Moreover, while California weedy rice shares some similarity to weedy rice from the southern US at several loci as expected with a similar genetic background, divergence at few specific loci highlights changes required for California weedy rice to thrive in this novel agricultural system. If weedy rice in California is newly derived from a temperate japonica crop ancestor in current commercial fields, this suggests that new feral ecotypes can evolve anywhere rice is under domestication. Our population genetic diversity analysis is consistent with recent establishment of the weed from a few individuals: low genetic diversity within and between California rice cultivars where weedy rice infestations occurred. Pairwise divergence estimates indicate high genetic divergence between California weedy rice and other groups. We examined the possibility that gourmetrice varieties could have been the source of California weedy rice because it may be an established cultivated or wild-weedy rice originating outside of North America that recently colonized California. Thus, vertical cannabis we sequenced 12 informative STS loci in red colored pericarp gourmet rice varieties grown in California and found no shared haplotypes with California weedy rice . In addition, California weedy rice is distinct morphologically from gourmet varieties scored in this study .
While both California weedy rice and its putative domestic progenitor share straw hull color, phenotypic traits that differentiate California weedy red rice from cultivars include purple pericarp, increased plant height, longer leaves, greater tillering capacity, protracted flowering time, more grains per panicle, long awns, and seed shattering. The de-domestication origin of weedy rice direct from rice cultivars is not unique to this study, as at least two cases of O. sativa f. spontanea have been documented in the Guangdong and Liaoning provinces of China. Weedy rice in California is derived from rice cultivar in a smaller-scale rice growing region isolated from wild relatives and compliant with very strict guidelines for seed purity as well as tracking and reporting infestations. An earlier US weedy rice population genetics study by Londo and Schaal included microsatellite data for a single Californiaweedy rice genotype, RR28, collected in California. Sequence analysis of the p-VATPase region of this genotype indicated that it was a unique, private haplotype genetically most similar to O. rufipogon—specifically O. rufipogon A100945-1 from southeast Asia used in crossing trials in California during the late 1970s. These M-101 crosses with O. rufipogon accessions produced weedy rice with red pericarp and shattering seedsto be used as a stem rot- resistant parent in breeding programs. California weedy rice RR28 appears to be a unique variant not found in our collection of thorough California weedy rice sampling. Moreover, included only one California cultivar in their study.
This recently released cultivar is likely not the exclusive source of domestication alleles, so our study was designed to capture a comprehensive set of crop alleles from a wider range of California cultivars. Londo and Schaal reported that RR28 shares alleles with NSGC 5936 and California cultivar accession M205. The California ‘red’ rice specimen in our study, from the same county as the one used by [22], are four gourmet varieties with red bran. A single genotype cannot explain the population-level evolutionary history of weedy rice in California. We employed an extensive, broad sampling of wild, weedy, and cultivated genotypes to test the hypothesis of a wild/domestic hybrid in California. This sampling approach enabled us to examine how global and gourmet specialty rice sources have contributed to the localized evolution of weedy rice. The intermediate morphology of California weedy rice alone—strawhull awned and pigmented pericarp—does not necessarily indicate a crop-wild hybrid origin. Indeed, we found no evidence to suggest an escaped O. rufipogon source of weedy rice . From an evolutionary standpoint, the amount of morphological variation exhibited by this emergent lineage of weedy rice demonstrates its rapid adaptive potential and ability to persist in agroecosystems. Zhang et al. also used UPGMA cluster analysis and principal component analysis to show that a spontaneously emergent weedy rice lineage is more closely related to rice cultivar grown in the sample field than with other neighboring cultivars or weedy varieties,supporting a de-domestication hypothesis that weedy rice can be derived from cultivated rice as we show in this study .
The possibility that a widely cultivated species has a propensity to feralize under selection pressure variation has implications for crop management and necessitates further investigation on both the agroecological and molecular evolutionary levels .Morphological traits used to classify major ecotypes of US weedy rice , including awnedness, plant height and culm abundance, seed shattering, spikelet fertility , flowering, grain weight, and leaf size, are readily identifiable in the field . However, determining the evolutionary pathways to weedinessis imperative but challenging because de-domestication can follow different trajectories and proceed cryptically. Some weedy rice are visually indistinguishable from cultivars except for the shattering phenotype because some weedy rice have the same overall appearance and grain size as the cultivar, and have white pericarp, but this is not the case of California or other US weedy rice . Also, seed morphology differences between weedy and cultivated rice in the field may only become apparent after hulling when the red caryopsis is visible,effectively concealing the weed during invasion. Emergence, establishment, and spread of weedy rice in places that have no wild Oryza provide clues to how feral forms cryptically evolve. For example, re-seeding with previously grown cultivated rice in Malaysia has selected for weedy ecotypes which shatter their seed. In instances where farmers cease cultivating a land race to take advantage of a new cultivar with better yield, the agroecological conditions are altered to prime the environment for de-domestication to proceed. Abandoned land race rice can establish, and because farmers are familiar with the similar appearance of volunteer land race varieties under cultivation, they may not be identified as de-domesticated lineages. This suggests that management strategies must include monitoring at a smaller scale to ensure that escaping individuals with slightly higher variance in weedy traits are immediately identified rather than considered environmental variants of the cultivar. The historical eradication of weedy rice from California was largely due to intensive management including control of water and use of certified seed. However, unintentional dispersal of weedy individuals via a connectivity corridor such as a river or irrigation system could be responsible for either resurgence or maintenance of weedy rice populations.Evolution of weedy rice by de-domestication is not simply “domestication in reverse,” and involves the interplay of a greater number of mechanistic drivers than rice domestication. Temporal variation in US weedy rice flowering strategies and shared haplotypes with crop ancestors suggest hybridization and evolution on a short timescale. The gene or processes conferring a wild or weedy trait during de-domestication may not be the same ones responsible during domestication. However, because variation is limited to ancestral standing variation and novel mutations, weeds evolving directly from crops consist of fewer de-domesticated haplotypes, making these cases ideal for testing hypotheses about adaptive evolution during dedomestication. Understanding the origin of weedy rice in California will be useful in managing this weed and controlling the evolution of future feral ecotypes. Pinpointing the molecular evolution and genomic factors involved in the weediness associated with this endoferal origin of weedy rice in California is currently underway . In the absence of directed husbandry, grow racks domesticated lines will maintain or acquire weedy or wild traits to ensure success in resource capture, survival, and fecundity. This dedomestication, or evolutionary reversion to wild-type morphology , can happen through processes involving hybridization with endemic or introduced relatives and involve either natural selection acting on standing genetic variation in the domesticated populations or gene flow from wild relatives.
