基于杜洛克猪全基因组重测序的InDel分析及重要经济性状基因定位

InDel Analysis and Gene Mapping of Important Economic Trait Genes Based on Whole-genome Resequencing of Duroc Pigs

本研究利用选择信号分析方法在美系杜洛克猪和丹系杜洛克猪中筛选与重要经济性状相关的候选基因。选取健康状态良好、饲养管理水平一致的成年美系杜洛克公猪33头、丹系杜洛克公猪11头,提取DNA并重测序,利用F_(st)&P_(i)的联合分析,保留候选区域,对注释基因进行GO功能和KEGG通路富集分析,进一步筛选与重要经济性状相关的相关候选基因。美系杜洛克猪和丹系杜洛克猪的全基因组重测序平均测序深度在13×以上,测序数据平均效率为99.82%,Q30平均值分别为91.91%、91.93%,G+C含量分别在42.90%~43.83%和42.48%~43.55%,均表明本次测序数据质量较高。以5%为筛选阈值,关联F_(st)&P_(i)提取相关候选区域,采用选择性消除方法检测到相应的选择信号区域,美系杜洛克猪和丹系杜洛克猪之间的F_(st)值为0.268,θ_(π)比值分别为0.495和-1.415,P_(i)值分别为4.206和3.506。在美系杜洛克猪的选择性消除分析中有557个受选择区域,注释到1323个基因;丹系杜洛克猪的选择性消除分析中有207个受选择区域,注释到338个基因。GO分析和KEGG通路富集分析发现,在美系和丹系杜洛克群体中初步筛选到ERLIN2、TMCO2、PITX2、SORCS3和SUFU等5个与精子发生、脂肪形成、生殖功能等性状相关的候选基因。在美系杜洛克猪中筛选到ATP1B1、LAMA4、EP300、ELOVL3、ECHS1、THEME5、PIP5K1A、PPT1、UBQLN1、IL2、CNTFR、ITGA10、SEC24D、MAP3K5和HSP90B1等15个与肉质、脂肪合成与代谢、精子发生、生长发育、骨发生和饲料效率等性状相关的候选基因。在丹系杜洛克猪中筛选到PDIA3、CBLIN2、CYCS和CDH7等4个候选基因,分别与产奶量、肉质性状、骨骼肌、饲料效率相关;BMI1、LHX8、ELL3、CATSPER2和CSMD1等5个与繁殖性状相关的候选基因。本研究发现美系杜洛克猪群体和丹系杜洛克猪群体间存在较大的遗传分化,为进一步研究杜洛克公猪的遗传特性提供了基因组数据支撑。

In this study,selection signal analysis methods were used to screen candidate genes related to important economic traits in both American and Danish Duroc pigs.A total of 33 healthy adult American Duroc boars and 11 Danish Duroc boars with consistent feeding management levels were selected,and their genomes were extracted and sequenced.A combined analysis of F_(st)and P_(i)were used to retain candidate regions,and performed GO functional and KEGG enrichment analyses on annotated genes to further screen candidate genes related to important economic traits.The average sequencing depth of whole-genome resequencing for American and Danish Duroc pigs was above 13×,the average effective rate of sequencing data was 99.82%,the average Q30 score was 91.91%and 91.93%,and the G+C content was between 42.90%-43.83%and 42.48%-43.55%,indicating that the quality of this sequencing data was high.A 5%screening threshold was used to associate F_(st)&P_(i)with related candidate regions and detected selective signals using the selective sweep method.The F_(st)values between American Duroc pigs and Danish Duroc pigs were 0.268,theθ_(π)ratio values were 0.495 and-1.415,and the P_(i)values were 4.206 and 3.506,respectively.In the selective sweep analysis of American Duroc pigs,557 selected regions were identified and annotated to 1323 genes;while in Danish Duroc pigs,207 selected regions were identified and annotated to 338 genes.Five candidate genes related to sperm maturation,adipogenesis,and reproductive functions were preliminarily screened by GO and KEGG pathway enrichment analyses in both American and Danish populations,including ERLIN2,TMCO2,PITX2,SORCS3,and SUFU.Fifteen candidate genes related to meat quality,fat synthesis and metabolism,sperm maturation,growth and development,bone development,and feed efficiency were screened in American Duroc pigs,including ATP1B1,LAMA4,EP300,ELOVL3,ECHS1,THEME5,PIP5K1A,PPT1,UBQLN1,IL2,CNTFR,ITGA10,SEC24D,MAP3K5,and HSP90B1.Four candidate genes related to milk production,meat quality,skeletal muscle,and feed efficiency were screened in Danish Duroc pigs,including PDIA3,CBLIN2,CYCS,and CDH7,as well as 5 candidate genes related to reproductive traits in Danish Duroc pigs,including BMI1,LHX8,ELL3,CATSPER2,and CSMD1,respectively.This study reveals significant genetic differentiation between American Duroc pig population and Danish Duroc pig population,providing genomic data support for further investigation into the genetic characteristics of Duroc boars.