猪发旋的全基因组关联研究。

Genome-Wide Association Studies of Hair Whorl in Pigs.

机构信息

Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.

State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.

出版信息

Genes (Basel). 2024 Sep 25;15(10):1249. doi: 10.3390/genes15101249.

DOI:10.3390/genes15101249

PMID:39457372

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11506845/

Abstract

BACKGROUND

In pigs, a hair whorl refers to hairs that form a ring of growth around the direction of the hair follicle at the dorsal hip. In China, a hair whorl is considered a negative trait that affects marketing, and no studies have been conducted to demonstrate whether hair whorl affects pig performance and provide an explanation for its genetic basis.

METHODS

Performance-measured traits and slaughter-measured traits of hair whorl and non-hair whorl pigs were differentially analyzed, followed by genome-wide association analysis (GWAS) and copy number variation (CNV) methods to investigate the genetic basis of hair whorl in pigs.

RESULTS

Differential analysis of 2625 pigs (171 hair whorl and 2454 non-hair whorl) for performance measures showed that hair whorl and non-hair whorl pigs differed significantly ( < 0.05) in traits such as live births, total litter size, and healthy litter size ( < 0.05), while differential analysis of carcass and meat quality traits showed a significant difference only in the 45 min pH ( = 0.0265). GWAS identified 4 SNP loci significantly associated with the hair whorl trait, 2 of which reached genome-significant levels, and 23 candidate genes were obtained by annotation with the Ensembl database. KEGG and GO enrichment analyses showed that these genes were mainly enriched in the ErbB signaling, endothelial apoptosis regulation, and cell proliferation pathways. In addition, CNV analysis identified 652 differential genes between hair whorl and non-hair whorl pigs, which were mainly involved in the signal transduction, transcription factor activity, and nuclear and cytoplasmic-related pathways.

CONCLUSIONS

The candidate genes and copy number variation differences identified in this study provide a new theoretical basis for pig breeding efforts.

摘要

背景

在猪中，发旋是指围绕着毛发生长方向的环状生长的毛发。在中国，发旋被认为是一种负面特征，会影响销售，并且没有研究表明发旋是否会影响猪的性能，并为其遗传基础提供解释。

方法

对有发旋和无发旋猪的性能测量性状和屠宰测量性状进行差异分析，然后采用全基因组关联分析（GWAS）和拷贝数变异（CNV）方法研究猪发旋的遗传基础。

结果

对 2625 头猪（171 头有发旋和 2454 头无发旋）的性能测量性状进行差异分析表明，有发旋和无发旋猪在活产仔数、总产仔数和健康产仔数等性状上存在显著差异（ < 0.05），而胴体和肉质性状的差异分析仅在 45 分钟 pH 值上存在显著差异（ = 0.0265）。GWAS 鉴定出 4 个与发旋性状显著相关的 SNP 位点，其中 2 个达到基因组显著水平，通过 Ensembl 数据库注释获得 23 个候选基因。KEGG 和 GO 富集分析表明，这些基因主要富集在 ErbB 信号、内皮细胞凋亡调节和细胞增殖途径中。此外，CNV 分析鉴定出有发旋和无发旋猪之间存在 652 个差异基因，这些基因主要涉及信号转导、转录因子活性以及核和细胞质相关途径。