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Genetic Dissection of Eating and Cooking Qualities in Different Subpopulations of Asian Cultivated Rice(Oryza sativa L.) through Association Mapping

赵春芳  Ling Zhao  Qingyong Zhao  Tao Chen  Shu Yao  Zhen Zhu  Lihui Zhou  Altafhusian B.Nadaf  Wenhua Liang  Kai Lu  Yadong Zhang  王才林  
【摘要】:[Background] Eating and cooking qualities(ECQs) of rice(Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. Genetic factors are required for development of rice varieties with excellent ECQs and association mapping is one of the promising approaches for discovering such associated genetic factors. [Material and method] A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica Asian cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. [Results] These markers amplified 747 alleles with an average of 3.57 alleles per locus. The structure, phylogenetic relationship, and principal component analysis indicated a strong population differentiation between indica and japonica accessions and association mapping was thus undertaken within indica and japonica subpopulations. All traits showed a large phenotypic variation and highly significant phenotypic correlations were present between most of traits. A total of 33 and 30 loci were located for 11 ECQs in indica and japonica subpopulations respectively. Most of associated loci were overlapped with starch synthesis-related genes(SSRGs), and the Wx locus gathered 14 associated loci with the largest effects on amylose content, gel consistency and pasting viscosities. Eight subpopulation specific markers, RM588, Wx-(CT)n, SSI and SBE1 for indica subpopulation and RM550, Wxmp, SSIIa and SBE4 for japonica subpopulation, were identified, suggesting alleles of SSRGs showed the subspecific tendency. Nevertheless, allelic variation in SSIIa showed no tendency towards subspecies. One associated maker RM550 detected in japonica subpopulation for amylose content and pasting viscosity was verified a potential novel and stably expressed locus and also indicated selection for further fine mapping. [Conclusion] This study illustrated the potential for dissecting minor-effect genetic factors of complex traits in domesticated rice cultivars and provided highly associated markers for breeding high-quality indica or japonica rice varieties.

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