Genetic Architecture Of Panicle Heterosis In Rice Based On Genome-Wide Association Study

Hetersosis has been widely used in aricultural animals and plants to increase their yield,enhance their stress-resistance and adapativity,and thus promoted the production efficiency in agriculture.Genetic mechanism of heterosis is still not clear,although plenty of efforts on its research have been made by in a century.The development of genomics and biology in recent decades supplied us more technology and the opportunity to uncover the mechanism of heterosis.As one of the crops which is successfully improved by the utility of heterosis,and also one model crop for genome research,comprehensive research on rice heterosis will not only guide the breeding of rice hybrids,but also shed light on the understanding of the genetic bases under heterosis.In this study,using japonica nipponbare and indica 93-11 as testers and the diverse and representative mini core collection of world wide cultivated rice as the crosser,we developed 450 F1.Using 5 panicle-related traits in two environments and 4632562 high-density and high-quality SNPs,we identified the QTL related to heterosis of five traits,and investigated the genetic bases under heterosis of these traits,and at last put forward to the methods to predict and evaluate rice heterosis.The main results are summarized as following:1.Parent phenotypes,F1 phenotypes and mid-parent heterosis for all traits and cross types showed significant difference among genotype main effect,environment effect and the genotype X environment interaction effect.Among five traits,traits related to grain number showed apparently stronger heterosis than grain weight.The inter-subspecific heterosis is distinctly stronger than the intra-subspecific one for grain number and secondary branch number,but no apparent difference for grain weight and panicle length.2.We identified 1237,172land 1436 QTL that control the parent phenotype,F1 phenotype and mid-parent heterosis.Comparison of those three types of QTL under two environments indicated that the proportion of QTL related to parent phenotype shared between two environments is higher than those related to F1 phenotype and mid-parent heterosis.In addition,the proportion of QTL related to both F1 phenotype and parent phenotype or both F1 phenotype and mid-parent heterosis is higher than the proportion of QTL related to both parent phenotype and mid-parent heterosis;as implied the different genetic bases under parent phenotype,F1 phenotype and mid-parent heterosis.3.According to the detection of additive and dominant effection of whole genome QTL,we distinguished the effect of the above detected QTL into additive,dominant and overdominant.In general,the difference of parent phenotype more attributes to QTL with additive effect,and most of the QTLs controlled F1 phenotype and mid-parent heterosis are dominant and overdorninant.But the relative proportion of three types of genetic effection varies under different genetic background,for different traits and under different environments;as indicated that the heterosis and especially the Fi phenotype are,in addition to,mainly under the control of domimant and overdominant,and also impacted by the additive and dominant genetic background,and also show somewhat cross-type-specific and trait-specific,and at the same time result from tibie different genetic response to the environment.4.We compared the power to predit the F1 phenotype and heterosis using whole genome SNP or SNP in heterosis QTL and according to their heterozygosity or effect.The results indicated that correlation coefficient between SNP hetersozygosity and F1 phenotype or heterosis are 0.21-0.4 at most,and the prediction power will increase to 0.6?0.89 when considering the effect of heterosis QTL.In addition,the predition power of dominant and overdominant QTL is distinctly higher than that of additive QTL,and the prediction accuracy for some traits is higher than 70%.In brief,using heterosis QTL rather than whole genome SNP and considering the genetic bases and mechanism can increase the prediction accuracy.5.Investigation on the possible heterotic group and evaluation on the utility potential of heterosis using the heterosis QTL indicated that tropical japonica and part of waxy cultivar pyramided much more superior alleles of the heterosis QTL and may be the heterotic group in japonica,and most of the temperate japonica contain much more inferior alleles and is difficult to forn cross with high heterosis,but potential mode with high heterosis could be developed relative easily by crosses tropical japonica X temperate japonica,tropical japonica X waxy japonica and waxy japonica X temperate japonica.In indica,there is no apparent heterotic group and aus contains more inferior alleles and is the apparent inferior group.The other types of indica cultivars contain different superior alleles of the heterosis QTL and thus supply diverse cross inodes with strong heterosis,but their prediction depends on the identification of heterosis QTL.