Occasionally, may weed , Wright’s ground cherry and volunteer tomato survived the 1.5 lb. a.i./acre rate of ethalfluralin. Weed species composition after the 0.75 lb. a.i./acre treatment of ethalfluralin was similar, but also included a few surviving seedlings of lambsquarters. Weed composition on plots that received no herbicide resembled the 1999 weed survey and included barnyard grass, black nightshade, hairy nightshade, redroot pigweed, annual sowthistle, Wright’s ground cherry, cheese weed , purslane and lambs quarters. Generally, higher weed-seedling survival after reduced herbicideapplication rates is typical. Griffin et al. reported lower weed control with reduced rates of soil herbicides in soybean fields. Preplant incorporated application of imazaquin at the full rate gave 95% control, whereas the half rate gave 88% control. Greater seedling survival after reduced herbicide rates may be due to the density thresholds used in this study. For example, Williams et al. used a reduced rate at or below one seedling per square yard of Polygonum aviculare in corn. A relatively high weed-density threshold used for the no-herbicide plots was probably responsible for the low success of the no-herbicide approach in this experiment. The threshold for the zero rate was defined as a seedling density below 10 plants per square yard and for mature plants, as less than one weed plant per square yard. Since treatment maps were based on counts of emerged plants, the threshold for the no-herbicide rate should be set to zero weed plants per square yard. In this experiment, areas treated with the medium rate had about 5% weed cover at 2 and 4 weeks after application and about 12% at 6 weeks; whereas, the high-rate plots had about 2% weed cover at 2 weeks, 5% at 4 weeks and 8% at 6 weeks. Increases in weed cover over time are due to herbicide decomposition in the soil, indoor grow table although ethalfluralin persists for a long time, with an average field half-life of 60 days . High or full herbicide rates should only be applied to high-density weed patches. However, even the full herbicide rate was not able to control weeds in highly infested areas.

Other researchers have also observed that weed clumps persist despite uniform full-rate treatment . High weed-density areas may require a slightly higher rate than what is currently considered full rate, assuming crop tolerance is sufficient. Variablerate herbicide applications could allow higher rates to be applied in high weed density areas, while still applying less herbicide to the field as a whole.When the herbicide application was based on the seedling map, 15% of the experimental area did not receive any herbicide and 63% received a medium rate. The treatment map indicated that 2.18 acres of the site were treated with 0.75 lb. a.i./acre, 0.75 acre with 1.5 lb. a.i./acre, and 0.52 acre with no herbicide. A 47% reduction in herbicide use was achieved with the seedling-map approach when compared with a uniform full-rate application. Reduced rates were applied to 78% of the experimental area. The treatment map that we developed based on mature plants recommended that 1.02 acres of the site be treated with 0.75 lb. a.i./acre, 1.77 acres with 1.5 lb. a.i./acre, and 0.66 acre with no herbicide. Nineteen percent of the experimental area did not receive any herbicide and 30% received the 0.75 lb. a.i./acre rate. A 34% reduction in herbicide use was achieved with the variable-rate application based on a mature-plant weed map when compared with a uniform full-rate application, and 49% of the experimental site received a reduced herbicide treatment. Since using no herbicide may present too much risk for many growers — particularly in the early stages of adoption for precision weed management — rates may be limited to medium and high applications, in which case the herbicide reduction would have been 39% for the seedling-map and 24% for the mature map approach.It took approximately 20 seconds to count mature weeds in each 32-squareyard measurement area. Depending on the level of experience, it would take 2.2 to 6.6 hours to count the weeds in 100 acres . In the variable-rate experiment, a 34% herbicide reduction was achieved with the mature-weed map approach. At a commercial price of $50 per gallon for the herbicide Sonalan, savings were $17. It would take $22 to produce a detailed weed map . In this scenario — based on a mature-weed map — no financial benefits would be achieved.

In the case of the weed-seedling map approach, where a 49% herbicide reduction and $24 herbicide cost savings was achieved, plus the approximate $22 cost of a weed map, variable-rate application brings some modest financial benefits of about $2 per acre. However, we did not account for the conversion of a weed map into an herbicide treatment map in this estimation of economic returns. Our economic analysis should be verified in another study before a firm decision is formed about the economic value of variablerate technology. The economic efficiency of site-specific herbicide application depends on the cost of herbicide, cost of producing the weed map and treatment map, and the spatial characteristics of the weed population. Since weed distribution within a field is slow to change, maps created in one year may be useful for several years. Additionally, there are research efforts currently examining the use of camera systems to mechanically map weeds, which will likely decrease the cost of weed mapping and improve its accuracy, since a greater portion of the field will be sampled.The results from this experiment show that when information about the spatial distribution of the previous year’s mature weeds is used, weed control in terms of subsequent weed cover is comparable to uniform one-rate herbicide application, while simultaneously the total amount of herbicide applied decreases. We conclude that variable-rate spraying based on maps created from estimating weed population density and levels of infestation just before harvest gave the best weed control. However, further improvement is likely when the prediction and modeling of weed-seed redistribution from harvest to application time is incorporated into treatment maps. The simulation of seed movement from the measurement event to herbicide application should be incorporated in any preemergent treatment map.In the modern era of global trade, species are being inadvertently and deliberately introduced widely beyond their historic ranges . A crucial focus of evolution‐ ary ecology of introduced species is to understand their pattern of spread and to identify their native origins and pathways of intro‐ duction to better prevent and manage biological invasions . Inferring the origins and spread of these exotic species is challenging and rarely are the true pathways or origins known. Thus, a fruitful approach may be to use documented intro‐ ductions, such as those performed in classical biological control, as model systems to provide greater insights into population genetic analyses, as well as insight into the consequences of population movement and ecological processes for the genetic structure and variation of a species .

Classical biological control uses natural enemies to control invasive populations of weeds, and arthropod pests and disease vectors in the introduced range . These natural enemies, as biological control agents, are often imported across disjunct geographic ranges for the long‐term control of the target invasive species. In the modern era, these importations are well‐regulated and well documented . Thus, they provide model systems to study the repercussions of invasion pathways and multiple intro‐ ductions—including their effects on inter‐ and intraspecific hybrid‐ ization, bottlenecks, inbreeding, genetic variation, and correlations of genetic diversity with population performance of the biological control agents . To enhance the establishment and success of biological control agents, often multiple separate introductions are made, and large numbers of individuals are released . Multiple introductions here refer to introducing individuals from more than one population, or of more than one species, or both into the same geographic areas. Multiple introductions can increase the genetic diversity in an introduced population due to genetic admix‐ ture of different source populations . Alternatively, multiple introductions of more than one population could interfere with local adaptation, particularly in the native range . Additionally, hybridization can occur when more than one closely related species or strain is introduced, which can poten‐ tially lead to hybrid breakdown or hybrid vigor . Hybrid vigor can result from positive epistatic interac‐ tions among loci, drying rack cannabis heterosis due to masking of deleterious alleles, or heterozygote advantage, whereas hybrid breakdown can occur from negative epistatic effects among loci and/or the under dominance of loci . Thus, the presence of multiple introductions and hybrids can greatly impact the growth and spread of introduced populations, and the efficacy of biological control programs. The introduction of large numbers of individuals is critical to im‐ prove establishment success, as it buffers against demographic sto‐ chasticity and helps minimize loss of genetic variation . Nonetheless, introduced populations often endure demographic bottlenecks , which can decrease allelic richness and heterozygosity, with the latter depending on the rate of population growth following the initial bottleneck . Certain alleles might increase or decrease in frequency by chance during bottlenecks, leading intro‐ duced populations to diverge from native populations . Genetic drift and inbreeding can also lead to increased homozygosity , which can be associated with reduced fitness . However, population bottlenecks do not always reduce genetic variation or lead to genetic differentiation from the native population , particularly if populations grow rapidly following introduction . Evaluating the effects of bottlenecks in population size on genetic diversity can enhance our understanding of the consequences of introductions and spread of species. Although great efforts are taken to introduce many individuals from the native range to enhance establishment success, regulatory processes can make this difficult. Thus, the number of individuals imported to a region ranges widely from 10 to more than 1,000.

While regulations vary by country , each collection from the native range for release typically passes through quarantine to prevent unintentional introductions of other species . In many countries, such as the United States, fur‐ ther screening to characterize host range is often required for each new collection from the native range, which can mean many additional generations in quarantine even for agents that have already been approved. During this time, inbreeding and adaptation to the quarantine and mass‐rearing environment can also occur . Following quarantine screening, population size is typically increased as much as possible in order to release hundreds to thousands of individuals . However, the proportion of individuals that survive in the field and contribute to the next generation may be low, resulting in another demographic bottleneck . Regulatory and logistical obstacles limit sampling from the native range; thus, biological control agents for release in new regionsare often collected from a population already in use for biological control rather than revisiting the native range. This introduction process is analogous to the movement of invasive species, whereby an introduced population becomes the source of several secondary introductions, and is therefore acknowledged as a “bridgehead population” . Similarly, biological control agents frequently undergo serial importation steps, and thus serial bottlenecks in population size. By using the known introduction pathways from biological control programs, we can evaluate our ability to reproduce the introduction pathways by analyzing data from molecular markers. Here, we examine the importation history, genetic diversity, and population structure of two closely related species introduced for biological control to gain insight into the consequences of population movement and ecological processes for the genetic structure and variation of these two species. Here, we ask: Is there evidence of hybridization between these species, and how do introduction processes affect the genetic variation and structure of these species? More specifically, are there indications of decreased heterozygosity and allelic diversity in the introduced populations relative to the native range, do increases in the number of in‐ dividuals initially released or genetic admixture from multiple introductions result in increased genetic diversity, do populations with more introduction steps between them and the source population in the native range exhibit greater loss in genetic variation com‐ pared to populations with fewer introduction steps, and despite originating from the same initial populations, have introduced populations differentiated from the native range and from each other? To address these questions, we use the documented importation history and polymorphic microsatellite loci of two weevils, Neochetina bruchi and N. eichhorniae Hustache from their native and introduced ranges.

A central challenge in agriculture is to harness the genetic variation controlling key traits in crops to produce stable populations that can be planted, managed, and harvested effectively. Evolutionary models frame and explain the domestication, continued improvement, and management of cultivated plants. Examining these processes sheds light on the roles of selection and demography on genetic interactions of populations and species during adaptation. During domestication and crop improvement, individuals are selected for predictable traits. The means and variances of these traits in breeding lines over generations depend upon the relative roles of genetics and the environment in shaping variation and the number of alleles at loci governing these phenotypes. Likewise,the additive genetic variance associated with a given domestication trait may control how easy it is to fix a population for a trait value, particularly for traits that are vastly different from wild or weedy close relatives. Domestication is a selection process for adaptation to agro-ecological niches favorable for human use, harvest, consumption, and management. Historical gene flow between wild progenitors and domesticated plant populations ensures that cultivated varieties vary in their composition of domestication versus wild traits. Domesticated lines and wild relatives that can interbreed are common among plants and animals. Genome-wide studies of these interbreeding complexes help us understand how genetic introgression modulates adaptation and the maintenance of species boundaries in the face of gene flow. Although weedy rice physiologically and phenotypically resembles cultivated rice, it differs in several important weedy traits, including seed shattering habit, seed dormancy, protracted emergence, clone trays and the presence of red pigmentation in the seed pericarp in many cases. Shattering furthers propagation of the weed because seeds scatter in the field before cultivated rice is harvested. Variation in gene sequence and expression has been shown in many genes related to seed shattering, including qSH1, sh4, and SHAT1 .

The shattering trait in weedy rice has been shown to re-evolve after fixation of the non-shattering sh4 allele in its domesticated ancestors. Additionally, QTL analysis indicates that shattering has reemerged independently and is controlled by different genetic locations in weedy rice. Variable seed dormancy makes control of weedy rice by crop rotation difficult due to the ability of weedy rice to remain dormant for extended periodsin the field. Protracted emergence patterns make control by chemical means difficult because late or early emerging individuals can escape herbicide applications. Prolonged and highly variable emergence also makes control by non-chemical means, such as cover crops, difficult. Finally, weedy rice is commonly referred to as red rice when characterized by a red-pigmented pericarp. Contamination of commercial rice with pigmented red rice seed significantly lowers its commercial value. Most traits distinguishing crop from weedy forms are determined by recessive alleles of major-effect loci. A subsequent focus on the molecular evolution of genes important in de-domestication can guide our understanding of the tempo and process of evolution in weedy and feralized crop populations, but first we must examine the evolutionary origins and morphologies that characterize emergent weed populations. This knowledge informs agricultural management strategies that account for how weeds evolve and mitigate infestation. Understanding the genetic interplay underlying these processes will predict their directionality, identify traits for crop improvement in the face of new or changing environmental constraints, and outline ecosystem management strategies for sustainability. Cultivated Asian rice and its progenitor O. rufipogon are both diploid AA genome species,which facilitates introgression and the maintenance of hybrid feral forms . There are two cultivated species of rice: African rice , which was domesticated from the wild progenitor O. barthii in Africa, and Asian rice , which was domesticated from the wild progenitors O. rufipogon and O. nivara in Asia. Asian rice is classified under two major subgroups, japonica and indica.

