利用紧缩线性模型和贝叶斯模型对猪总产仔数和产活仔数性状的全基因组关联研究

Genome-wide association study of total number born and number born alive in pigsusing both compressed mixed linear model and Bayes model

全基因组关联分析策略已逐渐成为家畜重要经济性状研究的强有力工具。文章使用猪60K SNP芯片对一个具多胎繁殖性状记录的商业母猪群(n=820)进行分型检测,共计57 814个SNP通过设定质控标准。主成分分析显示群体内不存在显著的群体分层现象,而后分别运用两种统计模型Compressed Mixed Linear Model(GAPIT程序包)、Bayes CPi(GenSel软件)进行第1和第2胎次总产仔数和产活仔数性状的全基因组关联分析。从两种分析方法所得结果中各取最显著的50个SNP位点进行比较:对于第1胎次总产仔数,两种方法分析结果存在31个重合SNP位点,对于第1胎次产活仔数,有20个重合SNP位点;且两种统计分析结果中最显著的SNP位点都在另一方法中得到验证。与第1胎次总产仔数显著关联的SNP位于1、2、3、7、13、16和18号染色体,与第1胎次产活仔数显著关联的SNP位于1、3、4、13和16号染色体上的11个区域内。在1、3、13和16染色体上共有5个区域同时与这两个性状显著关联。与第2胎次总产仔数和产活仔数显著关联的区域主要位于7、10、12、13、14和16号染色体的6个重叠区域内。

GWAS（Genome-wide association study） strategy has been extensively used for identification of economical trait loci in livestock animals.Using Illumina’s PorcineSNP60 BeadChip,a GWA study of 820 commercial pigs with reproductive traits recorded was performed.The PCA analysis showed that there was no significant population stratification.Two different statistical models Compressed Mixed Linear Model（GAPIT program package）and Bayes CPi（GenSel software） were used to implement GWAS on total number born and number born alive of the first and second parity.To compare the most significant 50 SNPs from each method,a total of 31 and 20 coincided SNPs for total number born in the first parity were identified,and there were 20 coincided SNPs for number born alive in the first parityinthe results of bothmethods.The most significant SNPs were also significant in the results of the other method.The most significantly associated regions for total number born in the first parity were located on SSC1,2,3,7,13,16,and 18.The most significantly associated regions for number born alive in the first parity were locatedon SSC1,3,4,13,and 16.There were 5 common regions significantly associated with bothtraits on SSC1,3,13,and 16.The most significantly associated regions forbothtotal number born and number born alive for the second parity were mainly located on six common regions on SSC7,10,12,13,14,and 16.