Heterotic Group Analysis And Fine Mapping Of Hull Silicon Content QTL QHUS6.1in Indica Rice

Seven hundred and thirty seven improved indica varieties/lines developed recently and/or widelyused by present indica breeding programs worldwide, were genotyped with384single nucleotidepolymorphism (SNP) assay. Model-based population structure analysis revealed the presence of twomajor groups with six subgroups. Over half of the accessions (51.8%) appeared to have less than0.6memberships assigned to any one of the six model-based groups, highlighting the wide range of geneflow within improved indica varieties/lines and the genetic integration of valuable alleles shared byancestries among improved high-yielding varieties/lines through germplasm exchanges and theincreasingly complex genetic background among improved high-yielding varieties/lines. Distance-basedclustering analysis showed Latin American cultivated indica lines have tended to form their ownecological cline, which could serve as a potential heterotic ecotype for hybrid rice breeding althoughthey are still closely related to Asian indica lines.A sample of17parents was selected from the panel of737improved cultivated elite varieties/lines,the parents represent the original genetic structure with6groups.17parents were crossed following adiallel mating design without reciprocals resulting136hybrids that were evaluated at five environments(Seasons and locations) in tropics, with the objectives of evaluating the magnitude of hybridperformance, yield heterosis, the consistency between marker-based group and heterotic performance ofhybrids, as well as the correlation between genetic distance (GD) with hybrid performance, yieldheterosis and combining ability. The analysis showed that1) the hybrids yielded20.4%higher than theparents;2) significant genotype environment effect for hybrid yield represented a challenge todevelop high yield hybrid rice with widespread for multi-environments in tropics;3) significant yield,yield heterosis and combining ability of inter-groups versus intra-group crosses suggested that groupsidentified by GD based on molecular marker could be a practical starting point for further breedingwork to develop useful heterotic groups;4) the correlations between the GD based on random molecularmarkers with hybrid yield, heterosis, SCA were insignificant or weak, GD cannot be used for hybridyield, heterosis and SCA prediction.Genome analysis based on re-sequencing of two indica accessions Zhenshan97(ZS97) andMilyang46(MY46), the parents of an elite three-line indica hybrid Shanyou10, has led to discovercomprehensive SNPs, short InDels and SVs variations. Compared with reference9311, a total of364488SNPs,61181InDels and6298SVs were detected in ZS97;364179SNPs,61984InDels and6408SVs were detected in MY46. Meanwhile,181737different SNPs,1205different short InDels wereobserved between ZS97and MY46. Out of1205different short InDels between ZS97and MY46,180InDels with3to8bp length were converted into PCR-based markers,160(88.9%) validated InDelmarkers can be amplified and showed significant plolymorphism between ZS97and MY46run in6%PAGE.A fine mapping strategy were used in the fine mapping of qHUS6.1for the silicon content in rice hull: a residual heterozygous plant (RH) was identified from RILs of ZS97/MY46; develop three sets ofNILs with overlapping target segregating chromosome segment; qHUS6.1was narrowed into an intervalwith only one ORF, as well as one set of single gene NILs (qHUS6.1) was developed using smallpopulation. Base one the fine mapping strategy with RH, totally,2441plants derived from selfedprogenies with seven generations from RH6were genotyped. Three sub-RHs with overlappingheterozygous segments were obtained by genoytyping only averaged348plants in every generation.Based on analyses of the phenotypic distribution and variance among the three sets of NILs derivedfrom the three sub-RHs, qHUS6.1was delimited to a region with only a single gene.