The japonica subgroup includes tropical japonica, temperate japonica, and aromatic rice, while the indica subgroup includes aus and indica rice. Rice cultivation in the US includes primarily tropical japonica cultivars in the Southern rice belt and temperate japonica in northern California. Recently, rice production in California has included ‘specialty’ varieties of temperate japonica rice . Although gourmet rice varieties are brought in, control of imported and specialty seed stocks in California has been tightly regulated to prevent the accidental introduction and dissemination of wild or weedy rice. Weedy rice interacts with rice in the US, mainly across the Southern rice belt in Arkansas, Louisiana, Mississippi, Missouri, and Texas. This weed most likely originated from early domesticated Asian rice that reverted to wild/weedy traits and was later introduced into rice cultivation in the US. In the southern US, there are two major weedy rice ecotypes that have been consistently well-defined,strawhull awnless and blackhull awned . SH and BHA weedy rice are most similar genetically to indica and aus rice varieties,respectively. Hybridization between weedy rice ecotypes and between weedy rice and cultivated rice has been shown to increase genetic diversity in these groups. Neither indica nor aus varieties were grown in the US at or before the time weedy rice was reported in southern US rice, indicating that both ecotypes arose in Asia and were brought in as contaminants of seed stocks during early rice production. Rice cultivated in California is largely of the straw hull variety, while the weedy rice infesting this region is straw hull awned . Morphologically, California SHA weedy rice is distinct from both SH and BHA weedy rice in the southern US , as it has a straw-colored hull with long awns . Moreover, California SHA weedy rice is morphologically distinct from cultivated rice in California as it has colored pericarp and fully developed awns. SHA weedy rice was widespread in California rice fields from the 1920s into the 1940s. Bellue proposed that California weedy rice in the early 1900s originated from contamination from other parts of the US . These Asian tropical japonica varieties are not present in the US, and no evidence has supported southern US weedy rice de-domestication from the co-occurring cultivated rice they infest. Swift management efforts through a direct,water-seeding system, herbicides, and certified seed mitigated infestations in the Sacramento Valley until complete elimination of weedy rice in California in the 1970s. California SHA weedy rice was eradicated until 2003 when a single field was infested. Since 2003, this weed has spread to several other fields in Colusa and Glenn counties. Possibilities for the origin of California weedy rice include hybridization between cultivated rice and other relatives, reversion of cultivated rice to weediness, or introduction of an already established weedy rice lineage by contamination of seed stock entering California. Because the southern US grows tropical japonica cultivars and California grows temperate japonica cultivars, contamination of seed stocks would most likely occur outside of the US. Weedy rice is commonly referred to as red rice when characterized by a red-pigmented pericarp. Weedy rice is very similar to the cultivated crops with which it grows, both genetically and phenotypically. The low genetic distance between cultivated, weedy, and wild forms maintains intermediates and in turn perpetuates hybridization between crop and weedy/wild rice. These similarities can result from the loss of crop-specific alleles in crops, resulting in weediness, hybridization between crops and wild relatives , or by selection for phenotypic mimicry of the cultivated plant growing in rice fields . When domesticated plants and weedy plants are genetically compatible, hybridization can potentially transfer alleles for weedy characteristics to the cultivated populations and cultivar-specific alleles into weedy populations.

One important example of this is when herbicide resistance alleles move into weedy species that hybridize with resistant crops. Indeed, cannabis drying room interactions among crops and weeds can impact the adaptive potential of a weed to a new environment by simultaneously increasing genetic diversity in the weed and imparting alleles from the crop that are already suited to survival in an agro-ecosystem. Although rice is a ‘model system’ for domestication studies and the evolutionary history of many global weedy rice ecotypesis well-established, the origin of this recently emergent weedy Oryza population in areas without endemic speciesis poorly understood.In this study, we elucidate the origins of California weedy rice and attempt to identify morphologies that confer weedinessin the de-domestication process. We used a genome-wide panel of48 sequence tagged sites , which are 400–500 bp portions of expressed genes that have already been sequenced in a thorough sampling of AA genome Oryza species. The STS loci we use in this study are an established and effective tool in the rice community for recapturing the population structure of weedy rice, and represent an unbiased sample of genomic SNP diversity across diverse Oryza, including similar varieties. Indeed, the data from these 48 STS markers enables quantification of nucleotide variation in weedy, cultivated, and wild rice, and enable the robust quantification of US weedy rice nucleotide variation and population structure as well as the determination of which Oryza have contributed to US weedy rice genomes and the role of de-domestication in weedy rice evolution. The Olsen et al. Publication provides thorough information as to how loci are distributed among the 12 rice chromosomes and the suitability of estimation of FST and all other genetic diversity parameters. The diverse panel of Oryza used in this study included wild species from Asia , Africa , Central America , and Australia , along with cultivated Asian rice and cultivated African rice . To these sequences,we added sequence information at the same loci for weedy and cultivated rice collected from California in order to identify the origin of this newly established weedy population. The population divergence history and variance in the many phenotypes used by the International Rice Research Institute to characterize rice life history stages are unknown in this recently reported weedy population. We show that weedy rice in California is genetically and morphologically distinct from other weedy, wild, and cultivated rice groups included in our sampling. Hybridization as the mechanism of origin is unlikely in this case due to the low level of sequence diversity, uniform haplotype grouping assignment within the California weedy group, and complete homozygosity at all loci for all individuals. Coalescent model-fitting indicates that California weedy rice diverged most recently from temperate japonica cultivars which are grown in California, possibly involving a recent regression of cultivated rice back to a weedy form since establishment in the US. The picture that emerges from our study is that, despite low diversity, weedy rice can harbor significant trait variance and be morphologically distinct from its domesticated progenitors. Understanding how and why crops turn weedy and the dynamics of feral forms in production agriculture will help ameliorate crop-weed competition,reduced yield and quality, contamination of harvested grain, and disease reservoirs due to these weeds.Mature seeds were collected from weedy rice plants growing in four fields in northern California in 2008. Collection of weedy rice seed was done with the help of rice extension agents, who obtained permission from growers to sample their fields. The elimination of weedy rice in California for decades prior to this recent discovery of weedy populations was made possible by the cooperation of growers. No endangered species were involved nor impacted by this activity. For genotyping, we included a total of 27 weedy rice individuals and 12 cultivars . Cultivars that we added to the existing STS sequence dataset were all temperate japonica grown in California.A collection of morpho-phenotypic traits was scored for both cultivated and weedy rice in California . Twenty seven California weedy rice plants were sampled from the four rice fields in the state reported to be infested with weedy rice. Seventy-nine once-selfedlines from the field collected mother plants were grown in the U.C. Davis outdoor facilitiesfor phenotyping. Approximately three offspring lines were obtained from each original California weedy rice line collected from the field. Only certain traits that were applicable to field-collected“mother” plants at harvest—such as grain size—were used in the analysis to incorporate the most representative features of this emergent weed in the field. Germinated seeds were transplanted on April 18, 2007, to 22-liter pots filled with saturated soil and placed inside basins. Fertilizer was added following field recommendations. Seedlings were thinned to one per pot soon after establishment and when seedlings reached the 3- to 4-leaf stage of growth, the basins were flooded as in a paddy field. Pots were spaced 50 cm apart and arranged in a randomized complete block design with six replicates per accession. Morphological traits evaluated in this study and measurement methods were based on rice descriptors for morpho-agronomic characterization published by the International Rice Research Institute.

The projected maximum temperature was calculated by adding 5°C to the current maximum . A difference of 6 °C between day and night temperatures was chosen in accordance with the current day/night temperature difference and with previous studies of C. album and C. canadensis . CO2 treatment levels were ambient and elevated , which corresponds to future climate projections and within the range of CO2 levels projected by the year 2100. Environmentally controlled growth chambers , equipped with non-dispersive infrared CO2 analyzers and valves injecting pure CO2 to the incoming air stream, were set at either the near normal ambient CO2 level or at the elevated CO2 level . Chamber CO2 concentrations were logged at 30 second intervals and averaged for each 24h period, showing that CO2 levels averaged 490±40 ppm for the ambient treatment and 720±5 ppm for the elevated CO2 treatment. Seeds from each C. album and C. canadensis population sampled were germinated in fats filled with commercial potting media . Seedlings of C. album at the two- to four-leaf stage and C. canadensis at the three- to four-leaf stage were transplanted into 5 by 5cm plastic pots filled with the same potting media and grown in a growth chamber set at 25/15 °C temperatures and 11-h photoperiod, representative of the day length for February/March in California, and a light intensity of 600 µmol m−2 s−1 provided by fuorescent and incandescent bulbs. Seedlings were watered daily. Tree days after transplanting, 20–40 healthy seedlings from each population were moved to two growth chambers that differed in the following temperature and CO2 conditions: LT/ACO2 – low temperature combined with ambient CO2 , and HT/ECO2 – high temperature combined with elevated CO2 but with the same photoperiod and light intensity as described above. Seedlings of C. album were grown to a height of 6–8 cm, clone trays whereas seedlings of C. canadensis were grown to the 8–10 rosette leaf stage , then treated with glyphosate at the labeled field rate of 867 g ae ha−1 using an automated spray chamber equipped with a fat-fan 8001E nozzle .

The sprayer was calibrated to deliver 187 L ha−1 of glyphosate solution at a pressure of 296 kPa. For each treatment, five unsprayed individual plants were designated as untreated controls. One hour after glyphosate treatment, plants were returned to their respective growth chambers. Plant survival was assessed 21 days after treatment . The experiment was repeated 2–3 times. Treatment combinations and experimental runs were rotated between the two chambers. In addition, seedlings of two populations were assessed for plant response to glyphosate under two additional temperature and CO2 combinations: LT/ECO2 – low temperature combined with elevated CO2 , and HT/ACO2 – high temperature combined with ambient CO2 . Photoperiod, light intensity, glyphosate application and data collection were the same as described above. Due to a shortage of available growth chambers in which CO2 levels could be regulated, only one population of each species could be tested at these environmental conditions.For each population of C. album and C. canadensis, 16 plants grown under LT/ACO2 and 16 plants grown under HT/ECO2 conditions [eight plants sprayed with glyphosate and eight unsprayed plants ] were measured for leaf greenness and an estimate of chlorophyll content using a portable chlorophyll meter , following the method of Yannicccari et al.. Tree independent measurements were taken at the middle section of the youngest fully expanded leaf four days following treatment with glyphosate. Chlorophyll content was calculated as the average of the three measurements and expressed for glyphosate-treated plants as a percentage of the respective values obtained for untreated control plants.Glyphosate absorption and translocation under different temperature and CO2 conditions was assessed using a completely randomized experimental design with four replicates. Seeds from C. album population CA1 and C. canadensis population CCS were germinated and seedlings grown as described above. Seedlings of C. album at the two- to four-leaf stage and C. canadensis at the three- to four-leaf stage were transplanted into 40ml vials and grown hydroponically with a dilute nutrient solution, as described in Moretti and Hanson, in the growth chambers maintained at LT/ACO2 and HT/ECO2 conditions.

A solution containing glyphosate at a fnal concentration that approximated an 867 g ae ha−1 spray solution at 187 L ha−1 carrier volume was prepared by mixing 14C-glyphosate and a commercial formulation of glyphosate . When plants reached a height of 6–7 cm for C. album and the 6–8 rosette leaf stage for C. canadensis, a 2µL volume of the solution was applied to the middle adaxial surface of the youngest fully expanded leaf of each plant using a blunt-edged syringe in the form of two droplets, as described in Nandula and Vencill. Plants were harvested at 6, 12, 24, 48 and 72hours after treatment . At each harvest time, the treated leaf was removed and gently rinsed for 30 seconds in vials containing 10mL of distilled water to remove the unabsorbed 14C-glyphosate from the leaf surface. After removing the treated leaf, plants were dissected into shoots and roots. Phosphor image analysis was used to visualize herbicide translocation. 14C-glyphosate treated and dissected plant parts were pressed between two layers of paper and dried at 60 °C for 72h. After cooling to room temperature, each sample was placed in a 20×40 cm exposure cassette and brought into contact with a standard storage phosphor screen for 24h. Glyphosate translocation was visualized using the Storm 860 PhosphorImager system . Image analysis was conducted using the ImageQuant 5.0 sofware . Following phosphor image analysis, 14C-glyphosate translocation was quantified at three harvest time points, 12, 24 and 48 HAT, for both species. To measure the amount of non-absorbed glyphosate, rinsate was evaporated to dryness and resuspended in 10 ml of scintillation cocktail . Rinsate radioactivity was quantified using a liquid scintillation spectrometer device . The oven-dried plant samples used for phosphor image analysis were also used to assess the distribution of 14C-glyphosate. Treated leaves and roots were combusted with no further dissection whereas shoots were divided into several subsections as illustrated in Supplementary Fig. S1. For C. album, each shoot was divided into three parts: 1) shoot apical meristems including young undeveloped leaves, 2) leaves+petioles below the treated leaf, and 3) stem. For C. canadensis, each shoot was divided into two parts: 1) shoot meristems including young undeveloped leaves and 2) the remaining rosette leaves.

