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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVING GENETIC PREDICTIONS IN DAIRY ANIMALS USING PHENOTYPIC AND GENOMIC INFORMATION

Location: Animal Improvement Programs

Title: Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle

Authors
item Cochran, S -
item Cole, John
item Null, Daniel
item Hansen, P -

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 23, 2013
Publication Date: June 7, 2013
Citation: Cochran, S.D., Cole, J.B., Null, D.J., Hansen, P.J. 2013. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BioMed Central (BMC) Genetics. 14:49.

Interpretive Summary: Semen from 550 Holstein bulls with high (n = 288) or low (n = 262) genetic merit for daughter fertility were used to identify single nucleotide polymorphisms (SNP) located in genes that are involved in reproduction. Those SNP may be useful for improving the reliability of predicted transmitting abilities for these lowly heritabile traits. Three types of SNPs were evaluated: those previously reported to be associated with reproductive traits or physically close to genetic markers for reproduction, those found in genes that are known to be involved in reproductive processes, and those in genes that are differentially expressed in a variety of tissues associated with reproductive function. Ten reproduction and production traits were analyzed. A total of 42 SNPs were associated (P < 0.05) with daughter pregnancy rate (DPR), a measure of daughter fertility. Among these were genes involved in the endocrine system, cell signaling, immune function and inhibition of apoptosis. A total of 10 genes were regulated by estradiol. In addition, 22 SNPs were associated with heifer conception rate, 33 with cow conception rate, 36 with productive life, 34 with net merit, 23 with milk yield, 19 with fat yield, 13 with fat percent, 19 with protein yield, 22 with protein percent, and 13 with somatic cell score. The allele substitution effect for SNPs associated with heifer conception rate, cow conception rate, productive life and net merit were in the same direction as for DPR. Allele substitution effects for several SNPs associated with production traits were in the opposite direction as DPR. Nonetheless, there were 29 SNPs associated with DPR that were also positively associated with production traits. It may be feasible to include these SNPs in genomic tests of reproduction and other traits. The large number of SNPs positively associated with DPR and production traits suggests that it may be possible to select for DPR without compromising production.

Technical Abstract: Identification of single nucleotide polymorphisms (SNPs) for specific genes involved in reproduction might improve reliability of genomic estimates for these low- heritability traits. Semen from 550 Holstein bulls of high (>= 1.7; n=288) or low (<= -2; n = 262) daughter pregnancy rate (DPR) was genotyped for 434 candidate SNPs using the Sequenom MassARRAY® system. Three types of SNPs were evaluated: SNPs previously reported to be associated with reproductive traits or physically close to genetic markers for reproduction, SNPs in genes that are well known to be involved in reproductive processes, and SNPs in genes that are differentially expressed between physiological conditions in a variety of tissues associated in reproductive function. Ten reproduction and production traits were analyzed. A total of 42 SNPs were associated (P < 0.05) with DPR. Among these were genes involved in the endocrine system, cell signaling, immune function and inhibition of apoptosis. A total of 10 genes were regulated by estradiol. In addition, 22 SNPs were associated with heifer conception rate, 33 with cow conception rate, 36 with productive life, 34 with net merit, 23 with milk yield, 19 with fat yield, 13 with fat percent, 19 with protein yield, 22 with protein percent, and 13 with somatic cell score. The allele substitution effect for SNPs associated with heifer conception rate, cow conception rate, productive life and net merit were in the same direction as for DPR. Allele substitution effects for several SNPs associated with production traits were in the opposite direction as DPR. Nonetheless, there were 29 SNPs associated with DPR that were not negatively associated with production traits. Conclusion: SNPs in a total of 42 genes associated with DPR were identified as well as SNPs for other traits. It might be feasible to include these SNPs into genomic tests of reproduction and other traits. The genes associated with DPR are likely to be important for understanding the physiology of reproduction. Given the large number of SNPs associated with DPR that were not negatively associated with production traits, it should be possible to select for DPR without compromising production.

Last Modified: 4/20/2014
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