Abstract
BackgroundIdentification 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. Eleven reproduction and production traits were analyzed.ResultsA total of 40 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.ConclusionSNPs in a total of 40 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.
Highlights
Identification of single nucleotide polymorphisms (SNPs) for specific genes involved in reproduction might improve reliability of genomic estimates for these low-heritability traits
Three types of SNPs were evaluated: SNPs previously reported to be associated with reproductive traits of dairy or beef cattle 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 reported to be differentially expressed between physiological conditions in a variety of tissues associated in reproductive function
Since the SNPs used for genotyping were chosen for their function in reproductive processes, a larger proportion of them would be associated with reproductive traits than for production traits
Summary
Identification of single nucleotide polymorphisms (SNPs) for specific genes involved in reproduction might improve reliability of genomic estimates for these low-heritability traits. There is a negative genetic correlation between milk yield and fertility in dairy cattle [1,2,3]. The large improvement in milk yield over the last 40 years was accompanied by a decline in fertility [4,5,6]. Genetic selection for fertility is hampered by low heritability. One possible way to improve the accuracy of genomic estimates of fertility is to incorporate SNPs for specific genes involved in reproduction into SNP panels. The bovine genome contains over 20,000 genes, and over 14,000 of those do not contain a single SNP on the BovineSNP50 chip [9]. Such an approach has been successful for improving ability to detect genomic associations with disease [10]
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