Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice ( Oryza sativa L.) thr
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RESEARCH ARTICLE
Open Access
Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice (Oryza sativa L.) through association mapping Chunfang Zhao1, Ling Zhao1, Qingyong Zhao1, Tao Chen1, Shu Yao1, Zhen Zhu1, Lihui Zhou1, Altafhusian B. Nadaf2, Wenhua Liang1, Kai Lu1, Yadong Zhang1* and Cailin Wang1*
Abstract Background: Eating and cooking qualities (ECQs) of rice (Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. The starch physicochemical properties, i.e. amylose content, gel consistency, gelatinization temperature and pasting viscosity are important indices for evaluating rice ECQs. 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. Results: A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. 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 could be selected for further fine mapping. (Continued on next page)
* Correspondence: [email protected]; [email protected]; [email protected] 1 Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing 210014, China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate c
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