Design and verification of a 25 K multiple-SNP liquid-capture chip by target sequencing for dairy goat

文献类型： 外文期刊

第一作者： Zhao, Jianqing

作者： Zhao, Jianqing;Wang, Yaling;Kamalibieke, Jiayidaer;Zhang, Fuhong;Shi, Huaiping;Wang, Wei;Luo, Jun;Gong, Ping

作者机构：

关键词： Dairy goat; Chip design; Genotyping by target sequencing; Liquid chip

期刊名称：BMC GENOMICS （ 影响因子：3.7； 五年影响因子：4.2 ）

ISSN： 1471-2164

年卷期： 2025 年 26 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundIn the genetic breeding research of dairy goats, traditional genotyping methods have limitations, and existing goat chips have shortcomings in functional loci and other aspects, which cannot meet the precise genetic analysis needs of dairy goats. Genotyping by Target Sequencing (GBTS) in the new generation of sequencing technology provides the possibility to solve these problems.ResultsA large number of candidate SNP sites related to important economic traits in dairy goats were identified through various analysis and screening methods. The chip ultimately retained 27,396 SNP sites for probe design, which can detect 46,459 SNPs. The site distribution is uniform, and the sequencing data efficiency, base quality, alignment rate, and other indicators are good. The chip SNP detection rate is high and the heterozygosity of gene typing is reasonable. GWAS was performed on 200 dairy goats for litter size and birth weight traits, and multiple genome-wide significantly related SNPs and related genes (litter size trait: SCAP, PTPN23, KIF9, ANTXRL, and GRID1. birth weight trait: NALCN, LRRN2, TMEM132D, COL5A2, and HS3ST1) were detected.ConclusionThe 25 K multiplex SNP liquid phase capture chip designed in this study has excellent performance and is of great value for genetic research and breeding of dairy goats, providing strong support for the development of the dairy goat industry.

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