Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat

Shengyu Guan; Weining Li; Hai Jin; Lu Zhang; Guoshi Liu

doi:10.3390/genes14051122

Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat

Genes (Basel). 2023 May 22;14(5):1122. doi: 10.3390/genes14051122.

Authors

Shengyu Guan¹, Weining Li¹, Hai Jin², Lu Zhang¹, Guoshi Liu¹

Affiliations

¹ State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
² Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China.

Abstract

As an important genotyping platform, SNP chips are essential for implementing genomic selection. In this article, we introduced the development of a liquid SNP chip panel for dairy goats. This panel contains 54,188 SNPs based on genotyping by targeted sequencing (GBTS) technology. The source of SNPs in the panel were from the whole-genome resequencing of 110 dairy goats from three European and two Chinese indigenous dairy goat breeds. The performance of this liquid SNP chip panel was evaluated by genotyping 200 additional goats. Fifteen of them were randomly selected for whole-genome resequencing. The average capture ratio of the panel design loci was 98.41%, and the genotype concordance with resequencing reached 98.02%. We further used this chip panel to conduct genome-wide association studies (GWAS) to detect genetic loci that affect coat color in dairy goats. A single significant association signal for hair color was found on chromosome 8 at 31.52-35.02 Mb. The TYRP1 gene, which is associated with coat color in goats, was identified to be located at this genomic region (chromosome 8: 31,500,048-31,519,064). The emergence of high-precision and low-cost liquid microarrays will improve the analysis of genomics and breeding efficiency of dairy goats.

Keywords: GBTS; SNP chip; dairy goat breeding; genotyping by target sequencing; sequence capture in-solution (liquid chip).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Genome
Genome-Wide Association Study*
Goats / genetics
Oligonucleotide Array Sequence Analysis
Polymorphism, Single Nucleotide* / genetics

Grants and funding

This research was funded by Inner Mongolia Autonomous Region Science and Technology Major Special Project, grant number (2021ZD0023-1); Biological Breeding Project-Topic4, grant number (2022ZD0401404); National Key Research and Development Program, grant number (2021YFD1300903).