Dissection Of Genetic Basis Of Yield Heterosis Between Indica And Japonica Subspecies In Rice

Heterosis exploitation of rice has made a great contribution to food security in China.Asian cultivated rice?Oryza sativa L.?is classified into indica and japonica,and the intersubspecies hybrid between indica and japonica subspecies often has stronger heterosis than the intrasubspecies hybrid.Studying the genetic mechanism of intersubspecies heterosis not only guides rice hybrid breeding,but also provides a reference for studying the heterosis theory of cereal crops.In this study,5 F₂ populations derived from 3 Yongyou series hybrids?Yongyou 4953,Yongyou 4949 and Yongyou4149?and 2 Chunyou series hybrids?Chunyou 295 and Chunyou 2915?were used for hybrid genome constitution analysis of origin of indica and japonica and QTL mapping of yield-related traits to analyze the genetic basis of intersubspecies heterosis.The main findings are as follows:1.Due to failed to obtain parental materials,we infer the F1 genotypes of the five combinations based on the sequencing data of the F₂ population.Then the genomes of male parents of the Yongyou hybrids were inferred with the available sequencing data of Yonggeng 49A.The parental genome of the two Chunyou hybrids was obtained by merging linkage segments in the population because no parental genome is available.According to the relationship matrix of 1000 cultivars,it is concluded that the female parents of the five hybrids belong to the japonica subgroup,and the male parents belong to the indica subgroup.2.The genome constitutions of 5 hybrids were inferred for the origin of indica and japonica genomes according to the information of subgroups of 1000 cultivars.The F1hybrid genomes contain not only heterozygous regions in most partial,but also homozygous indica and japonica regions in small partial,indicating that the parents are not typical indica or japonica varieties.The female parents of the Yongyou hybrids introgress indica genome accounting for about 20%of the whole genome,the male parents introgress japonica genome about 25%,and the hybrid F1 consisted of 10%indica and japonica homozygous region.While the female and male parents of Chunyou hybrids introgressed indica and japonica genome accounting for about 10%.5%of the hybrid F1 genome is japonica homozygous.3.GWAS analysis with the total of 5 F2 population,the synthetic F2 populations of 3 Yongyou hybrids and the synthetic F2 populations of 2 Chunyou hybrids was performed for spikelets per panicle?SPP?,thousand-grain weight?TGW?and panicle length?PL?.In the total of 5 F2 population,42,11,and 17 QTLs were detected for SPP,TGW,and PL,among which several cloned genes such as Gn1a,Os SPL14,GW5,and DEP1 were co-located with the associated sites.In the synthetic Yongyou population,6,3,and 4 QTLs were detected for SPP,TGW,and PL.In the synthetic Chunyou population,5,1,and 1 QTLs were identified respectively.The number of QTLs detected in the Yongyou population were significantly more than those in the Chunyou population.4.The bin maps of three Yongyou F2 populations were constructed,and genetic linkage maps were constructed using bin as genetic markers.17 QTLs for SPP,22 QTLs for TGW,10 QTLs for PL and 15 QTLs for TN were mapped.Of them,seven QTL?qSpp1,qSpp8.2,qTgw8.1,qTgw2.2,qPL6.3,qTn3?qTn8?were commonly detected in three populations.These QTLs have additive and/or dominant effects,and with varied genetic effects on different yield traits.5.GWAS and QTL mapping revealed that no relevant QTL was mapped for seed setting rate in Yongyou series populations.Genotype identification of the known genes controlling hybrid fertility between indica and japonica in F2 population showed that these fertility genes are fixed,indicating parents carried the same alleles.6.The correlation analysis between superior alleles and yield traits showed that the accumulation of more superior alleles has a higher phenotypic values of yield traits.Conclusion:The main genes controlling fertility of the hybrids between indica and japonica subspecies are homozygous in hybrids,which ensures the normal fertility in hybrids;the number of yield genes with dominance effects is large;and some major yield genes are homozygous with elite alleles in both parents.Therefore,the additive effect of the main yield genes ensures a higher mean value of the population,and the complementation of a larger number of dominant genes provides a larger heterosis value,so that intersubspecific hybrids have high yield performance,which can be released to farmers.