Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip
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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| Autores principales: | , , , , , , , , , , , , , |
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| Formato: | Artículo biblioteca |
| Idioma: | English |
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Elsevier
2021
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| Materias: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Genotyping by Sequencing, Multiplexing PCR, Sequence Capture in Solution, Liquid Chip, SINGLE NUCLEOTIDE POLYMORPHISM, GENOTYPING, PCR, LINKAGE DISEQUILIBRIUM, |
| Acceso en línea: | https://hdl.handle.net/10883/21729 |
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dig-cimmyt-10883-217292021-12-09T15:28:52Z Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip Zifeng Guo Quannv Yang Feifei Huang Hongjian Zheng Zhiqin Sang YanFen Xu Cong Zhang Kunsheng Wu Jiajun Tao Prasanna, B.M. Olsen, M. Yunbo Wang Jianan Zhang Yunbi Xu AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genotyping by Sequencing Multiplexing PCR Sequence Capture in Solution Liquid Chip SINGLE NUCLEOTIDE POLYMORPHISM GENOTYPING PCR LINKAGE DISEQUILIBRIUM 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. 2021-11-17T01:05:13Z 2021-11-17T01:05:13Z 2021 Article Published Version https://hdl.handle.net/10883/21729 10.1016/j.xplc.2021.100230 English https://www.sciencedirect.com/science/article/pii/S2590346221001322?via%3Dihub#appsec2 CIMMYT 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 Open Access USA Elsevier 6 2 2590-3462 Plant Communications 100230 |
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| access |
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| databasecode |
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biblioteca |
| region |
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| libraryname |
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| language |
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| topic |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genotyping by Sequencing Multiplexing PCR Sequence Capture in Solution Liquid Chip SINGLE NUCLEOTIDE POLYMORPHISM GENOTYPING PCR LINKAGE DISEQUILIBRIUM AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genotyping by Sequencing Multiplexing PCR Sequence Capture in Solution Liquid Chip SINGLE NUCLEOTIDE POLYMORPHISM GENOTYPING PCR LINKAGE DISEQUILIBRIUM |
| spellingShingle |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genotyping by Sequencing Multiplexing PCR Sequence Capture in Solution Liquid Chip SINGLE NUCLEOTIDE POLYMORPHISM GENOTYPING PCR LINKAGE DISEQUILIBRIUM AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genotyping by Sequencing Multiplexing PCR Sequence Capture in Solution Liquid Chip SINGLE NUCLEOTIDE POLYMORPHISM GENOTYPING PCR LINKAGE DISEQUILIBRIUM Zifeng Guo Quannv Yang Feifei Huang Hongjian Zheng Zhiqin Sang YanFen Xu Cong Zhang Kunsheng Wu Jiajun Tao Prasanna, B.M. Olsen, M. Yunbo Wang Jianan Zhang Yunbi Xu Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and 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. |
| format |
Article |
| topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genotyping by Sequencing Multiplexing PCR Sequence Capture in Solution Liquid Chip SINGLE NUCLEOTIDE POLYMORPHISM GENOTYPING PCR LINKAGE DISEQUILIBRIUM |
| author |
Zifeng Guo Quannv Yang Feifei Huang Hongjian Zheng Zhiqin Sang YanFen Xu Cong Zhang Kunsheng Wu Jiajun Tao Prasanna, B.M. Olsen, M. Yunbo Wang Jianan Zhang Yunbi Xu |
| author_facet |
Zifeng Guo Quannv Yang Feifei Huang Hongjian Zheng Zhiqin Sang YanFen Xu Cong Zhang Kunsheng Wu Jiajun Tao Prasanna, B.M. Olsen, M. Yunbo Wang Jianan Zhang Yunbi Xu |
| author_sort |
Zifeng Guo |
| title |
Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip |
| title_short |
Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip |
| title_full |
Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip |
| title_fullStr |
Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip |
| title_full_unstemmed |
Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip |
| title_sort |
development of high-resolution multiple-snp arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip |
| publisher |
Elsevier |
| publishDate |
2021 |
| url |
https://hdl.handle.net/10883/21729 |
| work_keys_str_mv |
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| _version_ |
1756087023109668864 |