Allele variation of yield trait genes in 13 hybrid rice parents
Increasing the rice yield per unit area is an important technical method for enhancing grain yield.Analyzing the molecular basis of yield traits is helpful for pyramiding superior alleles and improving traits for parents,which is beneficial for developing hybrid rice varieties with strong heterosis.In this study,the genomes of 13 newly bred parents(five male-sterile lines and eight restorers)were sequenced using second-generation genome sequencing technology.Ten yield traits of 13 parents and their F1 were investigated.Superior alleles related to yield traits and the combination of superior alleles in 13 parents and their F1 were analyzed using genotype-phenotype association analysis.Results showed that through a fuzzy search of the cloned yield-associated genes,16 180 polymorphic loci were identified among the 13 parental genomes,which included 404 yield-associated genes.When P≤6.18 × 10-8(0.001/16180=6.18 × 10-8),seven yield traits were considered to be significantly associated with 1 459 polymorphic sites of 107 genes,including 33 genes with polymorphic sites in their exon regions.When the level of P value was ≤ 6.18 × 10-8 in additive effect or dominant effect,there were 444 polymorphic loci with extremely significant additive effects associated with 45 genes that controlled the 1 000-grain weight,plant height,panicle length,grain length,and grain length/width ratio.Among these,22 polymorphic loci controlled both yield traits,including nine genes and three traits.There were 784 polymorphic loci with highly significant dominant effects associated with 41 genes that controlled the grain yield per plant,days to heading,and plant height.Of these,47 polymorphic loci were dominant in both traits,including five genes and two traits.A total of 216 polymorphic loci were not significantly additive or dominant loci,involving 42 genes associated with days to heading and plant height.Based on the mean phenotype and exon polymorphic sites of the associated genes,36 superior alleles were distinguished,and some superior allele variations showed differentiation between restorers and male-sterile lines.These results indicate that different combinations of superior alleles are important reasons for yield differences in hybrid F1,which provides theoretical reference information and gene resources for the molecular improvement of yield traits of hybrid rice.
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