Genome-wide detection of multiple variants associated with teat number in French Yorkshire pigs
文献类型： 外文期刊
作者： Lin, Danyang 1 ; Qiu, Yibin 1 ; Zhou, Fuchen 1 ; Li, Xuehua 1 ; Deng, Shaoxiong 1 ; Yang, Jisheng 1 ; Chen, Qiaoer 1 ; Cai, Gengyuan 1 ; Yang, Jie 1 ; Wu, Zhenfang 1 ; Zheng, Enqin 1 ;
作者机构： 1.South China Agr Univ, Coll Anim Sci, Guangzhou 510642, Peoples R China
2.South China Agr Univ, Natl Engn Res Ctr Breeding Swine Ind, Guangzhou 510642, Peoples R China
3.Guangdong Zhongxin Breeding Technol Co Ltd, Guangzhou 510642, Peoples R China
4.South China Agr Univ, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Guangzhou 510642, Guangdong, Peoples R China
5.Yunfu Subctr Guangdong Lab Lingnan Modern Agr, Yunfu 527300, Peoples R China
关键词： Teat number; Copy number variation; Genome-wide association study; French Yorkshire pigs
期刊名称：BMC GENOMICS （ 影响因子：3.5； 五年影响因子：4.1 ）
ISSN： 1471-2164
年卷期： 2024 年 25 卷 1 期
页码：
收录情况： SCI
摘要： BackgroundTeat number is a vital reproductive trait in sows, crucial for providing immunity and nutrition to piglets during lactation. However, "missing heritability" in Single Nucleotide Polymorphism (SNP)-based Genome-Wide Association Studies (GWAS) has led to an increasing focus on structural variations in the genetic analysis of complex biological traits.ResultsIn this study, we generated a comprehensive CNV map in a population of French Yorkshire pigs (n = 644) and identified 429 CNVRs. Notably, 44% (189 CNVRs) of these were detected for the first time. Subsequently, we conducted GWAS for teat number in the French Yorkshire pig population using both 80K chip and its imputed data, as well as a GWAS analysis based on CNV regions (CNVR). Interestingly, 80K chip GWAS identified two SNPs located on Sus scrofa chromosome 5 (SSC5) that were simultaneously associated with Total Teat Number (TTN), Left Teat Number (LTN), and Right Teat Number (RTN). The leading SNP (WU_10.2_5_76130558) explained 3.33%, 2.69%, and 2.67% of the phenotypic variance for TTN, LTN, and RTN, respectively. Moreover, through imputed GWAS, we successfully identified 30 genetic variants associated with TTN located within the 73.22 -73.30 Mb region on SSC5. The two SNPs identified in the 80K chip GWAS were also located in this region. In addition, CNVR-based GWAS revealed three significant CNVRs associated with TTN. Finally, through gene annotation, we pinpointed two candidate genes, TRIM66 and PRICKLE1, which are related to diverse processes such as breast cancer and abnormal vertebral development.ConclusionsOur research provides an in-depth analysis of the complex genetic structure underlying teat number, contributing to the genetic enhancement of sows with improved reproductive performance and, ultimately, bolstering the economic benefits of swine production enterprises.
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