Different plant parts were placed separately into a combustion cone and dried at 60 °C for 96h. Each cone was combusted in a biological oxidizer . The evolved 14CO2 was trapped in 10ml of a carbon dioxide adsorbent solvent and mixed with 10ml of scintillation cocktail . Radioactivity was quantified using the LSS device described above.The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 system has emerged as a powerful genome-engineering technology with success in diverse organisms. Cas9-mediated genome editing technology provides enormous advantages over other classical methods in crop improvement and plant research by generating desired modifications at a specific target sequence. In some cases, CRISPR/Cas9 permits the direct introduction of mutations conferring resistance in crop plants, without traditional back crosses or plant breeding. Cas9-DNA scissors makes site-specific double-strand cut in the genome, inducing modifications at targeted locus through homologous recombination or non-homologous end-joining repair mechanisms while Cas9 base editor have ability to alter a specific nucleotide into another. Te most frequently used CRISPR/Cas9 system, type II, has three components: Cas9 endonuclease, CRISPR RNA and trans activating crRNA . Cas9-mediated DNA cleavage is guided by a tracrRNA:crRNA duplex that is complementary to the target DNA. Recently the tracrRNA:crRNA complex is fused into a single chimeric RNA known as single guide RNA containing an 18 to 20-nucleotide sequence which determines the target DNA sequence. The NGG protospacer adjacent motif that is present at 3′-end of the target sequence was recognized by the CRISPR/Cas9 system. Use of CRISPR/Cas9 has been reported as a most effective tool for nucleotide sequence modification or editing in numerous crop species, including Arabidopsis, wheat, rice, sorghum, cotton, maize, soybean and tobacco. The genera of parasitic weeds, Orobanche and Phelipanche , the broomrapes, cannabis drying room consist of over 100 species and represent one of the most destructive and great challenge in agricultural production. These are obligate plant parasites that attack through the host roots of almost all economically important crops in the Solanaceae, Fabaceae, Asteraceae, Brassicaceae and Apiaceae plant families. The life cycle of P. aegyptiaca is divided into two stages, preparasitic and parasitic.

The germination of parasite seeds is triggered by a highly specialized detection system for strigolactones exuded by host roots. Te parasitic stage initiates with the parasite developing a special intrusive organ the haustorium- that connects directly to the vascular system of the host. Following successful attachment and invasion of the host root, the broomrape seedling grows into a structure known as tubercle and after 4–5 weeks of tubercle growth, a foral meristem is produced, which emerges above the ground to produce flower and seeds. SL is a plant hormone required for shoot branching and used as a signaling molecule for the rhizosphere microflora. SLs occur in all green lineages of the plant kingdom and its synthesis start with the all trans β-carotene, a carotenoid molecule which produce 9-cis-β-carotene by the activity of Dwarf 27 , after that Carotenoid Cleavage Dioxygenases 7 convert it into 9 cis β–apo 10′-carotenal and fnally Carotenoid Cleavage Dioxygenases 8 leads to the production of carlactone, then cytochrome P450 enzymes, More Axillary Growth 1 convert it into various SLs. Existence of homologs CCD7 and CCD8 have been reported in P. ramosa and P. aegyptiaca. In the rhizosphere, SL acts as a host-detection cue for symbiotic arbuscular mycorrhizal fungi and stimulates seed germination of parasitic plants. Different types of SLs, e.g., strigol, 5-deoxystrigol, sorgolactone, solanacol, didehydroorobanchol, orobanchol and others, are known as germination stimulants for root parasites. The altered SL production conferred resistance in the host by reducing the germination of parasite seeds. Host resistance to the Orobanchaceae root parasite Striga has been observed in crops with altered SL production. In addition, previous studies found that the tomato SL-ORT1 mutagenized by fast-neutron display highly resistant to Phelipanche and Orobanche spp, the resistance results from its inability to produce and secrete SLs regarded as natural germination stimulants to the rhizosphere. Diferent methods of parasitic weed-control have been applied in attempts to control broomrape, but difficulties are encountered in targeting specific plant–plant systems. Moreover, most control strategies are less effective and have considerable limitations. Here we report the development of tomato plants that are resistant to the parasitic weed P. aegyptiaca upon mutation of the SL-biosynthesis gene CCD8 using CRISPR/Cas9.To investigate the efficacy of using CRISPR/Cas9 to create host resistance in tomato plants against parasitic weeds, we chose to disrupt the SL-biosynthesis gene CCD8 in tomato. SLs are synthesized from plant carotenoids via a pathway involving CCD7 and CCD8. Te CCD8sgRNA construct was designed using the single sgRNA cassette in the pENTR vector, which was then recombined into the pDest vector to target the second exon of CCD8 with a BsrI restriction site located upstream to the protospacer adjacent motif . Fourteen independent T0 transgenic tomato lines were generated by Agrobacterium-mediated transformation at the Plant Transformation Facility of the University of California, Davis, USA. However, 10 out of 14 of the CCD8Cas9 transgenic plants showed mutation at SlCCD8 locus, as determined by PCR and restriction analysis . Mutants showed similar kind of mutation at genome level considered as one single line in our study. We chose to continue our study with only those lines that showed different kind of genome editing in the T0 generation such as line 1, 2, 5 and 11 and the presence of transgene Npt-II was confirmed by PCR .To detect mutations induced by the Cas9 nuclease in T0 plants, we assessed loss of the BsrI restriction enzyme site that might arise due to imprecise non-homologous end-joining repair. For each of the T0 plants, we PCR-amplifed the CCD8Cas9 target region using genomic DNA from the T0 lines and then digested it with BsrI and examined products on a 2% agarose gel. Digestion of the wild type PCR fragment with BsrI results in three products of 147 bp, 298 bp and 7 bp, while Cas9 editing of the target site will generally eliminate the BsrI site that is adjacent to the PAM, leading to a 445 bp fragment.

There are two cultivated species of rice: African rice , which was domesticated from the wild progenitor O. barthii in Africa, and Asian rice , which was domesticated from the wild progenitors O. rufipogon and O. nivara in Asia. Asian rice is classified under two major subgroups, japonica and indica. The japonica subgroup includes tropical japonica, temperate japonica, and aromatic rice, while the indica subgroup includes aus and indica rice. Rice cultivation in the US includes primarily tropical japonica cultivars in the Southern rice belt and temperate japonica in northern California. Recently, rice production in California has included ‘specialty’ varieties of temperate japonica rice . Although gourmet rice varieties are brought in, control of imported and specialty seed stocks in California has been tightly regulated to prevent the accidental introduction and dissemination of wild or weedy rice . Weedy rice interacts with rice in the US, mainly across the Southern rice belt in Arkansas, Louisiana, Mississippi, Missouri, and Texas. This weed most likely originated from early domesticated Asian rice that reverted to wild/weedy traits and was later introduced into rice cultivation in the US . In the southern US, there are two major weedy rice ecotypesthat have been consistently well-defined,strawhull awnless and blackhull awned . SH and BHA weedy rice are most similar genetically to indica and aus rice varieties,respectively. Hybridization between weedy rice ecotypes and between weedy rice and cultivated rice has been shown to increase genetic diversity in these groups. Neither indica nor aus varieties were grown in the US at or before the time weedy rice was reported in southern US rice, vertical grow system indicating that both ecotypes arose in Asia and were brought in as contaminants of seed stocks during early rice production. Rice cultivated in California is largely of the straw hull variety, while the weedy rice infesting this region is straw hull awned .

Morphologically, California SHA weedy rice is distinct from both SH and BHA weedy rice in the southern US , as it has a straw-colored hull with long awns . Moreover, California SHA weedy rice is morphologically distinct from cultivated rice in California as it has colored pericarp and fully developed awns. SHA weedy rice was widespread in California rice fields from the 1920s into the 1940s . Bellue proposed that California weedy rice in the early 1900s originated from contamination from other parts of the US . These Asian tropical japonica varieties are not present in the US, and no evidence has supported southern US weedy rice de-domestication from the co-occurring cultivated rice they infest. Swift management efforts through a direct,water-seeding system, herbicides, and certified seed mitigated infestations in the Sacramento Valley until complete elimination of weedy rice in California in the 1970. California SHA weedy rice was eradicated until 2003 when a single field was infested. Since 2003, this weed has spread to several other fields in Colusa and Glenn counties. Possibilities for the origin of California weedy rice include hybridization between cultivated rice and other relatives, reversion of cultivated rice to weediness, or introduction of an already established weedy rice lineage by contamination of seed stock entering California. Because the southern US grows tropical japonica cultivars and California grows temperate japonica cultivars, contamination of seed stocks would most likely occur outside of the US. Weedy rice is commonly referred to as red rice when characterized by a red-pigmented pericarp. Contamination of commercial rice with pigmented weedy red rice seed significantly lowers its commercial value. Weedy rice is very similar to the cultivated crops with which it grows, both genetically and phenotypically. The low genetic distance between cultivated, weedy, and wild forms maintains intermediates and in turn perpetuates hybridization between crop and weedy/wild rice.

These similarities can result from the loss of crop-specific alleles in crops, resulting in weediness, hybridization between crops and wild relatives , or by selection for phenotypic mimicry of the cultivated plant growing in rice fields. When domesticated plants and weedy plants are genetically compatible, hybridization can potentially transfer alleles for weedy characteristics to the cultivated populations and cultivar-specific alleles into weedy populations. One important example of this is when herbicide resistance alleles move into weedy species that hybridize with resistant crops. Indeed, interactions among crops and weeds can impact the adaptive potential of a weed to a new environment by simultaneously increasing genetic diversity in the weed and imparting alleles from the crop that are already suited to survival in an agro-ecosystem. Although rice is a ‘model system’ for domestication studies and the evolutionary history of many global weedy rice ecotypesis well-established, the origin of this recently emergent weedy Oryza population in areas without endemic species is poorly understood.In this study, we elucidate the origins of California weedy rice and attempt to identify morphologies that confer weedinessin the de-domestication process. We used a genome-wide panel of48 sequence tagged sites , which are 400–500 bp portions of expressed genes that have already been sequenced in a thorough sampling of AA genome Oryza species. The STS loci we use in this study are an established and effective tool in the rice community for recapturing the population structure of weedy rice, and represent an unbiased sample of genomic SNP diversity across diverse Oryza, including similar varieties. Indeed, the data from these 48 STS markers enables quantification of nucleotide variation in weedy, cultivated, and wild rice, and enable the robust quantification of US weedy rice nucleotide variation and population structure as well as the determination of which Oryza have contributed to US weedy rice genomes and the role of de-domestication in weedy rice evolution.

The Olsen et al. publication provides thorough information as to how loci are distributed among the 12 rice chromosomes and the suitability of estimation of FST and all other genetic diversity parameters. The diverse panel of Oryza used in this study included wild speciesfrom Asia , Africa , Central America , and Australia , along with cultivated Asian rice and cultivated African rice . To these sequences,we added sequence information at the same loci for weedy and cultivated rice collected from California in order to identify the origin of this newly established weedy population. The population divergence history and variance in the many phenotypes used by the International Rice Research Institute to characterize rice life history stages are unknown in this recently reported weedy population. We show that weedy rice in California is genetically and morphologically distinct from other weedy, wild, and cultivated rice groups included in our sampling. Hybridization as the mechanism of origin is unlikely in this case due to the low level of sequence diversity, uniform haplotype grouping assignment within the California weedy group, and complete homozygosity at all loci for all individuals. Coalescent model-fitting indicates that California weedy rice diverged most recently from temperate japonica cultivars which are grown in California, possibly involving a recent regression of cultivated rice back to a weedy form since establishment in the US. The picture that emerges from our study is that, despite low diversity, weedy rice can harbor significant trait variance and be morphologically distinct from its domesticated progenitors. Understanding how and why crops turn weedy and the dynamics of feral forms in production agriculture will help ameliorate crop-weed competition,reduced yield and quality, contamination of harvested grain, and disease reservoirs due to these weeds.A collection of morpho-phenotypic traits was scored for both cultivated and weedy rice in California . Twenty seven California weedy rice plants were sampled from the four rice fields in the state reported to be infested with weedy rice. Seventy-nine once-selfedlines from the field collected mother plants were grown in the U.C. Davis outdoor facilities for phenotyping. Approximately three offspring lines were obtained from each original California weedy rice line collected from the field. Only certain traits that were applicable to field-collected“mother” plants at harvest—such as grain size—were used in the analysis to incorporate the most representative features of this emergent weed in the field. Germinated seeds were transplanted on April 18, 2007, to 22-liter pots filled with saturated soil and placed inside basins. Fertilizer was added following field recommendations. Seedlings were thinned to one per pot soon after establishment and when seedlings reached the 3- to 4-leaf stage of growth, industrial grow the basins were flooded as in a paddy field. Pots were spaced 50 cm apart and arranged in a randomized complete block design with six replicates per accession. Morphological traits evaluated in this study and measurement methods were based on rice descriptors for morpho-agronomic characterization published by the International Rice Research Institute.Twenty-seven weedy rice plants were chosen for genotyping along with 12 accessions of temperate japonica varieties that are cultivated in California. Leaf tissue from the outdoor grown plants was excised and desiccated for shipment to Clemson University for DNA extraction. DNA was extracted from desiccated leaf tissue using the Macherey-Nagel NucleoSpin 96 Plant DNA extraction kit .

