杜长大商品猪肌内脂肪含量的全基因组关联分析

Genome-wide association study of intramuscular fat content in a Duroc-Landrace-Yorkshire pig population

  • 摘要: 【目的】通过全基因组关联分析,定位影响杜长大商品猪肌内脂肪含量的相关SNP位点及其重要候选基因,为利用分子生物学方法改良猪肌内脂肪含量提供科学依据。【方法】选取981头杜长大商品猪,包括阉割公猪447头、母猪534头,所有试验猪均在统一条件下饲养至150日龄后进行屠宰测定,屠宰后利用索氏浸提法对肌内脂肪含量进行测定。利用GeneSeek GGP 50K芯片进行基因分型,使用rMVP软件包的FarmCPU模型对肌内脂肪含量性状进行全基因组关联分析。【结果】杜长大商品猪平均肌内脂肪含量达2.27%,其变异系数为34.24%,基因组遗传力(h2)为0.39,属于中等遗传力性状,表明该性状具有较大的遗传改良空间。经质控后,剩余30600个SNPs位点用于全基因组关联分析,共发现有8个潜在SNPs位点与肌内脂肪含量相关,分别分布在2、3、5、11、12、13和14号染色体上。利用Gene Ontology数据库对可能影响肌内脂肪含量的候选基因进行GO功能注释分析,发现这些候选基因参与的代谢通路包括肌肉发育代谢过程、器官生长代谢、基因表达调控及RNA转录等生物学代谢过程,但主要以肌肉生长发育代谢通路为主,表明肌内脂肪含量与肌肉生长发育之间存在紧密联系。【结论】利用高密度芯片进行全基因组关联分析,发现有8个SNPs位点与肌内脂肪含量相关;根据基因生物学功能及相关研究文献,C2orf74、HS6ST3ROBO2基因主要参与细胞增殖分化及脂肪代谢等生物学过程,可作为影响肌内脂肪含量的重要候选基因。

     

    Abstract: 【Objective】Genome-wide association analysis was performed to locate SNP loci and their important candidate genes affecting intramuscular fat content in a Duroc-Landrace-Yorkshire pig population,thus providing a scientific basis for the improvement of intramuscular fat content in pigs by molecular biology.【Method】981 Duroc-Landrace-Yorkshire pigs were selected for the experiment,including 447 castrated boars and 534 sows. All pigs were reared under uniform conditions until 150 days of age and then slaughtered for determination of intramuscular fat content after slaughter using the Soxhlet leaching method. GeneSeek GGP 50 K was used for genotyping and the FarmCPU model of the rMVP software package was used to analyze the whole genome association of intramuscular fat content traits.【Result】The average intramuscular fat content of Duroc-Landrace-Yorkshire pig was 2.27%,with a coefficient of variation of 34.24%. Its genomic heritability(h2)was 0.39,which belonged to medium heritability trait,indicating that this trait has more room for genetic improvement. After quality control,the remaining 30600 SNPs were used for genome-wide association analysis and 8 potential SNP loci were found to be associated with intramuscular fat content and distributed on chromosomes 2,3,5,11,12,13 and 14. The GO function annotation analysis on candidate genes that may affect intramuscular fat content was conducted using the Gene Ontology database. It was found that these candidate genes were involved in the metabolic pathways of muscle development,organ growth and metabolism,gene expression regulation and RNA transcription,but mainly in muscle growth and development,indicating that there was a close relationship between intramuscular fat content and muscle growth and development.【Conclusion】Based on genome-wide association analysis that is conducted with high density chips,8 SNPs loci are found related to intramuscular fat content. According to the gene biological function and related research literature,it is further speculated that C2orf74,HS6ST3 and ROBO2 genes,mainly participating in cell proliferation and differentiation,fat metabolism and biological processes,can be used as important candidate genes affecting intramuscular fat content,which provides a reference basis for the breeding and improvement of pork quality traits.

     

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