Genome Wide Association Study And Candidate Genes Analysis For Semen Traits Of The Bulls In Chinese Holstein

In this paper, based on 129207 ejaculate records of 692 bulls from 8 bull stations, association test between five semen traits and 41,188 informative high-quality SNPs were achieved with GAPIT software using the Illumina BovineSNP50 Beadchip.Finally, based on the results of GWAS, two candidate genes were selected to screen SNPs in genes and perform the study on assocaiton of those SNPs with five semen traits of the bulls in Chinese Holstein. The conclusion are as follows:1.Association analysis between five semen traits and the 41,188 informative high-quality SNPs were achieved with GAPIT software. In total,19 suggestive significant SNPs associated with five semen traits were detected, which were within or close to the reported 20 candidate genes. Besides, by combining with our GWAS results and the biological functions of these genes,8 novel promising candidate genes were suggested to potentially relate to semen traits, including ETNK1, PDE3A, PDGFRB, CSF1R, WT1,DSCAML1, SOD1, and RUNX2. Our findings may provide a basis for further research on the genetic mechanism of semen production and marker assisted selection of such traits of the bulls in Chinese Holstein.2.Based on the results of GWAS, CSF1R and ETNK1 were selected as candidate genes to screen SNPs in genes using mixed pool DNA sequencing of the bulls in Chinese Holstein. The results indicated that 8 SNPs in CSF1R were identied, which were consistent with NCBI and 2 SNPs were found in ETNK1, one of them was new discovery.3.10 SNPs were genotyped by SNaPshot tenology and association of SNPs with five semen traits were analyzed by the MIXED procedure of SAS(9.3), testd by Bonferroni. The results indicated that 10 SNPs from CSF1R and ETNK1 were associated with at least two semen traits, and also, which were also associated with NSPE and NMSPE very significantly CP<0.01).Besides, haplotype analysis in CSF1R revealed the sme results as single marker analysis.4.After additive genetic effects, dominance effects and substitution effects, rs210296215,rs43518642 and rs 137825682 in CSF1R and rs208064031 from ETNK1 were associated with NSPE and NMSPE significantly (P<0.05) and very significantly (P<0.01),whose advantage alleles were C,G,A,and G, respectively.Those four SNPs may be used as molecular markers for semen traits in marker-assisted selection of the bulls in Chinese Holstein.