Purified genomic DNA was diluted 2:1 in nuclease-free water for polymerase chain reactions . PCR was carried out using standard conditions to amplify 48 gene fragments selected by [21] from 111 sequenced tagged sites developed by [38]. PCR products were checked by gel electrophoresis and cleaned up using Exonuclease and Antarctic phosphatase treatment following the method described in [39]. Direct sequencing in both the forward and reverse directions was carried out by the Clemson University Genomics and Computational Biology Laboratory. Sequences were assembled into contiguously aligned sequence ‘contigs’ and assigned quality scores using Phred and Phrap. Contigs were aligned and inspected visually for quality and heterozygous sites in BioLign version 4.0.6.2 . Heterozygous base calls were randomly assigned to two pseudo-haplotypes, which were then phased using PHASE version 2.1. Due to low levels of heterozygosity in the data set, haplotypes were inferred with very high probabilities and consistency across five runs. All sequences have been submitted to NCBI GenBank . Phased haplotypes were aligned with sequences obtained from [21]. These additional sequences consist of the same 48 STS loci for a broad range of AA genome Oryza species including 58 weedy rice accessions sampled over a 30 year period from Arkansas, Louisiana, Mississippi, Missouri, and Texas. Also included in this dataset are sequences from the major cultivated groups from Asia and Africa , as well as wild species sampled from Asia , Africa , Central America , and Australia .Summary statistics for each STS locus including nucleotide diversity at silent sites using the Juke’s Cantor correction, Watterson’s θ at silent sites, number of segregating sites S, and Tajima’s D were calculated in DnaSP version 5.0. Arlequin version 3.5 was used to calculate pairwise FST and ФST estimates with 10,000 permutations to assess significance.Bonferroni corrections were used to determine Pvalue cutoffs. The population-mutation parameter FST is an estimate of genetic divergence within and between groups and was used to test for the extent of genetic differentiation. To better estimate divergence between California weedy rice and other rice groups, the population mutation parameter ФST was used, which is similar to FST but uses distances between haplotypes, not just haplotype frequencies. Genetic diversity was measured by computing the average nucleotide diversity , total number of segregating sites, and Watterson’s θw within each field as well as within all fields combined. Population structure was inferred using InStruct, which was designed to allow for inbreeding by not assuming Hardy-Weinberg equilibrium within populations. Using STRUCTURE for inbreeding populations results in inappropriately higher rates of inferred splitting between populations . Five permutations for each number of populations were set from 1 to 22 with 500,000 steps and a burn-in period of 100,000 steps. In Structruns were completed on the Clemson University Condor computing cluster. Log likelihoods for each run were compared to determine the best fit K value. Distruct version 1.1was used to create the graphical display from the results obtained with InStruct. Isolation with Migration modeling was used to test for best fit models of isolation-migration and simultaneously estimate effective population sizes , migration between populations , ancestral population size and time since divergence . California weedy rice was compared on a pairwise basis to California cultivated rice , strawhull weedy rice, blackhull weedy rice, O. rufipogon and O. nivara.

To be most effective, these approaches demand landscape-scale perspectives on the mechanisms underlying invasive species spread and persistence over time . However, most studies on the effects of management on invasive species are conducted at the much smaller scale of 1-m2 plots. Such small plots can assess local responses to management but provide only a limited picture of landscape heterogeneity. Moreover, unless embedded within larger landscape assessments, small plots cannot readily quantify expansion, contraction, and persistence of invaded patches over time. At present, mapping with remote sensing generally requires that the invaders differ from the resident community in specific ways, such as in plant chemistry , texture/morphology, phenology, or canopy level. Thus, while remote sensing has been extremely effective in detecting changes in functional groups of plants , it is more difficult to detect invasion of a species that is similar in functional type to the resident community it is invading . Detecting the invasion of grasses into grassland communities is particularly challenging, with phenological differences so far proving to be the most helpful identifying features. However, when multiple images are required for phenological detection methods, drying rack for weed available low- or nocost public data has often come at a coarse spatial scale that fails to capture the smaller patch dynamics relevant to management . The use of data from commercial satellites in precision agriculture illustrates the power of finer-scale imagery , but such commercial satellite imagery has typically not been affordable for rangeland managers.

Even with the limitations of coarse-scale imagery, however, some studies have been able to use differences in phenology to map invasions, based on differences in season of green-up and timing of green-up after precipitation, or on seasonal variation in NDVI. In California’s semi-arid grasslands, two invasive weedy grasses have become particularly problematic, and are a high priority for mapping and control efforts: Elymus caput-medusae Nevski and Aegilops triuncialis L.. These annual grasses were introduced to California in the late 19th century from Eurasia and are now established throughout the Western United States. Both species produce unpalatable forage that is avoided by livestock, particularly as the plants mature, and generate a thick, mulching layer of litter that typically persists well into the next growing season . In California, broad-scale detection of these invaders is challenging because these annual grasses are invading a community already dominated by annual grass species, including Avena and Bromus spp. . In addition, for most of the growing season, the phenology of the invasive plants overlaps with the desirable annual forage grasses. Both groups germinate with fall rains in October and November and then grow throughout the rainy winter season into the spring months. However, the invasive weedy grasses differ notably from the forage grasses in their end-of-season phenology. The forage grasses typically reach peak greenness in March or early April and then senesce in late April and May , while the weedy species exhibit an extended late-season growing period that ends in late May or June. It is during late spring and early summer, when the invasive weedy grasses are green but the forage grasses are golden and senesced, that weed patches may be most easily identified on the ground by field observers . Our study focused on two key questions: How well can fine-grain phenologically-timed aerial imagery detect the invasion of medusa head and goat grass into naturalized California annual grasslands over time? and Using this method, how do the abundance and persistence of forage and weed-dominated patches vary in response to grassland management?

This study was conducted in partnership with private landowners and conservation practitioners, to assess the effectiveness of various weed mapping approaches in quantifying landscape-level impacts of land management actions on invasion in California grasslands .Our study examined invasive weedy grass distribution within a 6.8-km2 region of semi-arid grasslands on rolling hills on the west side of the Sacramento Valley, CA, USA. The study area included four different management units on three privately-owned ranches. The landowners of these private properties gave permission to conduct this work. These units had experienced different grazing intensities over recent years, ranging from none to intensive rotational grazing by sheep, goats, and cattle. The two weedy grasses medusa head and goat grass were well-established across all properties, alongside annual forage grasses . Much of the landscape matrix was thus a heterogeneous mixture of weedy and forage grasses, out of which emerged near-monospecific patches dominated by either weeds or forage. Our primary objective was to map the distribution of the strongly weed-dominated patches, which provide little forage or conservation value. At the study location, the dominant soil types are fine smectitic thermic Andic Haploxererts; fine, mixed, active thermic Typic Palexeralfs; and fine-silty mixed, superactive thermic Typic Haploxeralfs. The climate is Mediterranean, with a cool and rainy growing season that typically begins in September and extends into May when the summer drought begins. Peak precipitation typically occurs between December and February but patterns of precipitation are quite variable. Almost no precipitation falls during summer, when mean maximum temperatures can exceed 37 ˚C . The two growing seasons we studied differed both in total precipitation and its temporal distribution. In growing year 2008, total annual precipitation was close to average , with rains heaviest in January and February and very little falling thereafter . In contrast, total precipitation in growing year 2009 was only 81% of average , with the largest rain events occurring during the shoulder seasons and little in mid-winter; small rain events occurred later into late spring and early summer than in 2008 .

Our aim was to identify a robust method for mapping the distribution of weed-dominated patches that would work well even across years of different precipitation and then to use this approach to evaluate weed patch persistence or change across the four management units in our study site. The first challenge was to discern patches dominated by annual weedy grasses within the existing annual grassland, which is morphologically similar. To do this, we first characterized the phenological signature of the weeds based on subtle seasonal changes in their canopy greenness that could be discerned in contrast to the forage grasses or mixed communities of forage and weeds in which the weeds were not dominant. We considered the two weedy species as a group and did not attempt to distinguish between them. To characterize the weed group’s phenological signature, we evaluated how its greenness changed from the period of peak landscape greenness to the end of the growing season, and compared its signature to that of forage-dominated patches. To assess vegetation greenness, we used low-cost digitized color infra-red aerial photography familiar to many range managers and for which spatial resolution was fine enough to resolve small weed patches in this system. From this imagery, we derived values comparable to the Normalized Difference Vegetation Index , a classic index that identifies green vegetation. We then tested different combinations of imagery and classification approaches against ground truth data to identify the most robust mapping method, and then used this method to look in detail at weed patch distribution across the study site, as detailed below.Aerial imagery was acquired from a fixed wing airplane by Pacific Aerial Surveys between the hours of 12:30 and 1:30 pm, using Kodak Aerochrome III Infrared Film 1443 with a minus-blue filter at a scale of 1:34,200 or 1:35,000 . The imagery was acquired with a 22.9 cm x 22.9 cm negative format from a mapping camera with a focal length of 153 mm/6 inches. Flight lines were arranged north–south with less than 5% crab and less than 2 degrees tip and tilt. For each date, pipp mobile storage systems we used a single image that encompassed the entire study area, so the need for image mosaicking was avoided. The images were acquired on cloud-free days at a relatively low altitude, so atmospheric corrections were also not necessary. After processing, the film was scanned without color adjustment on a photogrammetric scanner to create a digital image with approximately 0.39–0.45-meter resolution. Spring images were taken on March 10 of 2008 and 2009, during the period of peak greenness when the canopy of forage grass species is typically greener than that of the invasive weeds . End-of-growing season imagery was acquired when the weed species were still green but forage grasses had senesced as judged from the ground . This date varied across years due to weather-driven variation in phenology. In 2008, the May image was acquired on May 13, and in 2009, images were acquired on both May 18 and 26 . Aerial images were orthorectified in the Leica Photogrammetry Suite in ERDAS Imagine 9.3 using recent camera calibration reports from the United States Geological Survey Optical Science Lab. Ground control points for orthorectification were georeferenced in the field with a Trimble GeoXH using a Trimble Beacon Receiver communicating with a U.S.

Coast Guard beacon and an antenna on a 2-m range pole. Point data were georeferenced in UTM10 with a WGS84 datum and then post-processed and adjusted for atmospheric conditions with reference data from the nearest National Geodetic Survey Continuously Operating Reference Station for greater positional precision. The navigational accuracy of point locations in the field and post-processed points was approximately 0.30 m, which was confirmed by benchmark tests. For effective orthorectification, a digital elevation model is also necessary. At the time of the project, the only existing DEM for the project area was the National Elevation Dataset produced by the USGS. This DEM had a spatial resolution of 30 m x 30 m. This meant that an elevation value was available every 30 m across the landscape. Because the project area contained considerable landscape relief, it was determined that the NED DEM would not allow for production of accurate orthoimagery needed for concurrent analysis of several image datasets. To ensure the accuracy of the final orthoimagery, it was necessary to create a new, more precise, DEM. The source for the elevation data was the georeferenced Digital Raster Graphic dataset created by the USGS from the USGS7.5-minute quadrangle maps . Individual contours were digitized in ESRI ArcMap 9.2 as polyline features. The elevation for each contour was entered into the database table as an attribute. After digitization was complete, a 2-meter DEM was created by interpolating the elevation values of the contours. The interpolation was completed using the Topo to Raster tool in ESRI ArcGIS Toolbox 9.2. The resulting 2-meter DEM represented a large increase in elevation precision over the National Elevation Dataset and was used in image orthorectification to correct for changes in terrain.The Normalized Difference Vegetation Index is a simple, well-tested metric derived from red and near-infrared radiances; it is calculated as . Green vegetation typically shows higher values than senesced or non-living materials. To minimize topographic and seasonal differences in illumination, we created an NDVI-like image from the red and near infrared bands of each digitized color infrared image, using ENVI 4.7 . The spectral properties of film differ from those of calibrated satellite instruments, but film-based NDVI estimates provide valuable utility. Historically, color infrared film was designed so that the red and infraredsaturation intensities appeared relatively similar to each other in order to produce an aesthetically pleasing image; as a result, NDVI values captured on film are typically lower than those captured by satellite sensors, in which the infrared saturation intensity is permitted to be greater. To evaluate different methods of capturing phenological signatures, we then used Modeler in ERDAS Imagine 9.3 to produce NDVI difference images for each year as ΔNDVI = NDVIMarch − NDVIMay . Mask. We created a 1-m resolution mask to remove from analysis the areas that did not include vegetation of interest . We digitized masked objects in ESRI ArcMap 9.3 and exported them to ERDAS Imagine, where a 5×5 neighborhood filter was used to remove spurious data and simplify the dataset. This image was then converted to vector polygons, compared to orthoimagery, and edited as appropriate. The polygon features were then simplified in ArcMap, converted to raster, and formatted for use in ENVI. Image layer stack for classification. To facilitate image classification, we created a layer stack in ENVI 4.7 using all of the NDVI and NDVI difference imagery, as well as the mask.

