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

Creator: Zifeng Guo
Creator: Quannv Yang
Creator: Feifei Huang
Creator: Hongjian Zheng
Creator: Zhiqin Sang
Creator: YanFen Xu
Creator: Cong Zhang
Creator: Kunsheng Wu
Creator: Jiajun Tao
Creator: Prasanna, B.M.
Creator: Olsen, M.
Creator: Yunbo Wang
Creator: Jianan Zhang
Creator: Yunbi Xu
Year: 2021
Language: English
Publisher: Elsevier
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Type: Article
Place of Publication: USA
Issue: 6
Volume: 2
DOI: 10.1016/j.xplc.2021.100230
Keywords: Genotyping by Sequencing
Keywords: Multiplexing PCR
Keywords: Sequence Capture in Solution
Keywords: Liquid Chip
Description: 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.
Agrovoc: PCR
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ISSN: 2590-3462
Journal: Plant Communications
Article number: 100230

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  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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