Abstract
Stigma exsertion and panicle enclosure of male sterile lines are two key determinants of outcrossing in hybrid rice seed production. Based on 43,394 single nucleotide polymorphism markers, 217 cytoplasmic male sterile lines were assigned into two subpopulations and a mixed-group where the linkage disequilibrium decay distances varied from 975 to 2,690 kb. Genome-wide association studies (GWAS) were performed for stigma exsertion rate (SE), panicle enclosure rate (PE) and seed-setting rate (SSR). A total of 154 significant association signals (P < 0.001) were identified. They were situated in 27 quantitative trait loci (QTLs), including 11 for SE, 6 for PE, and 10 for SSR. It was shown that six of the ten QTLs for SSR were tightly linked to QTLs for SE or/and PE with the expected allelic direction. These QTL clusters could be targeted to improve the outcrossing of female parents in hybrid rice breeding. Our study also indicates that GWAS-base QTL mapping can complement and enhance previous QTL information for understanding the genetic relationship between outcrossing and its related traits.
Highlights
The availability of affordable hybrid rice seeds is crucial to the success of hybrid rice commercialization
Among the three traits for stigma exsertion rate which was measured in 14DS only, the maximum coefficient of variation (CV) of 37.0% was detected for double stigma exsertion rate (DSE), followed by total stigma exsertion rate (TSE) and single stigma exsertion rate (SSE)
Using the rice single nucleotide polymorphism (SNP) chip consisting of 43,394 SNPs, the genetic diversity, linkage disequilibrium (LD) pattern, population structure, and kinship of a diverse panel of 217 rice cytoplasmic male sterile (CMS)-WA lines were characterized, and QTLs responsible for three key traits determining outcrossing in rice were identified
Summary
The availability of affordable hybrid rice seeds is crucial to the success of hybrid rice commercialization. In other Asian countries, it is 1.0–1.5 t ha−1 Such low yields in seed production have been a major constraint to hybrid rice dissemination. Improving outcrossing, which is an important and complicated trait in determining female parent seed yield, is always a priority in hybrid rice breeding. A more recent study extended the trait to stigma exsertion, showing that GS3, GW5 and GW2 play an important role in the genetic basis of stigma exsertion in rice[34]. None of these studies targeted at CMS line which is an essential category of rice cultivars for hybrid rice production.
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