Genetic Architecture Of Reproductive Isolation In Rice,Evolutionary Origination Of S5 And Utilization Of Inter-Subspecific Heterosis Via Genomic Prediction

Rice maintains high genetic diversity and the Asian cultivated rice(Oryza sativa.L)contains two major groups of Xian(indica)and Geng(japonica).The inter-subspecific hybrid between indica and japonica has a strong heterosis.However,hybrid sterility is a major obstacle in utilization of inter-subspecific heterosis.The cloned and mapped related genes do not fully explain the hybrid sterile behavior of indica-japonica hybrids.How to overcome the indica-japonica hybrid sterility disorders and make full use of the heterosis between indica and japonica subspecies remains to be further studied.On the other hand,hybrid sterility,one of the main forms of reproductive isolation,is both the indicator and a primary force of speciation.Understanding the processes of the origination and genetic molecular mechanisms controlling reproductive isolation has been a fundamental undertaking in evolutionary biology.For this central theme,this study is mainly carried out in the following three aspects:1.To detect the genetic architecture of reproductive isolation in rice,we selected three representative cultivars,Nipponbare(japonica),Zhenshan 97(indica)and Minghui 63(indica),to construct three F2 population.By RADseq,the high-density genetic linkage maps were constructed,and the three traits of embryo sac,pollen fertility and spikelet fertility were detailed phenotyped.A total of 27 QTLs(7 for embryo-sac,7 for pollen and 13 for spikelet fertility)in the three F2 populations were detected.Ten newly QTLs for inter-and intra-subspecific fertility were identified.A total of 16 regions were detected showing significant deviations from the expected allelic and genotypic frequencies by chisquare test.Using two-way ANOVA a total of 41 interactions pairs that had significant effects on fertility in three F2 population were identified.Genetic incompatibilities is another type of epistasis.It is expected that unfavourable allelic combinations will be under-represented,and this should precipitate a deviation from Mendelian proportions.169 pairs this types significant interactions were detected in all three F2 populations.2.The S5 locus was the first cloned loci,which control the embryo sacs fertility of indica-japonica hybrids.Using reciprocal BLASTN search a unique set of three genes on chromosome 5 was identified showing paralogy to ORFs3-5(chromosome 6).No paralogous genes other than ORFs3-5 and Ospara3-5 were identified between the two blocks.Both of which contained multiple partial sequences of the transposon Helitron suggested a possibility that the ORFs3-5 segment was derived by Helitron movement,carrying the internal Ospara4-5 fragment on chromosome 5,to insert them in the new location on chromosome 6 thus generating a new fragment containing ORFs3-5.We analyzed patterns of variation and diversity of these three genes in 635 rice accessions of the genus Oryza.The haplotype of ORF3+ORF4+ORF5+ was the most frequent type in the wild progenitors.We evaluated the genetic variation in regions flanking S5 locus in 529 rice accessions of O.sativa.A dramatic decrease in genetic variation was observed around S5 region in the indica subgroup.Significant selection at S5 locus was also detected by coalescent simulation analysis baised on the domography model of rice domestication in indica subgroup,suggesting that the spread of the indica haplotype might be driven by natural selection.Whereas the preservation of japonica haplotype might be due to the intense founder effect resulting from domestication of the japonica subgroup.3.A total of 21 rice accessions were selected to construct a half diallel population including 210 hybrids.We identified 2,621,064 SNPs across this panel of 21 rice accessions by high-throughput whole genome sequencing.We used the 5-cross-validation strategy to analyze the accuracy of genome-wide prediction with g BLUP method.The predictive accuracy for seven traits of grain length,grain width,grain weight,tiller number per plant,spikelet number per panicle,plant height and dry weight per plant were relatively high,0.946,0.956,0.784,0.819,0.824,0.405.Thus,we predicted the yield of indica-japonica inter-subspecific crosses,using indica-indica subspecies and japonica-japonica intrasubspecific crosses,and found that the predicted yield of hybrids with normal fertility were very close to their ture values.The parental materials associated with high predicttion yield hybrids might could be select as basic materials to future inter-subspecific hybrids breeding project.In this study,we first systematically detected the architecture of reproductive barriers in rice with respect to various forms at single-and multi-locus level using three F2 population.Second,we identified the transposon-induced gene duplication events and subsequent natural selection and founder effects in population domagraphy which contribute to establish the S5 reproductively isolated system in rice.Third,we apply a proof-of-concept study of whole genome selection showed that g BLUP is a promise method for selecting superior hybrids intra-subspecific hybrids.These research results can provide useful information in utilization of inter-subspecific heterosis.