Genome-wide association study of normal and atypical progesterone profiles in Holstein-Friesian dairy cows

Abstract

Female fertility has a major role in dairy production and affects the profitability of dairy cattle. The genetic progress obtained by traditional selection can be slow because of the low heritability of classical fertility traits. Endocrine fertility traits based on progesterone concentration in milk have higher heritability and more directly reflect the cow's own reproductive physiology. The aim of our study was to identify genomic regions for 7 endocrine fertility traits in dairy cows by performing a genome-wide association study with 54,000 SNP. The next step was to fine-map targeted genomic regions with significant SNP using imputed sequences to identify potential candidate genes associated with the normal and atypical progesterone profiles. The association between a SNP and a phenotype was assessed by a single SNP analysis, using a linear mixed model that included a random polygenic effect. Phenotypes and genotypes were available for 1,126 primiparous and multiparous Holstein-Friesian cows from research herds in Ireland, the Netherlands, Sweden, and the United Kingdom. In total, 44 significant SNP associated with 7 endocrine fertility traits were identified on Bos taurus autosome (BTA) 1-4, 6, 8-9, 11-12, 14-17, 19, 21-24, and 29. Three chromosomes, BTA8, BTA17, and BTA23, were imputed from 54,000 SNP genotypes to the whole-genome sequence level with Beagle version 4.1. The fine-mapping identified several significant associations with delayed cyclicity, cessation of cyclicity, commencement of luteal activity, and inter-ovulatory interval. These associations may contribute to an index of markers for genetic improvement of fertility. Several potential candidate genes reported to affect reproduction were also identified in the targeted genomic regions. However, due to high linkage disequilibrium, it was not possible to identify putative causal genes or polymorphisms for any of the regions.

Genetic parameters of endocrine fertility traits based on in-line milk progesterone profiles in Swedish Red and Holstein dairy cows

“…The low heritability estimates for the classical fertility traits could be attributed to a multitude of factors, including, for example, that the traits are truly under poor additive genetic control relative to nonadditive and nongenetic factors (Berry et al, 2012). It is also claimed that low heritability estimates together with an unfavorable relationship between production and fertility traits complicates genetic improvement (Nyman et al, 2019). Daetwyler et al (2008) pointed out that the level of heritability for a trait influences the success of genome-wide association studies.…”

Overview of SNPs Associated with Trans Fat Content in Cow’s Milk

“…JARID2 is a gene located within the QTL which is associated with the development of the hind quarter [112], and it is located in the window from the GWAS explaining >1% of the genetic variation of the performance traits of angus cattle in high-altitude regions (elevation at 2170 m) [113]. Nyman et al [114] point to JARID2 as a possible candidate gene for cow fertility traits.…”

Genome-wide association study for age at puberty and resumption of cyclicity in a crossbred dairy cattle population

“…In this study, we focused on a specific type of fertility traits, the endocrine traits. Quantitative trait loci studies regarding endocrine traits are much less common, and only a few studies have reported QTL (Berry et al, 2012;Tenghe et al, 2016;Nyman et al, 2019).…”