Romaine lettuce, spinach, and carrots were chosen as the subjects of this study and will be discussed in detail. Treatments were steam and steam + hydrogen peroxide applied by 3 different steam applicators. Pests monitored were lettuce drop and pythium wilt, crop yields, and soil temperature, weed control and hand weeding times, were conducted in plots in the Salinas Valley. Steam application and the cost were evaluated.Many soilborne pathogens affect vegetables; among them are Pythium spp., which weakens the roots of lettuce and Sclerotinia minor, which affects the lettuce crown and stems in contact with the soil causing them to breakdown, collapse, and die . There is little new research regarding the efficacy of steam on pathogens in leafy crops. Some studies have stressed that S. minor and Pythium spp. are important pathogens with the potential to affect crop health in lettuce, spinach and carrot production . Pythium wilt is caused by a fungal water mold that is most abundant in moist to wet field situations and can persist in the soil without a host and infect the roots of lettuce . Spinach and lettuce are susceptible to the fungus under moist field conditions, which can result in total crop collapse . The pathogen develops in soil temperatures of 5 °C to 43 °C, with optimal temperatures of 20-24 °C that are common in a Mediterranean climate, such as California . Depending on the environment, Pythium spp. can remain dormant in the soil for up to 8 years . Pythium zoospores travel through the soil via water and causing infection, drying marijuana whereas oospores are survival spores that allow the pathogen to persist in the soil . Lettuce drop is a fungal disease known as white mold and lettuce drop . The pathogen is most abundant in moist field settings and has a broad host range including weeds and other vegetables .

Lettuce drop affects the crown and stem of lettuce and persists in the soil as sclerotia that can last up to 8 years under dry conditions . The sclerotia are hard, black angular structures that can range in size depending on their developmental state but are smaller compared with S. sclerotiorum, which produce large smooth sclerotia . Under environments favorable to S. minor, the lettuce plants will start showing white mycelium on the crowns of the lettuce . The pathogen grows in temperatures of 6 °C to 30 °C and 18 °C is the optimal temperature for this pathogen . Lettucedrop is a serious problem in all lettuce production areas of the world and can cause crop losses up to 70% . Pinel et al., evaluated the control of S. minor and Pythium spp. with a self-propelled steam applicator in a leafy vegetable trial in Italy. They found a significant reduction of both pathogens to a soil depth of 10 cm. A similar study done by Triolo et al., which was treated once and followed for 5 years, observed the steam treatment reduced S. minor by 68.6% after treatment. Organic vegetable crops are valuable and weeds present a major risk to profitability, given the total value of high value crop production can cost up to $19,000 ha-1 . Some annual weed species can produce seeds more rapidly than others. For example, burning nettle can set seed in 45 days and thrive in a 65-day lettuce field . It is essential for organic growers to know the type of weeds that persist in their weed seed bank to know when to plant certain crops during the year. A worst-case scenario would be planting a high value organic crop in a severely infested weed field. For example, common purslane can remain viable in the soil for up to 20 years and a single plant can produce 52,300 seeds . In addition, perennial weeds such as yellow nutsedge can live short or long lives and white clover seed can persist 80 years or more .Over the years, horticultural studies and technology have been advancing. Olericulture is a branch of agriculture that relies on science to maintain profitable production in vegetable crops.

Many of the 400 commodities produced in California consist of high value crops like almonds and lettuce . In addition, these commodities are the products that make California one of the leading states in producing quality and high yielding specialty crops that boost California’s economy . Profitable high value vegetable crops, such as lettuce and spinach, are not only a cool season and a quick maturing crop but are an example of some important crops that are grown nearly year-round on the Coast of California. Lettuce People discovered in the early 1900s, that the Coastal areas of California have favorable soils and a Mediterranean climate which is well suited for growing high value crops throughout the year . Currently, iceberg, romaine, and leaf lettuces are commonly grown . Lettuce demand in the Western US increased during the 1930s, and the advent of refrigerated rail cars enabled the shipment of lettuce across the continent . While the industry benefited primarily from improved cooling facilities in the Salinas Valley and an accessible railroad, romaine and leaf lettuce became a popular crop by the 1950s that continues to be . Lettuce is the 8th most important commodity produced in California and together with Arizona, these states produce 95% of lettuce in the United States, with a $3.1 billion farm value . According to the 2020-2021 USDA/NASS overview, there was a 22% increase in firesh market romaine lettuce production from 2019 to 2020, with Monterey County continuing to be the leader accounting for 61.9% of the state gross value total. Lettuce producers use transplants for some of the lettuce plantings, but most plantings are direct seeded into 40-inch beds with two seedlines or 80-inch beds that can have 5 to 6 seedlines . With higher density plantings, 2.5 inches of space are established between rows to ensure good spacing and to maximize yield . After the crop is established, it is thinned at the two to four leaf stage by a thinning machine to ensure crops are not too crowded . Consequently, thinning too much or too little canpotentially affect the market quality of the product due to crop overlap or not having enough marketable plants to harvest. .The most common spinach types grown in California are firesh bunched, bagged spinach for salad mixes, and processed . Four states grow 98% of spinach in the United States: California, New Jersey, Texas, and Arizona . Most spinach produced in California is for the clipped and bagged spinach market, with California being the largest producer . Moreover, spinach is currently ranked the 23rd top commodity in California with a value of $281.8 million . The majority is grown in Monterey County, with 25% produced in Southern California and the San Joaquin Valley . All commercial spinach producers grow hybrid spinach that is direct seeded at a high density on 80-inch-wide beds with up to 42 seedlines . Spinach growers early on worked to ensure that there are no weeds present on bed tops because they use mechanical harvesters and have a very low tolerance for weeds, as they can contaminate packaged spinach .Carrots grown in California have a firesh market value of $643 million greater than other carrot-producing states like Michigan and Texas . As stated by the Crop Protection Research Institute, carrots are primarily grown in the Cuyama Valley, Kern, and Santa Barbara County areas and California production accounts for 85% of firesh market carrots in the United States . A disease that causes significant damage is carrot blight caused by Alternaria dauci, which can weaken the tops of the crop which are needed for mechanized harvesting. Therefore, farmers rely heavily on fungicide sprays and is the reason why only 10% of farmers grow carrots organically . Carrots are grown at high densities just like spinach, which makes cultivation difficult. Weeds can also be a problem by clogging machine harvesters .

Carlesi argues it is important that weeds are controlled during the early stages of carrot growth. Competition from weeds can reduce yield and because the crop canopy is not as dense, it can allow light penetration through the canopy, cannabis drying rack which can encourage additional weeds to emerge . Organic growers have few pesticides to control weeds and diseases. In addition, treated carrot seeds are used and are always seeded into the soil on 40-inch beds each with a total of six to eight rows . In addition, carrots are mostly started by sprinklers and then switch to furrow irrigation to prevent the spread of carrot blight and bacterial blight . Other diseases like Pythium spp. can also affect the crop in the early seedling stages causing early die off due to wet soils where overhead irrigation is used and later by causing cavity spot, which can result in major economic losses .Cover crops are used to not only trap soil nutrients and prevent it from leaching, but also to control weeds . In addition, using cover crops to control Pythium spp. in a 3-year interval can be effective because of improved soil fertility and its ability to suppress pathogens . Rotations with broccoli are very effective because once the crop residue is broken down in the soil it produces glucosinolates that can suppress pathogens . In addition, grain crops can also be effective, but legumes have poor performance in suppressing pathogens . Pathogen distribution can be influenced by irrigation and poor water drainage . There needs to be enough water for the zoospores of Pythium for successful infection and spread to other parts of the field . Pythium wilt primarily infects below the ground, causing roots to decay and turn gray and brown, causing damping-off in early plant development . A study by Pinel et al., was able to control Pythium spp. with steam 90-99% of the time in the first 5-10 cm of the soil and observed it did not recolonize during the 3-month trial duration. Prevention of weed seed maturity is necessary to reduce replenishment of the seedbank and cultural management of some weeds after crop harvest is crucial since weeds have already dispersed their seeds into the soil . Tillage immediately following harvest will minimize weed seed set . In addition, inadequate rotation programs, and continuous planting of lettuce can cause a reoccurrence of common purslane in the soil, especially because it can reroot in the ground and can continue to grow . Because crop rotations allow use of different weed control means, broccoli would allow use of oxyfluorfen post emergence herbicide in a integrated pest management program to control purslane, but growers do not make money on broccoli which is why they stick to growing lettuce and grow broccoli when they have to.Crop and weed competition are always at play and all control measures must be used to help the crop to out compete the weeds. The key to weed control is to act early to prevent weed establishment and promote crop competition with weeds. Integrated weed management takes advantage of the crops larger size, such as transplants and cover crops that can rapidly cover the soil surface. The transplants have the ability to establish earlier than the weeds . High density cover crops suppress weeds, and high density lettuce help suppress weeds, although cultivation and weed removal is difficult . Understanding weed seedbanks and integrating an ecological-based approach to weed management will allow growers to develop better weed control programs . These weed control programs can be improved in the future by looking at seed dispersal and emergence in terms of species and creating models of competition to better plan a weed field site program . Using living mulches can also aid in suppressing weed germination due to its ability to prevent light transmission into the ground and its ability to control the temperature of the soil . In addition, the cover crop can serve as an added allelopathic affect, which can also aid in impeding weed development and germination of annual weeds, but allelopathy is not a dependable tool since it is variable . Another pest management practice that is used is intercropping. This involves rotating crops and controlling weeds at the same time, resulting in yield increases . While using crop rotations to control weeds is effective, allowing fields to be fallow can also be of great benefit .

A shank fumigation trial was conducted in 2007 at the UC Kearney Agricultural Center , near Parlier, to determine the effect of two fumigation shank types and five soil surface treatments on 1,3-D emissions and control of representative soilborne pests following removal of a plum orchard. Soil texture at the site was a Hanford fine, sandy loam with pH 7.2, 0.7% organic matter, and a composition of 70% sand, 24% silt and 6% clay. The experiment included 10 treatments with 1,3-D in a split plot design with surface treatments as the main plots and two application shank types as the subplots, as well as an unfumigated control and a methyl bromide plus chloropicrin standard for comparison . Individual plots were 12 feet by 100 feet, and each treatment was replicated three times. Fumigant application. Fumigants were applied using commercial equipment on Oct. 2, 2007. Methyl bromide with chloropicrin was applied at 350 pounds per acre with a Noble plow rig set up to inject fumigants 10 inches deep through emitters spaced 12 inches apart while simultaneously installing 1-mil high-density polyethylene film. The 1,3-D treatments, at 332 pounds per acre, were applied using either a standard Telone rig with shanks spaced 20 inches apart and an injection depth of 18 inches or a Buessing shank rig with shanks spaced 24 inches apart and the fumigant injection split at 16- and 26-inch injection depths. The Buessing shank also had wings above each injection nozzle to scrape soil into the shank trace and minimize rapid upward movement of the fumigant . Following 1,3-D application, a disk and ring roller was used to level and compact the surface soil before surface seals were applied over the fumigated plots. Average soil temperature at 20 inches during fumigation was 70°F, grow rack with lights and soil moisture was 8.2% to 10.5% weight per weight in the top 3 feet. Surface treatments included HDPE film; virtually impermeable film, VIF ; and a series of intermittent water applications .

