Our study aligns with these studies in recommending active long-term management to enhance native populations and resist invasive populations. Instead of viewing restoration projects primarily as short term implementation efforts with only an auxiliary “maintenance phase,” the implementation phase of restoration could be primarily focused on establishing the biophysical conditions needed for native plant species establishment . This initiation of restoration is best followed by a long-term commitment to site stewardship, where community engagement could help defray long-term costs while providing ecosystem services. This directly aligns with indigenous land management practices, wherein humans are viewed as part of the annual and interannual dynamic of ecosystems . We suggest that “restoration” entails not only the initial restoration of native plants and animals and the exclusion of undesirable species but also the restoration of the symbiotic relationship between humans and nature via long-term human stewardship to create desirable ecosystems. Long-term adaptive management plans require ongoing monitoring so that management can pivot to address rising challenges. When funds are limited, cannabis drying engaging local community groups to help with ongoing restoration efforts can achieve both ecological goals and social goals . Shifting the focus toward viewing restoration as a long-term relationship with the land may thus allow us to realize more resilient and resistant socioecological systems.
Plant domestication is the process of conversion of wild plants into domesticated crop plants through artificial selection. Domestication leads to plant varieties that are distinctly different from their wild ancestor, typically selecting for a suite of traits including the ability to grow in densely planted environments, easily controlled mating, reduced seed dormancy and seed shattering, good nutritive or fiber quality, and adaptation to local growing conditions . However, in the process, some cultivated plants may escape cultivation and evolve in unintended ways. Plant de‐domestication is an evolutionary process separate from domestication, in which plants develop genetically and phenotypically distinct “feral” populations through hybridization and/or adaptation . During dedomestication, weedy populations typically re‐acquire traits that were lost in the process of domestication such as seed shattering and seed dormancy while retaining some crop‐specific traits such as crop growth form and ability to thrive in a densely planted managed field environment . These weedy populations pose a problem for crop cultivation because they are often similar enough to the crop to escape weed management practices, but can reduce the yield and value of the crop. Compared to the evolutionary process of domestication, de‐domestication is far less well understood,especially in terms of how these de‐domesticated plants came to be and how their populations and genomes are evolving . Asian domesticated rice originated in South and Southeast Asia from the wild rice species Oryza rufipogon Griff.
Several distinct types of cultivated rice, including japonica, indica, and aus varieties, have evolved through multiple domestication events, ad‐ aptation to environment and rice‐growing practices, and selection for agronomic and culinary traits . Cultivated rice has been a model genetic system for agricultural plants because of its small genome, ease of genetic manipulation, and importance as a food source globally . This has led to a wealth of developed genetic resources, which can be used for the study of plant evolution. In the United States, two major rice‐growing regions, the Mississippi River flood plain in the southern United States and the Sacramento Valley region of California, produce tropical japonica and temperate japonica rice, respectively. Weedy rice , also known as red rice, is a major problematic weed of rice agriculture in many regions . It is considered to be the same species as cultivated rice, O. sativa . While populations of weedy rice vary, it can generally be distinguished from cultivated rice by the red seed pericarp it is named for, high seed shattering, and increased seed dormancy . This weed competes with cultivated rice in the field, leading to yield losses of up to 49% in the southern United States . Weedy rice is phenotypically similar to cultivated rice during the vegetative stage, making it difficult to identify until late in the growing season. The phenotypic and biological similarities of weedy rice with cultivated rice make it difficult to control in‐season with either hand‐weeding or chemical weed control methods. Because weedy rice is conspecific with cultivated rice, the abundant genetic resources developed for cultivated rice can also be applied to weedy rice.
With diverse populations found in rice‐growing regions around the world, weedy rice can be used as a model system to study weedy plant evolution as well as understanding the process of de‐domestication. As early evolutionary biologists considered the origins of weeds that are related to crops, various hypotheses were proposed for evolutionary pathways to weediness . The endoferal hypothesis states that weedy crop relatives are derived directly from the crop as a result of de‐domestication . Local weedy populations could have descended either from locally grown cultivars or from distantly located cultivars transported through movement of contaminated seed. Endoferal weedy rice populations that likely originated from local rice varieties have been identified in China . Some of these weed populations may have arisen through hybridization of indica and ja‐ ponica cultivars, followed by environmental adaptation . Weedy rice populations from the southern United States have been found to be descended from Asian indica and aus rice cultivars not grown in the United States . New weedy rice biotypes may also arise by hybridization of cultivated rice with existing weedy rice biotypes. Some populations of weedy rice in the southern United States originally derived from Asian cultivated sources have hybridized with each other and with local cultivars resulting in distinct weedy rice populations . DNA sequencing of southern United States weedy rice and Asian weedy rice revealed that some populations contain a functional allele of the Rc gene responsible for both red pericarp and increased seed dormancy, indicating possible relationship to wild rice or Asian rice landraces never selected for white pericarp . In contrast to the endoferal hypothesis, the exoferal hypothesis states that weedy populations are the result of hybridization of the crop with its wild relative , in the case of rice most likely with O. rufipogon or O. nivara. Domesticated rice and its wild ancestor O. rufipogon have some reproductive barriers, but gene flow is possible between domesticated, weedy, drying cannabis and wild rice . Some studies have proposed that some southern United States weedy rice populations evolved from crop–wild hybridization in China , although there is limited empirical evidence for this. One final hy‐ pothesis is that weedy rice populations may not be derived from cultivated rice at all, but rather derived directly from wild rice species such as O. rufipogon or O. nivara, and that these populations have adapted to the environment of the cultivated rice agroeco‐ system, evolving phenotypic similarity with cultivated rice while retaining the seed shattering and seed dormancy traits of the wild species . Some south Asian populations of weedy rice are likely descended from a wild rice ancestor .
