Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip

文献类型： 外文期刊

第一作者： Guo, Zifeng

作者： Guo, Zifeng;Xu, Yunbi;Yang, Quannv;Wang, Yunbo;Xu, Yunbi;Huang, Feifei;Xu, Yanfen;Zhang, Cong;Wu, Kunsheng;Tao, Jiajun;Zhang, Jianan;Zheng, Hongjian;Xu, Yunbi;Sang, Zhiqin;Xu, Yunbi;Prasanna, Boddupalli M.;Olsen, Michael S.;Zhang, Jianan

作者机构：

关键词： multiple single-nucleotide polymorphisms; mSNPs; genotyping by target sequencing; GBTS; multi-plexing PCR; sequence capture in-solution (liquid chip); linkage disequilibrium; LD

期刊名称：PLANT COMMUNICATIONS （ 影响因子：8.625； 五年影响因子：8.625 ）

ISSN： 2590-3462

年卷期： 2021 年 2 卷 6 期

页码：

收录情况： SCI

摘要： Genotyping platforms, as critical supports for genomics, genetics, and molecular breeding, have been well implemented at national institutions/universities in developed countries and multinational seed companies that possess high-throughput, automatic, large-scale, and shared facilities. In this study, we integrated an improved genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology to develop a multiple single-nucleotide polymorphism (mSNP) approach in which mSNPs can be captured from a single amplicon. From one 40K maize mSNP panel, we developed three types of markers (40K mSNPs, 251K SNPs, and 690K haplotypes), and generated multiple panels with various marker densities (1K-40K mSNPs) by sequencing at different depths. Comparative genetic diversity analysis was performed with genic versus intergenic markers and di-allelic SNPs versus non-typical SNPs. Compared with the one-amplicon-one-SNP system, mSNPs and within-mSNP haplotypes are more powerful for genetic diversity detection, linkage disequilibrium decay analysis, and genome-wide association studies. The technologies, protocols, and application scenarios developed for maize in this study will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals, plants, and microorganisms.

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[1]Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip. Guo, Zifeng,Xu, Yunbi,Yang, Quannv,Wang, Yunbo,Xu, Yunbi,Huang, Feifei,Xu, Yanfen,Zhang, Cong,Wu, Kunsheng,Tao, Jiajun,Zhang, Jianan,Zheng, Hongjian,Xu, Yunbi,Sang, Zhiqin,Xu, Yunbi,Prasanna, Boddupalli M.,Olsen, Michael S.,Zhang, Jianan. 2021

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