The Study Of Origin Of Weedy Rice Based On Chloroplast Genome Sequence Polymorphism And A Preliminary Research In Seed Shattering Of Weedy Rice

Weedy rice(Oryza sativa f. spontanea) is one of the most unsavory weeds which compete aggressively with crops, reduce yields and contaminate harvests, and which occurs in rice-planting areas worldwide. Weedy rice is morphologically similar to the cultivated rice in plant and seed characteristics. It shares a common gene pool with cultivated rice. Thus, the weedy rice has adapted to the habitat of crop fields. It has early and heavy seed shattering and dormancy traits that make it persisted in rice fields and difficult to control. According to the properties of the weedy rice, its multi-origins hypothesis has been proposed. It is well-known that the high genetic diversity occurred in the populations of weedy rice through the genomic sequence comparison between cultivated, wild and weedy rice and these researches showed the most of the weedy rice populations have a close lineage with cultivate rice. But further evidence is needed to support the multi-origins hypothesis of weedy rice. Especially the wild-origin of weedy rice is still a puzzle. No matter which evolutionary process(exo- or endo-ferality) is involved, reacquiring seed shattering characteristics is the key for the origin of weedy rice. Therefore, research on the genetic control of shattering is a way to solve this problem. Bycomparing sh4 gene sequences in wild, weedy, and cultivated rice accessions, it has been found that the weedy rice and cultivated rice have the same genotype of sh4. The strong shattering of weedy rice makes the origins of weedy rice more complicated. First, we detected the sequences differentiation of chloroplast DNA in three sets of rice populations that included wild, cultivated and weedy rice. The aim of this experiment was to figure out the origination of weedy rice. Another experiment was to determine the genetic basis of seed shattering trait involving an F2 population derived from a cross between a rice variety Minghui86(MH86) of seed persistence and a weedy rice accession(WD1292) with strong seed shattering. These results are included as follows:1: The theta_π values of wild, weedy and cultivated rice samples were 0.0020, 0.0023 and 0.0024, respectively, although the comparably low genetic diversity in chloroplast DNA of the genus of Oryza, the values of Fst=0.108 indicated the differentiation between wild and cultivated rice populations.2: The differentiation between weedy and cultivated rice populations(Fst=0.047) was lower than the differentiation between weedy and wild rice populations(Fst=0.144). This result was consistent with the results where the nuclear genome was used as an object to detecting the differentiation in rice.3: Through the haplotype analyses, we found that wild and cultivated rice samples have no sharing haplotypes. Further analysis indicated that individuals of weedy rice shared one haplotype(H18) with wild rice and seven haplotypes(H1, H2, H5, H6, H8, H9, and H13) with cultivated rice.4: these individuals of weedy rice that share the same haplotypes or have high affinity with wild were mainly distributed in the areas where the wild rice grows naturally.5: there were some weedy rice individuals that share no haplotypes with wild rice and cultivated rice and far away from them(the haplotypes of wild and cultivated rice) indicated the event of fast evolution in weedy rice populations.6: Three QTLs(designated as wd-qsh1, wd-qsh3, and wd-qsh5) were identified based on the analyses. The major QTL with the greatest effect was located on chromosome-3 and explained 31.41 % of the phenotypic variance, whereas the two remaining QTLs with a smaller effect were located on chromosome-1 and-5 and explained phenotypic variation ranging from 11.61 % to 16.85 %.These results provided strong evidence to the multi-origins of weedy rice. Especially, this research provided evidence of the wild-origin of weedy rice. Not only the multi-origins of weedy rice, a story of cultivated rice and the genetic relationships between them were narrated by our results. The independent haplotypes of weedy rice give the view of the fast evolution since the weedy rice differentiated from wild rice or cultivated rice. Through the detection of genetic diversity of rice chloroplast we found the obvious differentiation between rice subspecies. This could be useful for the research of rice origin and evolution. Mapping of novel shattering genes in weedy rice and a comparison of locations of shattering genes or shattering loci, suggest that distinct genetic mechanisms may evolves independently in different weedy rice groups, which allowed weedy rice to adapt to the diverse agricultural environments. De-domestication played a significant role in generating weedy rice without the involvement of wild rice in agro-ecosystems. Our study shows a complexity in the origins of weedy rice. And the knowledge in the shattering of weedy rice was beneficial to the controlling of weedy rice.