Genome-wide association study for calving traits in Holstein–Friesian dairy cattle

Abstract

Dystocia and perinatal mortality are quantitative traits that significantly impact animal productivity and welfare. Their economic importance is reflected by their inclusion in the national breeding goals of many cattle populations. The genetic architecture that influences these traits, however, has still yet to be thoroughly defined. Regions of the bovine genome associated with calving difficulty (direct and maternal) and perinatal mortality were detected in this study using a Bayesian approach with 43 204 single nucleotide polymorphisms (SNPs) on up to 1970 Holstein-Friesian bulls. Several SNPs on chromosomes 5, 6, 11, 12, 17,18 and 28 were detected to be strongly associated with these calving performance traits. Novel genomic regions with previously reported associations with growth, stature, birth weight and bone morphology were identified in the present study as being associated with the three calving performance traits. Morphological abnormalities are a known contributor to perinatal mortality and the most significantly associated SNP for perinatal mortality in the present study was located in a region in linkage disequilibrium with the gene SLC26A7. This gene, SLC26A7, has similarities and colocalises with SLC4A2, which has previously been associated with osteoporosis and mortality in cattle populations. The HHIP gene that is known to be associated with stature in humans was strongly associated with direct calving difficulty in the present study; large calves are known to, on average, have a greater likelihood of dystocia. A stemloop microRNA, bta-mir-1256, on chromosome 12, involved in post-transcriptional regulation of gene expression was associated with maternal calving difficulty. Previously reported quantitative trait loci associated with calving performance traits in other populations were again identified in this study; with one genomic region on chromosome 18 supporting very strong evidence of an underlying causative mutation and accounting for 2.1% of the genetic variation in direct calving difficulty. Overlapping genomic regions associated with one or more of the calving traits were also detected substantiating the known genetic covariances existing between these traits. Moreover, some genomic regions were only associated with one of the calving traits implying the selective genomic breeding programs exploiting these regions could help resolve genetic antagonisms.Keywords: dystocia, mortality, calving difficulty, genomic, quantitative trait loci ImplicationsThis study contributes to the understanding of the underlying genetic architecture and aetiology of dystocia and perinatal mortality both of which are quantitative traits that have a significant economic farm impact. Moreover, the detection of quantitative trait loci associated with only one calving trait can help resolve genetic antagonisms if targeted in genomic breeding programs -for example, selecting for decreased calving difficulty without impacting maternal calving difficulty.

A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits

“…Many studies have reported on QTL affecting calving traits in several populations of Holstein cattle (Kühn et al, 2003;Schnabel et al, 2005;Holmberg and Andersson-Eklund, 2006;Kolbehdari et al, 2008;Thomasen et al, 2008;Seidenspinner et al, 2011;Purfield et al, 2014), and there appears to be a major gene on BTA18 affecting dystocia, stillbirth, conformation, and lifetime economic merit (Cole et al, 2009b;Brand et al, 2010;Sahana et al, 2011;Purfield et al, 2014). Qanbari et al (2011) also identified a signature of selection in the same region of the cattle genome.…”

Effects of a novel missense polymorphism within the SIGLEC5 gene on fertility traits in Holstein‐Friesian cattle

“…They verified previous QTL studies for calving ease, foetus size and calf mortality and concluded that chromosome 18 contains many significant SNP markers for fertility traits. Two years later, Purfield, Bradley, Kearney, and Berry () in GWAS confirmed the significant influence of SNP rs109478645 within SIGLEC5 on calving traits.…”

Genetic improvement in cattle—are we sacrificing reproduction in favor of production?

“…Positive correlations of dystocia with calf birth weights, 200-d weights, and post-weaning gain suggest that selection for carcass yield can have negative implications on reproductive performance in the cow herd due to increases in dystocia (Bennett & Gregory 2001a, Bennett & Gregory 2001b. A genome-wide association study identified chromosomal regions associated with calving traits in Holstein-Friesian cows (Purfield et al 2013). A polymorphism in the hedgehog interacting protein (HHIP) gene that is associated with stature in humans was associated with direct calving difficulty, although polymorphisms in the bovine HHIP gene were not associated with stature in cattle (Pryce et al 2011).…”