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

dc.creatorZifeng Guo
dc.creatorQuannv Yang
dc.creatorFeifei Huang
dc.creatorHongjian Zheng
dc.creatorZhiqin Sang
dc.creatorYanFen Xu
dc.creatorCong Zhang
dc.creatorKunsheng Wu
dc.creatorJiajun Tao
dc.creatorPrasanna, B.M.
dc.creatorOlsen, M.
dc.creatorYunbo Wang
dc.creatorJianan Zhang
dc.creatorYunbi Xu
dc.date2021-11-17T01:05:13Z
dc.date2021-11-17T01:05:13Z
dc.date2021
dc.date.accessioned2023-07-17T20:08:18Z
dc.date.available2023-07-17T20:08:18Z
dc.identifierhttps://hdl.handle.net/10883/21729
dc.identifier10.1016/j.xplc.2021.100230
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/7513500
dc.descriptionGenotyping 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.
dc.languageEnglish
dc.publisherElsevier
dc.relationhttps://www.sciencedirect.com/science/article/pii/S2590346221001322?via%3Dihub#appsec2
dc.rightsCIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
dc.rightsOpen Access
dc.source6
dc.source2
dc.source2590-3462
dc.sourcePlant Communications
dc.source100230
dc.subjectAGRICULTURAL SCIENCES AND BIOTECHNOLOGY
dc.subjectGenotyping by Sequencing
dc.subjectMultiplexing PCR
dc.subjectSequence Capture in Solution
dc.subjectLiquid Chip
dc.subjectSINGLE NUCLEOTIDE POLYMORPHISM
dc.subjectGENOTYPING
dc.subjectPCR
dc.subjectLINKAGE DISEQUILIBRIUM
dc.titleDevelopment of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip
dc.typeArticle
dc.typePublished Version
dc.coverageUSA


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