The intermittent water seals treatment was applied using a temporary sprinkler system installed in the plots following fumigation and the post fumigation tillage operation; water was applied four times in the first 2 days after fumigation: 0.5 inch after 3 hours, 0.2 inch after 12 hours, 0.2 inch after 24 hours and 0.2 inch after 48 hours. All plastic films were removed 10 days after fumigation. Fourteen days after the initial 1,3-D fumigation, the metam sodium treatment was applied through sprinklers at 160 pounds per acre in 2.75 inches of water. For the dual application treatment, 21 days after the initial treatment, soil was inverted with a moldboard plow and an additional 1,3-D treatment was applied with the previously described Telone rig and rolling operation. Emissions data collection. Fumigant emissions from eight 1,3-D treatments — two application shank types times four surface seal methods — were monitored in three replicate plots for 10 days following the initial application. Emission of 1,3-D from the soil surface was monitored using previously described dynamic flux chamber techniques . Briefly, a flow-through flux chamber with a 10-inch-by-20-inch opening was installed on the surface following fumigant injection and installation of the films or after the initial water seal treatment . These chambers allow semi-automated, continuous sampling of fumigant concentrations in the air above the surfaces. The cis– and trans-isomers of 1,3-D were trapped in charcoal sampling tubes . The two 1,3-D isomers were summed as total 1,3-D for data analysis and reporting. Individual tubes were removed from the flux chambers every 3 to 6 hours and stored frozen until laboratory processing. Emission flux and cumulative emission during the 10-day monitoring period were calculated based on surface area and air flow rates through the flux chambers, and treatment differences were compared using analysis of variance . The concentration of 1,3-D in the soil-gas phase was determined 6, 12, 24, 48, 120 and 240 hours after treatment. At each time point, samples were collected using a multiport sampling probe and a system of gas-tight syringes to draw air from eight depths through charcoal sampling tubes. Samples were stored frozen until analysis. In the laboratory, all samples were processed using procedures described by Gao et al. . Briefly, sample tubes were broken and trapped fumigants were extracted from the trapping matrix with ethyl acetate and analyzed using a gas chromatograph equipped with a micro electron capture detector .

Pest control data collection. Pest control efficacy was evaluated using citrus nematode bioassay counts, fungal dilution plating, and weed emergence counts and biomass collections from each replicated plot. The pest control data from this research station emission flux experiment were reported in Jhala et al. . Rose and tree nursery trials In addition to the emission flux and efficacy study conducted at KAC, two field trials were conducted in commercial nurseries to evaluate pest control efficacy and nursery stock productivity. Fumigation and surface treatments in the nursery experiments were the same as in the flux study with minor exceptions . The commercial nursery trials were arranged as randomized complete block experiments with a split plot arrangement of 1,3-D treatments. The whole plot factor was surface treatment, and the split plot factor was the shank type. Individual plots in these experiments were 22 feet by 90 feet, and each treatment was replicated four times. Fumigant application. In 2007, the experiment was established in a garden rose nursery near Wasco. The soil at the rose nursery site was a McFarland loam with pH 6.2, 0.9% organic matter and 74% sand, 13% silt and 13% clay. Treatments were applied on Nov. 7, 2007, when the soil temperature was 64ºF and soil moisture averaged 9.2% w/w from 2 to 5 feet. The experiment was repeated in 2008 in a deciduous tree nursery near Hickman, in a Whitney and Rocklin sandy loam soil with pH 6.5, 0.8% organic matter, and 66% sand, 23% silt and 11% clay. Treatments in the tree nursery trial were applied on Aug. 13, 2008, when the soil was 80ºF and soil moisture ranged from 5.0% to 12.6% w/w in the top 5 feet. Immediately following 1,3-D application, a disk and roller were used to compact the soil and disrupt shank traces and HDPE and VIF were installed using the Noble plow rig. For the water seal main plots, a temporary sprinkler system was installed after the post fumigation tillage operation and intermittent water seals were applied: 0.5 inch after 3 hours, and 0.2 inch each after 12, 24 and 48 hours.

The dual application 1,3-D treatments were applied in the garden rose experiment on Nov. 28, 2007, but were not included in the 2008 tree nursery experiment. Metam sodium was applied in 2.75 inches of irrigation water through sprinklers 14 to 30 days after the initial 1,3-D treatment in both experiments. All plastic films were removed 2 to 3 weeks after fumigation at both sites. Crop production and data collection. Both nursery trials were managed by the cooperating growers using their standard practices for planting, fertilization, in-season tillage and budding and harvest operations. In the 2007 rose experiment, two rows each of the rose rootstock ‘Dr. Huey’ and the own-rooted garden rose variety ‘Home Run’ were planted as hardwood cuttings in December 2007. Rose nursery stock was planted 7 inches apart in furrows spaced 3 feet apart, and the field was furrow irrigated during the 2008 and 2009 growing seasons. The own-rooted cultivar was harvested after one growing season in January 2009, and the unbudded ‘Dr. Huey’ rootstock was harvested in February 2010 after an additional growing season. At both harvest dates, all plants in one 90-foot row were lifted using a singlerow undercutting digger, plants were bundled and tagged by plot, and graded in a commercial packinghouse. In the 2008 tree nursery trial, two rows each of the peach rootstock ‘Nemaguard’ and the plum rootstock ‘Myro 29C’ were planted with 8 inches between plants and 5 feet between rows in December 2008. The tree nursery plots were sprinkler irrigated during the 2009 growing season. Due to the market needs of the cooperating nursery, the rootstocks in the tree trial were not available for harvest and grading as a part of the experiment. Pest control efficacy and crop productivity were evaluated during the 12- or 26-month nursery production cycle. Nematode control was determined using a citrus nematode bio-assay in which two sets of muslin bags containing 100 grams of soil infested with citrus nematode were buried at 6, 12, 24 and 36 inches below the soil surface in each plot prior to fumigation. The initial population of citrus nematodes in infested soil was 4,086 and 3,876 nematodes per 100 cubic centimeters of soil in 2007 and 2008, respectively. The bags were recovered 1 month after fumigation, nematodes were extracted from 100 cubic centimeters of soil using the Baermann funnel protocol, indoor grow rack and surviving nematodes were identified and counted. To evaluate the effect of fumigation treatments on soil fungal populations, ten 1-inch-by-12-inch soil cores were collected from each subplot 2 weeks after fumigation. Soils were homogenized, and a subsample was assayed for Fusarium oxysporum Schlecht. and Pythium species using dilution plating techniques on selective media. Pythium species samples were plated on P5ARP medium for 48 hours, and F. oxysporum samples were plated on Komada’s medium for 6 days. Emerged weeds in a 1-square-meter area were identified and counted twice in the winter following the fall fumigation and several times during the subsequent summer growing season. Nursery stock establishment, vigor and growth were monitored during the season. Visual evaluations of crop vigor were made on a scale of 1 to 7, where 7 was the most vigorous and 1 was dead or dying plants. Near the end of the growing season, trunk diameter of 10 plants in each subplot was measured 3 inches above the soil surface using a dial caliper. As previously described, rose nursery stock was harvested and graded to commercial standards ratings, but tree nursery stock was not harvested as a part of the experiment. Data were subjected to analysis of variance, and initial analyses indicated that the shank types did not differ in their effect on any of the pest control or crop growth parameters measured. Thus, data from the two shank type treatments were grouped together within surface treatments and reanalyzed with seven treatments and six treatments . The nematode, pathogen and weed density data were transformed [ln ] to stabilize the variance prior to analysis; however, means of untransformed data are presented for clarity. Treatment means were separated using Fisher’s protected least significant difference procedure with α = 0.05.Emission flux. Within a surface treatment, there were no statistical differences in emission flux between the two application shank types, thus data were combined over application rig. However, significant differences in 1,3-D emission flux were observed among surface treatments . Fumigant emission flux from bare plots was two times higher than from water seals and HDPE and nearly 15 times higher than from VIF within 48 hours after treatment. Emission from water-sealed plots was reduced during the sequential water applications, but flux was similar to bare soil plots after 48 hours. HDPE film continued to give lower emission rates than the bare soil and water seals but was significantly higher than VIF. Throughout the monitoring period, VIF-covered plots had the lowest 1,3-D emissions; maximum flux was 11 micrograms per square meter per second , which was at least 90% lower than that from the bare soil plots. Relative to the bare soil treatment, estimated cumulative 1,3-D emission losses for water seals, HDPE and VIF were 73%, 45% and 6%, respectively, which were similar to reports from a previous field study . Headspace 1,3-D concentration. Concentration of 1,3-D immediately below the plastic film indicated that 1,3-D retention is much greater under VIF film than under HDPE . Several other studies have shown that VIF can retain substantially higher fumigant concentrations without negatively affecting nematode, pathogen and weed control efficacy or crop yield . Fumigant distribution in soil. Initial analysis of fumigant distribution in the surface 90 centimeters indicated that there were no differences between the application shanks within a surface treatment in this zone; thus data were combined over application shank types . The 1,3-D concentration was highest near the injection depth, at 45 centimeters and lowest near the soil surface, at 5 centimeters , and at 90 centimeters , but this difference diminished over time.

Plots that had been planted with field peas and vetches in mid-summer were associated with lower flag leaf nitrogen than plots that had received spring plantings of field peas and vetches. Grass cover crops were associated with the lowest leaf nitrogen, suggesting that the ability of grass decomposition to tie up nitrogen can be persistent. Visual growth differences were apparent throughout the winter wheat growing season; wheat in spring field peas and vetch cover crop treatments were taller and much greener than other treatments. This suggests that nitrogen release from legume cover crops can continue for more than 1 year and can potentially have cumulative effects in crop rotations.Chicken manure amendments were the most effective fall-applied amendments for increasing soil nitrate levels at potato planting . Soil nitrate at potato planting in soil amended with chicken manure was greater than 75 pounds of nitrogen per acre , similar to levels in plots treated with field peas and vetches. Potato petiole nitrate levels for plots amended with chicken manure were over 19,000 ppm at early tuber bulking, similar to levels produced by many field peas and vetches. Potato petiole nitrate at early bulking for blood meal and soy meal amendments was similar to levels associated with both chicken manure and 150 pounds per acre of urea fertilizer . Green waste compost applied at all rates, as well as composted steer manure, led to lower soil nitrate at potato planting than did chicken manure, and these amendments did not increase soil nitrate at potato planting compared to the fallow treatment . Green waste compost and steer manure did not increase potato petiole nitrate at early bulking and vine maturity compared to the fallow treatment, flood drain table suggesting that nitrogen in these amendments mineralized too slowly for a single application to benefit a potato crop .

Potato establishment and early season vigor did not differ significantly among treatments, but differences in potato vigor were significant at row closure and tuber initiation . Treatments producing high potato petiole nitrate produced taller, greener potato plants than did treatments producing low potato petiole nitrate. Russet Norkotah total potato yield, average tuber size and cull yield were influenced by cover crops and amendments while Yukon Gold potato yield was similar for most treatments . This trend was not surprising given that Russet Norkotah is more responsive to nitrogen fertilizer than Yukon Gold. For Russet Norkotah, vetch species , chicken manures, steer manure, blood meal and soil protein fertilizer produced higher total potato yields than did the untreated fallow. These treatments, along with five field pea varieties, resulted in a larger average tuber size than did the untreated fallow . Total yield for the treatment with 150 pounds per acre of urea fertilizer was similar to that produced with vetches, chicken manures and blood meal, suggesting that soil nitrogen availability was a primary factor in increasing potato yield . Nitrogen’s important role is also supported by a strong positive correlation between total Russet Norkotah potato yield and potato petiole nitrate at early bulking. The r value for this correlation equaled 0.656 when Russet Norkotah and Yukon Gold data were combined. The only treatment-related effect on total Yukon Gold potato yield was that cover-cropping with spring wheat and fall triticale produced lower total yield than did cover-cropping with legumes . Grass cover crop treatments led to numerically lower soil nitrogen at planting and lower potato petiole nitrate at early bulking, compared to the untreated fallow .

This suggests that the low potato yield following grass cover crops could be due to nitrogen immobilization during potato growth and development. Cover crop and amendment treatments did not cause a substantial increase in tubers with knobs or growth cracks in either Russet Norkotah or Yukon Gold , but the percentage of cull potatoes based on total yield for Russet Norkotah differed among treatments . Both chicken manure treatments, as well as blood meal and soy protein, resulted in higher percentages of culls than did the untreated fallow. An increase in cull percentage often occurs as total yield increases, but Perfect Organic Blend chicken manure also produced a higher percentage of culls than did the treatment with 150 pounds per acre of urea fertilizer. All cover crop treatments led to a percentage of culls similar to or lower than was associated with the treatment with 150 pounds per acre of urea fertilizer . Yukon Gold was chosen for the 2017 trials because Rhizoctonia black scurf and black dot tuber blemish, common problems for organic potato growers, are easy to see on yellow varieties. The severity of black scurf and black dot did not differ according to cover crop species, but in potatoes grown after spring-planted cover crops , 27% exhibited black scurf — compared to 13% in potatoes grown after mid-summer and fall plantings of cover crops. On the other hand, spring plantings of cover crops led to lower black dot severity on tubers than did mid-summer plantings .Economic issues play a major role in the feasibility of using legume cover crops to boost soil nitrogen in a crop rotation. Organic growers must consider the opportunity cost involved in growing cover crops instead of a cash crop as well as the cost of applying an amendment such as chicken manure. The economic analysis required to weigh all benefits and lost opportunity costs is complex, and beyond the scope of this study, but a comparison of monetary costs shows that cover crop production is more expensive than synthetic fertilizer, similar to applying chicken manure and less expensive than applying blood meal and soy meal.

