GWAS on imputed whole-genome sequence variants reveal novel candidate mutations affecting feed efficiency and body composition traits in a crossbred swine population

IF 3.7 2区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE

Journal of animal science Pub Date : 2026-09-29 DOI:10.1093/jas/skag315

B N Keel, H L Bradford, W T Oliver, A K Lindholm-Perry, G A Rohrer

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引用次数: 0

Abstract

A pig’s ability to convert consumed feed into saleable meat is an important component of production efficiency in the swine industry. Given the polygenic and environmentally influenced nature of feed efficiency and body composition traits, conventional selection approaches have limited ability to pinpoint causal genetic factors driving variation. In this study, we performed a single-step genome-wide association study, with whole-genome sequence data (imputed from 50 to 60K SNP arrays), for feed efficiency and body composition traits using a multi-generational crossbred swine population. Overall, the three-generation pedigree consisted of 14,242 pigs, of which 9,336 pigs were phenotyped and 7,339 were genotyped. Whole-genome sequence variants were clustered into 705,923 linkage disequilibrium (LD) blocks, ranging from 0.001 to 9981.80 kb in size. A total of 133 LD blocks were significantly associated with the studied traits, several with potentially large pleiotropic effects. A total of 453 candidate genes were identified in the genomic regions of significant LD blocks. Four functional candidate genes (SIRT2, RYR1, MC4R, and LEPR) were found to harbor moderate to high impact variants, expected to affect protein function.

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全基因组序列变异的GWAS揭示了影响杂交猪群体饲料效率和体组成性状的新的候选突变

猪将消耗的饲料转化为可销售肉类的能力是养猪业生产效率的重要组成部分。考虑到饲料效率和体成分性状的多基因性和受环境影响的性质，传统的选择方法确定驱动变异的因果遗传因素的能力有限。在这项研究中，我们使用多代杂交猪群体进行了一项单步全基因组关联研究，使用全基因组序列数据（从50到60K SNP阵列输入），研究饲料效率和体成分性状。总体而言，该三代家系由14,242头猪组成，其中表型猪9,336头，基因型猪7,339头。全基因组序列变异聚集在705,923个连锁不平衡（LD）块中，大小从0.001到9981.80 kb不等。共有133个LD片段与研究性状显著相关，其中一些具有潜在的多效性效应。在显著LD块的基因组区域共鉴定出453个候选基因。四个功能候选基因（SIRT2, RYR1， MC4R和LEPR）被发现含有中等到高影响变异，预计会影响蛋白质功能。

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来源期刊

Journal of animal science 农林科学-奶制品与动物科学

CiteScore

4.80

自引率

12.10%

发文量

1589

审稿时长

3 months

期刊介绍： The Journal of Animal Science (JAS) is the premier journal for animal science and serves as the leading source of new knowledge and perspective in this area. JAS publishes more than 500 fully reviewed research articles, invited reviews, technical notes, and letters to the editor each year. Articles published in JAS encompass a broad range of research topics in animal production and fundamental aspects of genetics, nutrition, physiology, and preparation and utilization of animal products. Articles typically report research with beef cattle, companion animals, goats, horses, pigs, and sheep; however, studies involving other farm animals, aquatic and wildlife species, and laboratory animal species that address fundamental questions related to livestock and companion animal biology will be considered for publication.