Genome Wide Association Study For Milk Production Traits And Body Conformation Traits In The Chinese Holstein Cattle

Genome wide association study(GWAS)is an important approach for genetic improvement of agricultural animals.This study used the geneseek GGP bovine 26 K SNP chips and two statistical mldels to investigate milk production traits and body conformation traits of 445 chinese holstein dairy cows with GWAS.The aim of this study is to identify causative SNPs which could be associated with phenotypic traits by GWAS approach.The project includes three phases.In part I,the population structure analysis of chinese holstein cows.we assessed the population structure of chinese holstein cows using principle component analysis(PAC)available from the PLINK(v1.07)software.All autosomal SNPs were pruned using the indep-pairwise option,resulting in 8,703 independent SNP markers.Pairwise identity-bystate(IBS)distances were calculated between all individuals using the 8703 independent SNP markers,and principle components were obtained using the mds-plot option based on the IBS matrix.The result shows that population structure of different farms have a little stratification,but most of the groups are mixed together.So,the influence of population structure effected on the association analysis is small,and we can disregard the influence of the population structure or use the first principal component as a covariate of the subsequent association analysis.In part?,genome-wide association study of milk production traits in chinese holstein cows.Genome-wide association analyses were carried out in PLINK and GCTA software.Linear regression model and mixed linear model analyses for milk production traits were performed with the first princile component,calving interval,batch,and lactation period as covariates.Four common SNPs were found by the two models and the traits were also consistent,which indicated that the mixed linear model was more strict to the correction of influencing factors.At the same time,the nearest genes EEF2 K,KLHL1 and SLC22A8?ATP11B can be used as the candidate genes for milk yield,lactation persistence and mature equivalency,and then to verify and analyze the genes function.In part ?,genome-wide association study of body conformation traits in ChineseHolstein cows.GWAS was carried out to identify SNPs that are association with body conformation traits,using marker data of the GGP bovine SNP 26 beadchip.Linear regression model and mix linear model were applied to detect the remarkable SNPs for 29 body conformation traits.The association results of two models have a great difference.Using the linear regression model,we found 87 significant SNPs,while one significant SNP was found association with breast width and trunk simultaneously for the mixed linear model.This study used different models of two kinds of software to analyze the milk production traits and body conformation traits with GWAS for Chinese Holstein cows.The results show that the mixed linear model is a relatively optimal model.At the same time,using two different models,we also find some common significant loci providing a basis for the next step of verification and analysis of gene function.Finally,this study also provides some SNPs data for the marker assisted selection of cattle genetic research in Shandong region.