The average cost of bulk urea fertilizer from local suppliers in Northern California in 2018 was $365 per ton, or $60 to supply one acre with 150 pounds of nitrogen . The average cost of bulk dried poultry manure from local suppliers in Northern California was $145 per ton, or $272 dollars to supply one acre with 150 pounds of nitrogen . The cost of bulk blood meal and soy meal represented a nitrogen cost of greater than $3.40 per pound, or over $500 to supply one acre with 150 pounds of nitrogen. The cost of certified organic blood meal, packaged in 50-pound bags, was greater than $7 per pound of nitrogen, or more than $1,000 to supply one acre with 150 pounds of nitrogen. The total cost of field pea and vetch production is estimated at $175 dollars per acre, including the cost of seed, planting, irrigation, management and incorporation .Vetch, field peas, blood meal, soy meal and chicken manure, because they produced potato yields and potato petiole nitrate similar to those produced in plots treated with 150 pounds per acre of urea fertilizer , were feasible alternatives to synthetic fertilizer. Whether organic producers favor cover crops or chicken manure as a nitrogen source depends on several factors, including land availability and the opportunity to grow cash crops. Producers who grow high-value cash crops requiring a full growing season may favor amendments because they can be quickly applied after harvest or before planting. Producers with idle land or with time between cash crops during the growing season may prefer cover crops, as many legumes in this study added over 150 pounds of nitrogen per acre and provided multi-season carry-over of soil nitrogen, and also offer protection from soil erosion. For hay producers, it’s extremely important to leave above ground biomass from legume cover crops in place, instead of haying the residue, because most added nitrogen is contained in legumes’ leaves and shoots rather than their roots. Regardless, both options offer benefits in soil health, and in our study the added nitrogen in both cases broke down into mineralized form in adequate amounts to meet early-season and late-season potato nitrogen needs. The economic benefit of using cover crops and chicken manure is more difficult to justify in conventional potatoes because, in our research, both practices entail higher costs and greater difficulty of application than synthetic fertilizer, which produced similar yields. For organic potato production, using either grass cover crops or a one-time application of compost to increase soil nitrogen is difficult to justify economically. In our research, grow tables 4×8 these treatments had a neutral or negative effect on soil nitrogen compared to fallow treatments. Organic nitrogen in these treatments failed to convert into mineralized form in adequate amounts to increase either potato yield or yield of wheat planted the year after potatoes. Mustard, arugula and radish had a neutral-to-positive effect on potato yield and nitrogen.

Several Brassica species have also been shown to have biofumigation properties, although a reduction in soilborne potato diseases Rhizoctonia solani, Colletotrichum coccodes and Verticillium wilt was not evident in this study. Fallowing for an entire year, starting in spring the year before growing potatoes, is another option that growers with idle land or limited water can consider. In this research, the spring fallow treatment resulted in mineralized nitrogen at potato planting similar to or higher than levels that resulted from the summer fallow and fall fallow treatments . In potatoes, the spring fallow treatment produced petiole nitrate at early bulking similar to that produced by a treatment with 150 pounds per acre of urea fertilizer following barley . The additional nitrogen in the spring fallow treatment was likely related to natural mineralization of soil organic matter, as organic matter in Tulelake soils is naturally high .Rice is one of the most important sources of human energy worldwide and is grown in a wide range of agroecosystems, though paddy systems are the most prevalent . In California, more than 200,000 ha of flooded rice are grown in a waterseeded, continuously flooded system that has successfully suppressed certain nonaquatic weed species such as barn yard grass [Echinochloa crus-galli Beauv.] and bearded sprangletop . Currently, rice growers in California flood fields at the beginning of the growing season and then direct seed pregerminated rice seed into the flooded fields from airplanes. A flood depth of 10 to 15 cm is maintained until approximately 1 mo before harvest, when the field is drained to allow rice harvesting. Repeated use of flooded irrigation in the California rice agroecosystem has since selected for weed species such as late watergrass [Echinochloa oryzicola Vasinger] that are well adapted to the system. In recent years, California has experienced unprecedented drought, with the 2012 to 2014 period being the driest on record . Accordingly, concerns about water usage have increased, particularly for crops like rice that have high water use. Due to the flood irrigation, rice is a visible water user, receiving attention from both the general public and policy makers, and there is increased pressure on rice growers to reduce water use. In California, the only alternative to water seeding currently in use is dry seeding followed byflooding after early postemergent herbicide applications. Recent research, however, indicates that drill seeding into dry soil as practiced in California rice systems does not necessarily reduce crop evapotranspiration, crop coefficient, or irrigation delivery in comparison with the continuously flooded system . A number of alternatives to flood irrigation exist in other rice-growing regions of the world, including an alternate wet and dry system , which reduces water use over the crop growth period through alternating periods of flooding with periods of drying, and saturated soil culture , which reduces water use over the crop growth period by maintaining the soil at the saturation point . Yields in aerobic systems are often lower due to the reduced ability of rice to compete with weeds , and this may be an obstacle to adoption of alternative irrigation systems by growers. In addition to changing the competitive ability of rice with respect to weeds, alternative irrigation systems can shift weed species composition, selecting for some species over others. In California, differences in irrigation during the seedling recruitment period have been shown to shift the emergence of certain weed species when comparing wet- versus dry-seeded systems . In these systems, water seeding favored sedges and broad leaves, whereas dry seeding favored grasses, particularly watergrass and sprangletop species . Later in the season, sedges and grasses dominate over aquatic weeds in saturated, non-flooded soils . For continuously flooded systems, water depth also affects the presence of certain species. Grasses are suppressed by continuous flooding to a depth of at least 5 cm, whereas a deeper flood of about 15 cm suppresses most sedges .

The recommendations comprehensively address bio-fuel production and use, as well as the necessity of agency and private sector stakeholder cooperation for effective implementation of the recommendations . Initially, all federal agencies with authority relevant to bio-fuel production should be identified, their likely responsibilities on the invasiveness issue determined, and their ability to minimize the risk of bio-fuel escape and invasion strengthened as necessary. To reduce the risk of escape, the bio-fuel crops that are promoted should not be currently invasive or should pose a low risk of becoming invasive in the target region. In addition, bio-fuel crops should be propagated in production sites that are least likely to impact sensitive habitat or create disturbances that would facilitate invasion. Most importantly, effective mitigation protocols need to be developed to prevent dispersal of plant propagules from sites of production, transportation corridors, storage areas and processing facilities. Minimizing harvest disturbance can also reduce the potential for dispersal and off-site movement of propagules. Prior to wide scale planting, multi-year eradication protocols should be developed that are based on integrated pest management strategies. Such practices should be readily available, and appropriate information should be distributed with the purchase of bio-fuel crop seeds. These control methods are not only critical for preventing the dispersal of bio-fuel crops from abandoned production sites, they are a necessary component of an effective early detection and rapid response system for bio-fuel crop populations that do escape active management. Throughout this entire process , flood and drain table all stakeholder groups should be engaged, from bio-fuel development to conversion.The question of how species successfully invade new areas has fascinated scientists for over a century .

By studying ruderal and agricultural weeds invading empty niches, Herbert Baker began to identify characteristics associated with invasiveness, which resulted in a list of traits describing the ‘ideal weed’ . Work in subsequent decades examined a wide range of traits using comparative approaches of taxonomically-related species and regional floras . With these studies came an increasing realization that factors contributing to invasiveness are strongly influenced by the stage of invasion, characteristics of the introduced range, and which species groups are being compared. These realizations, combined with discrepancies across studies, resulted in some skepticism that traits associated with invasiveness could be generalized . However, there is support for the idea that invasive species differ from non-invasive native and non-native species in key attributes depending on the environmental context . Here, we explore how ecological and evolutionary theory has refined our understanding of the ‘ideal weed’. We do not provide an exhaustive review of all traits but rather an overview of key functional and evolutionary frameworks in which progress has been made.Baker’s ‘ideal weed’ possessed a general-purpose phenotype , life history traits that permit reproduction from a single individual , rapid growth, and high, continuous seed output . Several of these characteristics are well studied and appear to be common when evaluated across different invasive taxa such as high germination success across environments , selfing , and rapid growth rate , while others are less studied . In recent decades, researchers have broadened the search for ‘weedy’ characteristics to include traits related to resource acquisition and use that underlie rapid growth, competitive ability, and even stress tolerance. Syntheses of regional and global for as have demonstrated that, relative to non-invasive species, invasive species are generally larger, have higher specific leaf area , allocate relatively more biomass to leaves and stems at the expense of roots, and use resources more efficiently .

However, there are exceptions to every rule. Identifying traits associated with invasive species is hindered by differences in how invasiveness is defined, bias in species selection for experiments, and challenges comparing species at different stages of invasion . However, several useful frameworks have been developed to evaluate traits within relevant contexts. First, many researchers recommend controlling for a species’ commonness when selecting species for experiments as comparisons among common invasives and rare non-invasive species may lead to spurious conclusions . For example, invasive species appear to be more competitive than co-occurring natives ; however, many of these studies focus on particularly aggressive and common invaders. In a comparison of annual plants in Germany, Zhang and van Kluenen found that invasive species were stronger competitors only when comparing common invaders with rare natives. In essence, comparing species that are similarly successful should allow researchers to identify traits that promote invasion in particular, rather than commonness more generally. In another effort to standardize how invasiveness is defined, Catford et al. proposed comparing traits of invasive species within invasiveness categories based on four demographic dimensions: local abundance, geographic range, environmental range, and spread rate. One trait may promote invasiveness along one dimension but limit invasion along another . Time since introduction and propagule pressure would ideally be incorporated into invasiveness categories , but these data are not available for many species. Perhaps the most comprehensive effort to link traits to different stages of invasion is that of van Kluenen et al. who proposed a nested, multi-scale approach . Identifying a universal set of traits that explains invasiveness is challenging because traits are dependent on environmental context, including specific abiotic and biotic factors arising from, for example, climate and community composition .

By accounting for spatial scale, the framework proposed by van Kluenen et al. avoids inappropriate comparisons of traits across different stages of invasion and resolves inconsistencies associated with context dependency. For example, studies have found that invasive species can have smaller, similar, or larger seeds compared to native or non-invasive species . However, this inconsistency likely reflects different ecological filters or processes across stages: smaller seeds are likely to be dispersed to new sites, but larger seeds have more resources for establishment and growth . Conversely, some traits may enhance invasiveness at multiple stages of invasion. For example, fast growth rates can assist with colonization of new or disturbed habitats , lead to priority effects , and ultimately affect competition outcomes in established communities . Finally, a trait-based community assembly framework may also elucidate mechanisms of invasion . Community assembly theory allows for both stochastic and niche-based processes at various scales. Species composition within a community is determined by a series of ecological filters that sort species based on their traits . As an example, seed predation is a strong biotic filter on recruitment in some systems and this may favor species with smaller seeds that are more likely to evade predation from rodents . Investigating how trait-performance relationships change when a filter is manipulated can indicate if non-native invaders are succeeding by acting like the natives or by doing something different . Trait analyses can also determine if invasive species occupy empty niches. Work in desert annual communities in the southwest U.S. show that invasive annuals have unique trait combinations that allow them to grow fast and use water efficiently . Below, we expand on how traits and trait plasticity interact with abiotic and biotic filters to regulate invasion.Many invasive species thrive in resource-rich environments . Environments with ample light, water, or nutrient availability could favor fast-growing species that quickly take up available resources. Species associated with a resource acquisitive strategy have trait values aligned with the ‘fast-return’ end of leaf, plant, and root economic spectra . This includes cheaply constructed, short-lived tissues designed for high rates of carbon and nutrient assimilation and biomass allocation patterns that favor light interception and growth . These species may alter the system in a way that prevents slower-growing species from establishing and dominating. For example, hydroponic flood table the proliferation of invasive grasses in many systems suppresses woody seedling establishment via competition for limiting resources or increased fire firequency leading to a type conversion or invasion by other species . Many species can also invade low resource environments and they succeed by employing a wide range of strategies . Community assembly theory predicts that strong abiotic filters in stressful environments will result in co-occurring species with similar traits and there is some evidence for this in invaded systems. For example, species invading low resource systems are similarly or more efficient at using limiting resources relative to native species adapted to those systems .

