Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing

文献类型： 外文期刊

第一作者： Chen, Wei

作者： Chen, Wei;Chen, Haodong;Yu, Renbo;Deng, Xing Wang;He, Hang;Chen, Haodong;Yu, Renbo;Deng, Xing Wang;He, Hang;Zheng, Tianqing;Li, Zhikang;Xu, Jianlong;Yu, Renbo;Deng, Xing Wang;Terzaghi, William Bryan;Li, Zhikang;Xu, Jianlong

作者机构：

期刊名称：THEORETICAL AND APPLIED GENETICS （ 影响因子：5.699； 五年影响因子：5.565 ）

ISSN： 0040-5752

年卷期： 2014 年 127 卷 2 期

页码：

收录情况： SCI

摘要： Key message A new time- and cost-effective strategy was developed for medium-density SNP genotyping of rice biparental populations, using GoldenGate assays based on parental resequencing. Since the advent of molecular markers, crop researchers and breeders have dedicated huge amounts of effort to detecting quantitative trait loci (QTL) in biparental populations for genetic analysis and marker-assisted selection (MAS). In this study, we developed a new time- and cost-effective strategy for genotyping a population of progeny from a rice cross using medium-density single nucleotide polymorphisms (SNPs). Using this strategy, 728,362 "high quality" SNPs were identified by resequencing Teqing and Lemont, the parents of the population. We selected 384 informative SNPs that were evenly distributed across the genome for genotyping the biparental population using the Illumina GoldenGate assay. 335 (87.2 %) validated SNPs were used for further genetic analyses. After removing segregation distortion markers, 321 SNPs were used for linkage map construction and QTL mapping. This strategy generated SNP markers distributed more evenly across the genome than previous SSR assays. Taking the GW5 gene that controls grain shape as an example, our strategy provided higher accuracy (0.8 Mb) and significance (LOD 5.5 and 10.1) in QTL mapping than SSR analysis. Our study thus provides a rapid and efficient strategy for genetic studies and QTL mapping using SNP genotyping assays.

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