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Design and characterization of a high-resolution multiple-SNP capture array by target sequencing for sheep

文献类型： 外文期刊

作者： Guo, Yingwei 1 ; Bai, Fengting 1 ; Wang, Jintao 1 ; Fu, Shaoyin 2 ; Zhang, Yu 1 ; Liu, Xiaoyi 1 ; Zhang, Zhuangbiao 1 ; Shao, Junjie 1 ; Li, Ran 1 ; Wang, Fei 1 ; Zhang, Lei 1 ; Zheng, Huiling 1 ; Wang, Xihong 1 ; Liu, Yongbin 3 ; Jiang, Yu 1 ;

作者机构： 1.Northwest A&F Univ, Coll Anim Sci & Technol, Key Lab Anim Genet Breeding & Reprod Shaanxi Prov, Yangling 712100, Peoples R China

2.Inner Mongolia Acad Agr & Anim Husb Sci, Inst Anim Sci, Hohhot 010031, Peoples R China

3.Inner Mongolia Univ, Sch Life Sci, Hohhot 010070, Peoples R China

关键词： chip design; genotyping by target sequencing; GWAS; sheep breeding

期刊名称：JOURNAL OF ANIMAL SCIENCE （ 影响因子：3.3； 五年影响因子：3.1 ）

ISSN： 0021-8812

年卷期： 2023 年 101 卷

页码：

收录情况： SCI

摘要： The efficiency of molecular breeding largely depends on inexpensive genotyping arrays. In this study, we aimed to develop an ovine high-resolution multiple-single-nucleotide polymorphism (SNP) capture array, based on genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology. All the markers were from 40K captured regions, including genes located within selective sweep regions, breed-specific regions, quantitative trait loci (QTL), and the potential functional SNPs on the sheep genome. The results showed that a total of 210K high-quality SNPs were identified in the 40K regions, indicating a high average capture ratio (99.7%) for the target genomic regions. Using genotyped data (n = 317) from liquid chip technology, we further performed genome-wide association studies (GWAS) to detect the genetic loci affecting sheep hair types and teat number. A single significant association signal for hair types was identified on 6.7-7.1 Mb of chromosome 25. The IRF2BP2 gene (chr25: 7,067,974-7,071,785), which is located within this genomic region, has been previously known to be involved in hair/wool traits in sheep. The results further showed a new candidate region around 26.4 Mb of chromosome 13, between the ARHGAP21 and KIAA1217 genes, that was significantly related to teat number in sheep. The haplotype patterns of this region also showed differences in animals with 2, 3, or 4 teats. Advances in using the high-accuracy and low-cost liquid chip are expected to accelerate sheep genomic and breeding studies in the coming years.

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