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
作者： Guo, Zifeng 1 ; Yang, Quannv 2 ; Huang, Feifei 3 ; Zheng, Hongjian 4 ; Sang, Zhiqin 5 ; Xu, Yanfen 3 ; Zhang, Cong 3 ; Wu, Kunsheng 3 ; Tao, Jiajun 3 ; Prasanna, Boddupalli M. 7 ; Olsen, Michael S. 7 ; Wang, Yunbo 2 ; Zhang, Jianan 3 ; Xu, Yunbi 1 ;
作者机构： 1.Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100081, Peoples R China
2.Foshan Univ, CIMMYT China Trop Maize Res Ctr, Sch Food Sci & Engn, Foshan 528225, Guangdong, Peoples R China
3.MolBreeding Biotechnol Co Ltd, Shijiazhuang 050035, Hebei, Peoples R China
4.Shanghai Acad Agr Sci, CIMMYT China Specialty Maize Res Ctr, Crop Breeding & Cultivat Res Inst, Shanghai 201403, Peoples R China
5.Xinjiang Acad Agr Reclamat, Shihezi 832000, Xinjiang, Peoples R China
6.Int Maize & Wheat Improvement Ctr CIMMYT, El Batan Texcoco 56130, Mexico
7.CIMMYT Int Maize & Wheat Improvement Ctr, ICRAF Campus,United Nations Ave, Nairobi, Kenya
8.Hebei Acad Agr & Forestry Sci, Natl Foxtail Millet Improvement Ctr, Inst Millet Crops, Minor Cereal Crops Lab Hebei Prov, Shijiazhuang 050035, Hebei, Peoples R China
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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