Modes of weed evolution include a domesticate origin with genetic contributions from weedy or wild relatives , or solely domesticate-derived forms . Seed dispersal is pivotal to the establishment and maintenance of grasses, where the level of shattering is directly related to a weed’s fitness. Because non-shattering is selected for in domesticated grasses, weeds evolving from crops would have to revert to shattering either through gene flow or by re-evolving the trait, assuming there is no standing variation for this trait in domesticated populations. Extended seed dormancy could also increase fitness of a weed, but would be selected against in a crop because cultivation would be difficult.Therefore, the reversion to seed dormancy would be selected for in weedy species.In addition, it is possible that pigmented pericarp may be selected for in weedy rice evolution due to its association with the ability of seedsto remain dormant for long periods of time.Weedy rice emerging in cultivated rice populations could be explained by the quick loss of a few domestication alleles in regions of the genome that experienced relaxation of selective pressure. Based on an evolutionary dynamic described in [75], the evolutionary genetic dynamics we observe here could be those of deep divergence of non-endemic wild species at neutral loci but allele-sharing at key wild-like loci, which necessitates a closer look at candidate genes. An interesting further avenue of research will be to sequence known genetic regions that confer weedy characteristics and whose patterns have been identified in both weedy and cultivated rice to have a better understanding of the evolution of weediness as manifested in the California ecotype . The Rc locus would be a good candidate because most rice cultivated in California would carry the loss of function mutation, resulting in a white pericarp. We can determine if California weedy rice shares polymorphisms associated with the loss of function allele , but has re-evolved pigmented pericarp either by reversion or by changes at another locus. We could also test if California weedy rice has captured the ancestral functional allele through gene flow from another source such as cultivated rice with a red pigmented pericarp or wild or weedy relatives present outside of the US. In closing, we present compelling evidence of rapid independent origin of weedy races of rice from cultivated relatives and contribute to our understanding of adaptive evolution under domestication. The use of divergence population genetics to track crop and weed interactions, as done in this study, is useful in understanding how weeds evolve and what approaches can be used to best control their spread. However, there is still much to learn about the extent to which contemporary populations diverge in genetic and morpho-physiological background from their non-wild progenitors during de-domestication.Weeds cause significant crop yield and economic losses in agriculture. Worldwide, the potential loss in overall yield of our major crops due to weeds is higher than that due to other crop pests, including insects, pathogens, viruses, and animal pests . Treatment with herbicides is a highly effective means of controlling weeds as herbicides can kill 90 to >99% of the weeds targeted. However, the evolution of herbicide resistance is reducing the overall efficacy of chemical weed management. Presently, more than 250 herbicide-resistant weed species and almost 500 unique cases of resistance have been reported. Changing environmental conditions are expected to have major effects on plant physiological processes such as stomatal conductance, photosynthetic efficiency and growth rate. Negative impacts of climate change on agricultural productivity has been widely recognized, mainly in the form of potential 6–13% decreases in crop yields. Mounting evidence suggests that changing climate conditions may also reduce the sensitivity of weeds to some herbicides. Glyphosate is the most commonly used herbicide in the world. It has a unique mode of action inhibiting 5-enolypyruvylshikimate-3-phosphate synthase , a key enzyme in the biosynthesis of aromatic amino acids. Glyphosate was found to be less effective under either high temperatures [e.g. in Conyza canadensis or elevated carbon dioxide levels [e.g. in Chenopodium album, Cirsium arvense and Glycine max] but no studies, to our knowledge, have examined the joint effects of both increased temperature and elevated CO2 level on plant response to glyphosate. Reduced glyphosate efficacy is mainly correlated with changes in the translocation and distribution of the herbicide. Vacuolar sequestration, limited cellular uptake and rapid necrosis were all found to play a role in reduced plant sensitivity to glyphosate. Even though photosynthesis is not the primary inhibitory target of glyphosate, it has been reported to be affected by this herbicide.