Impact of gene introgression and de domestication processes on the origin of weedy rice  (Oryza sativa f. spontanea) populations in Sri Lanka 

Majority of genetic studies of Domesticated Wild-Weedy Complexes (DWWC) have examined only a portion of the natural ecosystem, focusing on the spontaneous one-way introgression of  crop alleles into wild or weedy populations. Rarer still are studies that attempt to measure multi-way gene flow among all members of the DWWC. An ideal system to measure the role of multilateral gene flow in the evolution of a DWWC occurs in the large island nation of Sri  Lanka. The DWWC is incredibly rich, involving six evolutionarily discrete groups in the genus  Oryza that share common ancestry. Two different potential DWWC participants, traditional cultivars and modern improved cultivars represent the cultivated rice. Cross-compatible free-living relatives of the cultivated rice include the two wild species, the annual O. nivara, and the perennial O. rufipogon. Self-sustaining feral populations resulting from relatively recently abandoned cultivated fields represent another kind of free-living lineage class. The sixth category is one of the world’s worst weeds, weedy rice (Oryza sativa f. spontanea: Poaceae). Thirty-three neutral SSR markers were used to characterize the six evolutionarily discrete Oryza groups. It aims to explore multi way gene flow, population genetic structure, and the role of gene introgression and de domestication for the origin of the most noxious weed, weedy rice in Sri Lanka.  Results revealed that Oryza groups have relatively large effective population sizes and high inter-group long-term gene flow among Oryza groups. Significant asymmetric gene flow was found between wild and weedy rice groups, indicating considerable introgression from weedy rice to wild rice and vice versa. Complex genetic admixture among different Oryza lineages shows its dynamic nature and continuous evolution. Sharing patterns of rare alleles further provide evidence to the long-term interaction and sharing of genetic material among components of DWWC. Moreover, DWWC components have subsequently mixed over generations, that resulted in a high level of genetic diversity at population and species levels. Weedy rice populations that were genetically distinct from other populations with a close spatial distance collected from the same geographical regions indicate that Sri Lankan weedy rice populations did not follow the rule of “isolation-by- distance”. Studied weedy rice populations were genetically structured into two distinct groups and genetic diversity was not evenly distributed among populations. The history of invasive weedy rice is so complex thcan be difficult to determine. Therefore, each weedy rice population was compared with its putative progenitors using STRUCTURE analysis which revealed that the majority of weedy rice populations’ origin is probably due to the primary contribution of traditional rice and improved rice respectively. The primary contribution of annual O. nivara and secondary contribution of O. rufipogon is evident in the origin of some weedy rice populations while feral rice primarily contributes to the origin of weedy rice. Therefore, Sri Lankan weedy rice originated from different pathways. Such as inter-cultivar hybridization via de domestication. Wild rice adapted to take advantage of cultivated rice habitats, forming a hybrid between cultivated rice and their reproductively compatible wild relatives. Moreover, abandoned rice domesticates evolve to weedy forms with a less intimate relationship with humans and take advantage of contamination to the rice ecosystem.at its origins