Genome-wide Association Analysis Of SCS In Chinese Holstein Cows And The Association Between Candidate Gene SNPs And Production Performance

Chinese Holstein cow is the most important dairy cow breed in China and has important economic value.The production performance of dairy cows is affected by many factors.The purpose of this study was to explore the effects of different candidate gene SNPs and some non-genetic factors on the production performance of Chinese Holstein cattle in Jiangsu area,and to further explore candidate genes significantly related to dairy cow mastitis,and to reveal more mastitis-related genetic variations.It provides a reference for the molecular breeding of disease-resistant mastitis in Holstein cattle.In this study,the multivariate analysis of variance model was used to analyze the collected DHI measurement data to reveal its changing law.Secondly,this study used the recorded data of 86,281 test days of 8,580 Holstein cow in Jiangsu,and used the random regression measurement day model to estimate the genetic parameters of Holstein cow SCS.At the same time,the adjusted phenotype was used to perform a genome-wide association analysis of dairy cow somatic cell scores using the FarmCPU method to screen for significant SNPs and candidate genes.Based on the results of genome-wide association analysis,three candidate genes（ABCG2、CD44、SPP1）were selected in this study for SNPs association analysis with production traits in Holstein cow.The specific results are as follows:1.This study analyzed the non-genetic factors affecting the production performance of Holsteins in Jiangsu,and found that different parity,measurement season,calving season,and lactation month all affected the milk production,milk fat rate,milk protein rate,milk urea nitrogen and somatic cell score had extremely significant effects（p<0.01）.There was very significant negative correlation between milk yield,milk fat rate,milk protein rate and somatic cell score（p<0.01）.2.Genetic parameter estimation and genome-wide association analysis of Chinese Holstein somatic cell score in Jiangsu area were performed,and the heritability of somatic cell score was found to be 0.18;the additive genetic variance and heritability of the SCS of dairy cows both increased firstly and then decreased;The permanent environmental variance of SCS showed a decreasing trend throughout the lactation period;The genetic and permanent environmental correlations of somatic cell scores in different varieties of dairy cows between different DIMs decreased with the increase of time interval;Six SNPs（rs135806474、rs41256968、rs41566683、rs109267271、rs134115197 and rs109756462）were significantly associated with dairy cow SCS（p<0.05）;Through the enrichment analysis of genes related to significant SNPs,a total of 8 significantly related pathways（bta04512、bta04620、bta04510、bta00970、bta05169、bta05417、bta04215、bta04010）were found on the KEGG pathway,covering a total of 7 genes;In the GO enrichment analysis,22 GO terms enriched by 8 genes were retained.There are eight genes（PKD2、KCNAB1、SPP1、IBSP、ABCG2、SLC35A4、CD14 and CD44）can be used as candidate genes for somatic cell scoring in dairy cows for further exploration.3.The association analysis of ABCG2、CD44 and SPP1 genes and dairy cow production performance was carried out.Among them,4、4 and 2 SNP loci were detected in the ABCG2、CD44 and SPP1 genes.The different genotypes of these 10 SNPs loci significantly affected the milk production、milk fat rate、milk protein rate、somatic cell score and urea nitrogen content.Among them,different genotypes of ABCG2-g.80952G>T site、ABCG2g.120017G>A site and CD44-g.2294G>C site had extremely significant effects on the somatic cell score of dairy cows（p<0.01）.Cows with GG genotype at ABCG2-g.80952G>T site、AA and GG genotype at ABCG2-g.120017G>A site and GG genotype at CD44-g.2294G>C site had lower somatic cell scores.