Studies On The Genetic And Genomic Basis Of Heterosis In An Elite Rice Hybrid,Shanyou 63

Rice is an ideal model for functional genomic research of crops and a staple food that feeds half of the world.The molecular basis of heterosis is still vague after a century of debates despite the tremendous contribution of heterosis to the increased productivity of world crops.Utilization of heterosis in rice has greatly improved rice yield in China in the last two decades.With the simplest genome in crops and the rapid development of rice functional genomic studies,rice is a good model for the study of heterosis.Shanyou 63 was the most widely cultivated rice hybrid in the 1980 s and 1990 s and was still used with reduced area in recent years in China.We compared the genome sequences of the parents of Shanyou 63,Zhenshan 97 and Minghui 63 based on high-coverage genomic sequencing data.We identified 971,883 SNPs and 198,152 InDels between the genomes of Zhenshan 97 and Minghui 63.A total of 13,147 protein-coding genes harbored SNPs or InDels between the parental genomes.GO enrichment analysis showed that genes associated with the terms “cellular protein modification process”,“protein modification process” and “macromolecule modification” were enriched in these 13,147 protein-coding genes.We identified 686 genes present only in the genome of Zhenshan 97 and 762 genes present only in the genome of Minghui 63.These findings indicated that the hybrid harbored more genes and sequence diversity than its parents.We compared the expression profile across 18 tissues of an elite rice hybrid with its parents.We found that 379 genes were expressed in the genome of Zhenshan 97 but not expressed in Minghui 63 while 330 genes were expressed only in the genome of Minghui 63.Most of these genes were expressed in the hybrid,implying that more genes were expressed in the genome of the hybrid.A total of 7,450 genes were non-additively expressed across the 18 selected samples.Genes associated with GO term “photosynthesis” were enriched in the non-additively expressed genes identified from the leaf samples.Genes associated with the GO term “biosynthetic process” and genes associated with GO terms “cell growth” and “growth” were enriched in the non-additively expressed genes identified in the root and stem samples respectively.We also found genes including OsMPS,OsEXPA8 and OsFOR1,the non-additively expression of which were beneficial to the growth of the hybrid.We found evidence for the contribution of allele complementation to heterosis.At Bin1006,the yield per plant for IMF2 s with Minghui 63 genotype were better than IMF2 s with Zhenshan 97 genotype.On the other hand,the yield per plant for IMF2 s with Zhenshan 97 genotype were better than IMF2 s with Minghui 63 genotype at Bin1087.The yield per plant for IMF2 s that were both heterozygotes at the two bins were better than IMF2 s which were both homozygote at the two bins.Allele specific expression?ASE?is the preferential expression of one allele of genes in the genome of hybrid.Allele specific expression of genes provides potential superiority for the hybrid relative to its parents.Although it was believed that ASE was probably involved in the formation of heterosis,the mechanisms are still elusive.We reported the quantification of allele-specific gene expression in an IMF2 population derived from the cross between the parents of Shanyou 63.A total of 284 genes of the hybrid while an average of 153 genes of the IMF2 population were identified as allele specific expressed.A total of 2,351 genes were detected as ASE in at least one of all the 97 IMF2 s.Taken together,2,369 genes were identified as ASE in at least one of all the IMF2 s and the F₁ hybrid.Comparisons of ASE in the IMF2 population and the F₁ hybrid showed that the occurrence and orientation of ASE for the majority genes in the IMF2 population were in accordance with that in the F₁ hybrid.We detected 1,656 local-eQTLs and 2,303 distant-eQTLs for 3,807 genes by mapping the mRNA sequencing data to the Minghui 63 genome.Comparison of ASE and eQTL confirmed ASE as a good indicator of local-eQTLs.We further identified 126 QTLs regulating the levels of allele-specific expression of 123 distant genes,designated as aseQTLs.Comparisons of aseQTLs and eQTLs indicated different regulating mechanisms for expression level and the ASE of genes.In the F₁ hybrid,a gene is regarded as dominantly or non-additively expressed if its expression level in the hybrid is significantly different from that of the mean of the parents.In the IMF2 population,the dominance effect of the expression level of genes were defined as the average expression levels of the heterozygotes minus that of the mean expression levels of the homozygotes.By comparing the expression level of genes in the hybrid and that of the mid-parent level,we identified 1,672 non-additively expressed genes.For the IMF2 population,we identified 3,544 genes with dominance effect significantly different from 0 utilizing h-test as was performed in previous studies.The dominance effect of a total of 16,852 genes were subject to QTL analysis.As a result,1,349 QTLs were recovered for 1,340 traits.A QTL on chromosome 8 were found to regulate the dominance effect of the expression of Gn1 a located on chromosome 1 while another QTL on chromosome 9 were identified to explain the variations in the dominance effect of the expression of SNAC2 on chromosome 1.Further comparisons of these QTLs with eQTLs identified using the same mRNA sequencing data indicated the existence of different regulating mechanisms for gene expression and the dominance effect of gene expression.We further performed a genetic analysis of sRNA abundance in flag leaf from IMF2 population derived from the cross between Zhenshan 97 and Minghui 63.We identified 53,613,739 unique s RNAs and 165,797 sRNA expression traits.A total of 66,649 s-traits mapped 40,049 local-sQTLs and 30,809 distant-sQTLs.By defining 80,362 sRNA clusters,22,263 sRNA cluster QTLs were recovered for 20,249 of all the 50,139 sRNA cluster expression traits.The expression levels for most of s-traits from the same genes or the same sRNA clusters were slightly positively correlated.Some s RNA biogenesis genes were located in distant-sQTL hotspots and showed correspondence with specific length classes of sRNAs suggesting their important roles in the regulation and biogenesis of the sRNAs.In summary,we conducted a detailed analysis of the cross between Zhenshan 97 and Minghui 63 based on genome sequencing,transcriptome sequencing,sRNA sequencing data and whole genome expression profile.We systematically compared the genome sequences and gene expression between the hybrid and its parents.We found that the hybrid harbored more genes and more genes were expressed in the hybrid.We found evidence of the contribution of non-additive expression to the growth vigor of the hybrid.We further dissected the genetic regulation of ASE and sRNA expression in an IMF2 population derived from the corss between Zhenshan 97 and Minghui 63.The occurrence and orientation of ASE in the IMF2 population were generally in accordance with that in the F₁ hybrid.In addition,the genetic regulation of ASE and gene expression were different from each other.QTL analysis of sRNA expression indicated the existence of DNA sequences contributed to the variation of sRNA expression.sRNA biogenesis genes were found to be involved in the regulation of sRNA expression.These results were helpful for future dissection of heterosis in the cross between Zhenshan 97 and Minghui 63.