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.