中国肉用西门塔尔牛生长曲线参数的全基因组关联分析

Genome-wide Association Study of Growth Curve Parameters in Chinese Simmental Beef Cattle

旨在通过对中国肉用西门塔尔牛纵向体重性状的全基因组关联分析(genome-wide association study,GWAS),定位与肉牛生长发育性状显著关联的候选基因。本研究利用808头中国肉用西门塔尔牛公牛0、6、12、18月龄的纵向体重数据,采用Gompertz、Logistic和Brody 3种非线性模型拟合个体的体重预测模型,估计参数A(成熟体重)、b(达到最大生长率的时间)和K(成熟率),然后以参数值为表型,BovineHD(770K)芯片数据质控后剩余671991个SNPs,利用GAPIT进行关联分析,结合基因注释筛选影响肉牛发育的候选基因。选取拟合度最高的Gompertz模型(R^(2)=0.954)确定相应参数估计值,GWAS共筛选到了9、49和7个显著的SNPs分别与A、b和K关联,且主要分布在2、3、7、9、11、14、22和25号染色体上。基因注释结果发现,PLIN3、KCNS3、ANGPTL2和ALPL与生长发育过程相关,其中KCNS3被认为是肌内脂肪含量的候选基因;IGF-1、TMCO1、PRKAG3和SHISA9影响肌肉发育过程,其中IGF-1被报道为生长发育过程的核心调控元件;ASPH基因参与调控肉牛胴体发育和肉质性状。本研究利用体重预测模型的参数估计值作为表型进行GWAS分析,定位到了一些与生长发育性状相关的候选基因,为其他纵向数据的研究提供了参考,也为调控肉牛生长发育进而提高产肉量的育种工作提供了新的候选分子标记。

The objective of this study was to explore candidate genes which are significantly associated with growth and development traits of beef cattle by performing genome-wide association study(GWAS)for body weight longitudinal data of 808 Chinese Simmental beef cattle.The longitudinal body weight data of 808 Chinese Simmental beef bulls aged 0,6,12 and 18 months were used to fit the individual body weight prediction model using 3 nonlinear models(Gompertz model,Logistic model and Brody model),and the parameters A(mature body weight),b(time-scale parameter)and K(maturity rate)were estimated.Then,the parameter values were used as phenotypes.After the quality control using the BovineHD Beadchip(770K),671991 SNPs were generated.GAPIT was used for association analysis,combined with gene annotation to identify candidate genes associated with development traits of beef cattle.Gompertz model with the highest goodness of fit(R^(2)=0.954)was selected to determine the parameter estimates.A total of 9,49 and 7 significant SNPs associated with parameters A,b and K were identified by GWAS,respectively.These SNPs were mainly mapped on BTA 2,3,7,9,11,14,22 and 25.Gene annotation results showed that PLIN 3,KCNS 3,ANGPTL 2 and ALPL were associated with fat deposition process,and KCNS3 was considered as a candidate gene for intramuscular fat content;IGF-1,TMCO 1,PRKAG 3 and SHISA 9 were associated with growth and development,and IGF-1 was reported to be central to the growth and development process;ASPH was involved in regulating carcass development and meat quality traits of beef cattle.In this study,the estimated parameters of the weight prediction model were used as phenotypes for GWAS,and some candidate genes associated with growth and development traits were identified,which provided a reference for other longitudinal data studies and new candidate molecular markers for regulating the growth and development of beef cattle to improve meat production in breeding.