There is also evidence that invasive species can succeed in low resource environments by possessing resource acquisitive traits. While native and invasive non-native annuals in semi-arid Mediterranean-climate ecosystems are similar with respect to most traits, invasive annuals were taller and had larger seeds and thinner roots—which likely enhances establishment and resource acquisition . Phenological differences, such as early germination, may allow invasive species to avoid competition from co-occurring species in low resource environments . Early phenology coupled with high resource-use efficiency or rapid growth may be particularly effective in low resource environments, such as deserts and coastal sage scrub in the southwestern U.S. . In sum, the fast growth rates and competitive strategies hypothesized by Baker appear to promote invasion in a range of habitats, but the specific physiological traits underlying these strategies differ across environments. Resource acquisition traits may be particularly useful in high resource environments, while efficient resource use or competitive strategies like early phenology may lead to invasion success in low resource environments. Finally, a central tenet of Baker’s ideology is that some invaders display broad environmental tolerance and are able to move past environmental filters by possessing traits that promote high fitness under low and high resource conditions. Some invasive species exhibit broad environmental tolerance by not conforming to growth-stress tolerance tradeoffs. For example, Norway maple is a common invader in North American forests and has high survival under low light conditions and high growth rates in full sun . Tree of heaven is one of the most invasive woody species in Europe and North America and its broad geographic distribution is driven by a combination of traits aligned with high resource acquisition as well as the ability to alter morphological traits and biomass allocation patterns across environments . During the invasion process plants may escape specialist enemies that limit their population growth in the native range . Such escape is typically transient, however, as invaders accumulate new enemies over time . The initial escape from enemies could allow for rapid establishment but, over longer timescales, three traits of invaders may make them particularly adept at overcoming the biotic filter created by enemies and promoting invasion. First, ruderal invaders can escape their enemies by virtue of their high dispersal, short lifespan, and low allocation to defense, fireeing up resources for rapid growth or competitive ability . Second and relatedly, many invaders appear to have high growth rates, which tend to reduce the cost of damage . This high growth rate means that invaders can withstand high amounts of enemy damage with limited effects on fitness . Consistent with this idea, in a multi-species study, invasive vines received just as much herbivory as natives or naturalized species, but were also more tolerant of damage , although other multispecies studies and metaanalyses find that invasives are similarly or even less tolerant to herbivory than natives . Third, native generalist enemies may have reduced preferences for non-native species with which they have no evolutionary history , although this appears not to be a general phenomenon across invasive species . Thus, both innate traits of the invader that Baker hypothesized would facilitate invasion and the match between invader traits and the invaded community may reduce the capacity for enemies to limit invader population growth. Like enemies, mutualists may also be left behind during the invasion process. As a result, successful invaders might be less dependent on mutualists , more generalist and able to interact with a wide variety of partners as predicted by Baker , or rely on co-invasion of mutualist partners . For example, selfng was one of Baker’s ‘ideal weed’ characteristics because it would allow reproduction in the absence of suitable pollinators and at low population densities. Selfers do appear to be over represented in invasive taxa although it is not clear whether this is because of the advantages of selfng when suitable pollinators aren’t available or because of Allee effects. For other species that fail to meet Baker’s criteria of generalized dispersal or pollination mechanisms , like that of highly specialized fgs which require a specific species of wasp pollinator or pines limited by appropriate mycorrhizae, invasion can still occur but only once the mutualist also invades.

Where other buyers exist, producers may try to increase property rights and bargaining power by retaining ownership of any surplus yield. For example, the contract could explicitly reserve any production surplus over the maximum to the producer or preserve the right of the end-user to request surplus biomass priced under the contract’s default compensation provision. On the other hand, contracts also must consider allocation of catastrophic risk. Over time, it is likely that weather, pests, drought, flooding, wind, or hail will impact biomass production on a given farm. No such product exists for biomass as of this writing. End-users require a consistent supply to accommodate conversion facilities, but a biomass farmer that fails to harvest a crop 243 has no revenue to perform the contract via spot market purchases—especially when there is no spot market for biomass. Accordingly, contracts should specify conditions for performance excuse and contingency provisions. Moreover, in the absence of a government safety net along the lines of crop insurance, biomass contracts should consider minimum revenue provisions to provide the farmer with some compensation. One way to soften this effect on the end-user is through the use of an amortized payment schedule. Producers would receive a guaranteed cash flow during all years of production to cover costs, but later payments could be diminished to allow the end-user to recover the costs throughout the life of the contract. Contracts could also require crop insurance, once available, botanicare trays and use insurance proceeds to offset initial contingency provisions.Once the crop is established, producers face a number of issues during the growing phase.

Some production contracts may require very specific production practices in order to decrease end-user supply risk and require monitoring of crop quality. These requirements decrease producer autonomy, and diminish potential gains from producers’ individual management skills and experience. Heavy requirements may also restrict the producers’ flexibility to adjust management practices to various production environment scenarios. On the other hand, considerable production risk arises from inexperience and lack of knowledge with producing energy crops. Inexperience or ignorance may cause a producer to adopt a production practice harmful to the crop or environment. In addition, the producer may be unsure how to address new production hazards, such as a new pest, drought conditions, or invasiveness. Thus, inexperience and lack of knowledge creates risks and costs for producers. End-users may desire to increase producer control through the biomass production agreements. As a general rule, however, contracts should allow producers as much freedom as possible to choose production practices. A principle of the Sociological Compatibility perspective is that producers value autonomy and demand compensation in some form for the loss of autonomy to satisfy participation constraints. Moreover, adjusting cultural practices is a traditional risk management tool for producers. For example, producers may choose to apply fertilizer in the fall to avoid higher prices in the spring, decide to plant later to avoid risk of a late frost and insect pests, and producers may choose to plant herbicide resistant crops and apply herbicides rather than mechanically cultivate crops to reduce weed competition. Because incentive contracts enhance producer risk, and rigid production practices foreclose other risk management strategies, other methods of dealing with end-user production risk are preferable. In other words, production practices have very poor separability, and thus respond poorly to incentives.

A better strategy may be for biomass production agreements to employ the use of generalized legal standards rather than specific practices to control production, which would shift contracting costs from the front to back end, while providing greater producer autonomy. A singular focus on incentives to maximize yield, however, is fraught with potential downside risks to long-term sustainability and suitability with end-user needs. For example, there is a tradeoff between corn stover removal, soil erosion, and fertilizer inputs. Removing high percentages of crop residues increases the risk of soil erosion from water and wind. Excess stover removal to increase per acre yield in one year will require additional fertilizer for the following crop year. Excess fertilizer can then impact the composition of the resulting biomass, especially its mineral content, which can then impact the ethanol conversion process. Additional fertilizer application also shifts the carbon footprint of the biomass feedstock or precipitates other environmental externalizes . Research also has suggested that the loss of soil organic carbon serves as an additional constraint for corn stover harvest. Similarly, harvest timing and cutting depth of both corn stover and perennial biomass crops must balance yield, moisture content, nutrient storage in the rootstock, soil compaction, and wildlife habitat over the winter. At the establishment stage, producer discretion in initial crop variety selection could impact potential invasiveness or migration of genetically engineered plants.  Accordingly, incentives in biomass supply contracts should provide producers sufficient flexibility to manage production and harvest decisions within the context of their other farming operations and long-term environmental values. As discussed in more detail in Section IV, infra, sustainability standards address many of the environmental tradeoffs identified above and embed balancing criteria to allow for producer autonomy within the context of environmental, social, and economic sustainability. Incentive contracts could look to or even incorporate third-party sustainability certification programs for guidance in allocating risks and responsibilities among producer and end-users with respect to balancing yield with environmental impacts.

In addition to, or complementary with, third-party sustainability certification, monitoring through the use of fieldmen may provide the most favorable strategy to address moral hazard during establishment and maintenance. Although developing the fieldmen model may take time, the benefits discussed in the framework likely outweigh the costs. Contracts can incorporate this model by elaborating on the “cooperation provision” outlined in the information sharing section. In addition to requiring notification of any material change in circumstances that may affect performance of either party’s obligations, the contract could create a right of the end-user to inspect the producer’s premises. In order to be of value to producers, end-users should employ the services of agronomists or individuals with knowledge and experience in biomass crop production, a requirement likely worth adding into the contract. Qualified fieldmen also can provide an excellent avenue for information sharing and education—an important risk management tool. In addition to inspections, the contract should authorize producers to request fieldmen services. Moreover, fieldmen could be enabled to authorize contract modifications or excuse performance. This strategy enhances producers’ social interaction factors, and could be coupled with assistance for sustainability standard certification.End-users deploy biomass production agreements to secure a stable supply of biomass, as well as other important characteristics, such as moisture level, foreign matter, mineral profile, BTU content, size and shape, and its environmental footprint. Risk arises when the producer is required or incentivized through penalties or bonuses for these crop attributes. While the producer may have control over some attributes, others evade manipulation. Strict consequences, such as rejection or price docking, create large risks for producers. Moreover, when minimum requirements are defined loosely, end-users may be able to engage in opportunistic behavior. To minimize holdup, biomass contracts should incorporate reasonable margins of error to account for normal environmental characteristics, as well as procedures for third-party verification and re-measurement.Storage and transportation of the low-density, high-volume biomass from the producer to the end-user presents unique challenges and should be considered carefully in the biomass supply contract. Assigning responsibility for storing and transporting implicates both risk- and cost-minimization strategies of contract design. For example, a set delivery date in the contract provides certainty, but indirectly assigns the storage burden—perhaps to both parties—and requires careful planning. On the other hand, an “on end-user demand” clearly shifts responsibility for storage to the producer and may dictate harvest timing despite other agronomic or environmental considerations. In contrast, an on-harvest delivery term places storage responsibility—and attendant risk of loss—on the enduser. Transportation responsibilities tie directly into product specifications and storage. If the contract requires certain harvesting methods or preprocessing requirements, flood table such as pelletizing or densification, the farmer may incur significant upfront equipment costs to produce the required result. However, some producers seek flexibility to minimize processing and transportation costs, such as forage chopping, directly into road transportable wagons, or pelletizing biomass in the field to decrease volume. In sum, up-front consideration should be given in the contract to linking product specifications with optimal storage methods to minimize post-harvest loss and maximize transportation efficiencies. The very high level of asset specificity, along with specialized equipment, places significant post-harvest risk in the farmer who has little bargaining power in a single-buyer market.

Accordingly, a more complete contract to minimize hold-up risk may be necessary to induce contract acceptance by the farming community.From a producer perspective, several factors influence the choice of land for biomass production. Perhaps most important is opportunity cost. In the Midwest, where much of the land is highly productive and can support currently higher value crops , energy crops, such as Miscanthus and switch grass, are unlikely to compete for scarce land resources. Biomass may be relegated to more marginal lands with lower opportunity cost, such as pasture or hay ground. Perennial biomass crops do provide, however, a number of environmental benefits, such as erosion control, improved soil and water quality, increased wildlife habitat, and increased soil organic carbon. Producers, therefore, may want to take advantage of these benefits and grow energy crops on at least marginal land to provide these long-term and environmental benefits. In addition, studies have shown that soil types can affect the composition of biomass plants, such as the percentage of lignin, cellulose, ash, and mineral content. In this way, land choice can significantly influence the quality and value of the resulting biomass crops. End-users have two strong preferences concerning the choice of land. First, in order to secure a stable biomass supply, endusers would prefer to tie biomass production to land title, rather than tying production requirements to individual producers. This strategy permits end-users to be less concerned with producer default, as land resources remain dedicated for biomass production. Other than outright purchase of land by the enduser, more creative avenues exist, such as equitable servitudes, covenants, or easements, to produce biomass that would attach to land title and provide more supply security than long-term lease agreements. Second, end-users prefer that biomass production be located near the end-user’s facility to decrease transportation costs. Where the end-user assumes the responsibility of transporting the biomass, local production is especially important. Longer transportation routes also increase greenhouse gas emissions, thereby decreasing the energy balance of the crop. Local production creates cost and risk for producers in two main ways, however. First, producers lose the traditional agriculture risk management strategy of geographical diversification; they cannot spread out production over larger areas to decrease weather and pest risk. Second, requiring local production limits the producer’s ability to produce energy crops on marginal ground or land exiting the Conservation Reserve Program. These production dynamics create a number of concerns for producers. First, as discussed in the Sociological-Compatibility Perspective, a producer may be unwilling to relinquish that level of control over his land; producers’ land is usually their most critical asset. Second, the greater the degree the land title is locked into biomass production, the greater the level of asset specificity, increasing the risk of holdup or renegotiation. Moreover, most producers grow crops on a combination of owned and leased land, with farmers depending on rental land resources to achieve economies of scale. Tying biomass production to land title, therefore, tightens the producers’ participation and incentive compatibility constraints and necessitates higher compensation.On the other hand, the multi-year production cycle for perennial biomass crops injects unique risk concerns into the farmland rental market. Producers may have difficulty securing leases for the duration of the production contract or even the life cycle of crops, such as switch grass and Miscanthus. Moreover, landowners may be concerned with the short- and long-term effects of biomass production on the land itself, or how to remediate the land back to its prior use if the end-user defaults on the biomass supply contract—a particular concern due to asset specificity. To provide safeguards and regulate producer practices, traditional leases have often relied on legal standards and duties .