Development of High-resolution Multiple-SNP Arrays for Genetic Analyses and Molecular Breeding Through Genotyping by Target Sequencing and Liquid Chip

Overview

Journal Plant Commun

Specialty Biology

Date 2021 Nov 15

PMID 34778746

Citations 32

Authors

Zifeng Guo

Quannv Yang

Feifei Huang

Hongjian Zheng

Zhiqin Sang

Yanfen Xu

Cong Zhang

Kunsheng Wu

Jiajun Tao

Boddupalli M Prasanna

Michael S Olsen

Yunbo Wang

Jianan Zhang

Yunbi Xu

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

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