All of these hypotheses for the origins of de‐domesticated populations are non-mutually exclusive, and it is possible that a weedy population may have genetic contributions from several wild, weedy, or domesticated ancestors. It is clear from these previous studies that weedy rice around the world has evolved through several independent origins from diverse sources. The suite of phenotypic traits characteristic of weedy rice has evolved multiple times through convergent evolution of diverse genetic mechanisms . These studies highlight the need to investigate the evolutionary origins of weedy rice in individual regions to gain a greater understanding of weedy rice evolution as a whole . In California, weedy rice was reported in the early 20th century shortly after the beginning of commercial rice production and was hypothesized to have originated from contaminated seed from the southern United States . In the 1950s, weedy rice was thought to be eradicated. The use of a continuously flooded system and the widespread adoption of a certified seed program involving third‐party field inspections and rice variety certification were credited as the reasons for the disappearance of weedy rice. In 2003, however, weedy rice of a single biotype was reported in a dry‐seeded rice field . Since then, weedy rice has been identified in at least 60 fields and on over 4,050 ha in 2016 . While weedy rice in the southern United States has been well‐characterized , weedy rice in California is a recent and growing problem with previous studies limited to one or two biotypes . It is unclear whether California weedy rice is derived from the weedy rice present in the southern United States, from cultivated rice inside or outside of California, from Asian wild rice, or from hybridization of any of these groups. In this study, we seek to investigate the genetic diversity and relationships of California weedy rice, in order to gain insights into its evolutionary origins. We used microsatellite markers and a Rc gene‐specific marker to genotype 48 California accessions of weedy rice, as well as weedy rice from the southern United States, wild rice, and cultivated rice at 99 loci. We used phylogenetic, population structuring, and genetic distance‐based approaches to examine possible relationships and evolutionary hypotheses for the origin of California weedy rice. We hypothesized that genetic diversity of weedy rice biotypes and their relationships to other rice groups would indicate multiple independent evolutionary ori‐ gins of California weedy rice.Weedy, wild, and cultivated rice samples selected for genotyping analysis totaled 96 samples. Forty‐six weedy rice samples from California included 18 accessions collected in 2006 and 28 samples collected in 2016 . Samples were obtained from commercial rice fields in five of the nine major rice‐producing counties in the northern Sacramento Valley region of California. The majority of the 2006 collections were strawhull awned type or bronzehull awnless type, while several phenotypic types were present in 2016 collections . Four of the 2006 accessions were also used to produce plant mate‐ rial for other studies . To enable comparison with other weedy and wild rice, we included 20 weedy rice accessions from the southern United States and 8 wild rice accessions. We also included a total of 22 cultivated rice accessions: 6 temperate ja‐ ponica, 4 tropical japonica, 5 indica, 5 aus, 1 aromatic group V, and 2 red‐pericarp specialty rice accessions. Samples of cultivated rice, southern weedy rice, and wild rice were obtained from USDA col‐ lections and from the Rice Experiment Station .Genomic DNA was extracted from a 4‐cm‐long piece of leaf tissue from each plant sample using a modified TE‐potassium acetate extrac‐ tion protocol . Extracted genomic DNA was used directly for genotyping with 98 microsatellite markers and 1 Rc gene‐specific marker . PCR amplification was performed with 0.1 µM labeled for‐ ward and reverse primers, 0.06 µM unlabeled dNTPs, 1× PCR buffer, and 0.08 units BioReady Taq polymerase , and 10 ng DNA in a 8 µl PCR reaction. PCR reactions were run in a thermocycler with an initial denaturing step of 5 min at 94°C, fol‐ lowed by 35 cycles of 15 s at 94°C, 15 s at 55°C, and 30 s at 72°C, and a final extension of 5 min at 72°C. Products were resolved in a 6% poly‐ acrylamide gel using an ABI 377 DNA sequencer . Allelic differences between samples were scored based on allele size for genetic diversity and population STRUCTURE analyses. Genetic data were also scored as present or absent for each allele for the construction of phylogenetic trees. To examine the biotypes of weedy rice existing in California and the southern United States, genetic diversity and differentiation indices, including the mean number of alleles detected per locus, Shannon diversity index, observed and expected heterozygosity, unbiased expected heterozygosity, and inbreeding coefficient were assessed for weedy rice biotypes using GenAlEx v6.5 software . Genetic differences among groups of California weedy rice were also inferred by conducting an analysis of molecular variance in GenAlEx software. To assess relationships between all rice samples, phylogenetic analysis of all 96 samples of California weedy rice, southern United States weedy rice, wild rice, and cultivated rice was conducted using neighbor‐joining analysis with 1,000 bootstrap iterations in DARwin v.6 software with allelic data from 99 genetic markers. To assess the membership of individual genotypesinto clusters allowing for genetic admixture, allelic genotype data were analyzed for genetic structure using STRUCTURE software using 98 microsatellite markers, excluding the Rc gene‐specific marker as STRUCTURE analy‐ sis is only appropriate for neutral genetic variation.