Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height

Abstract

BackgroundBirth weight (BW) is an economically important trait in beef cattle, and is associated with growth- and stature-related traits and calving difficulty. One region of the cattle genome, located on Bos primigenius taurus chromosome 14 (BTA14), has been previously shown to be associated with stature by multiple independent studies, and contains orthologous genes affecting human height. A genome-wide association study (GWAS) for BW in Brazilian Nellore cattle (Bos primigenius indicus) was performed using estimated breeding values (EBVs) of 654 progeny-tested bulls genotyped for over 777,000 single nucleotide polymorphisms (SNPs).ResultsThe most significant SNP (rs133012258, PGC = 1.34 × 10-9), located at BTA14:25376827, explained 4.62% of the variance in BW EBVs. The surrounding 1 Mb region presented high identity with human, pig and mouse autosomes 8, 4 and 4, respectively, and contains the orthologous height genes PLAG1, CHCHD7, MOS, RPS20, LYN, RDHE2 (SDR16C5) and PENK. The region also overlapped 28 quantitative trait loci (QTLs) previously reported in literature by linkage mapping studies in cattle, including QTLs for birth weight, mature height, carcass weight, stature, pre-weaning average daily gain, calving ease, and gestation length.ConclusionsThis study presents the first GWAS applying a high-density SNP panel to identify putative chromosome regions affecting birth weight in Nellore cattle. These results suggest that the QTLs on BTA14 associated with body size in taurine cattle (Bos primigenius taurus) also affect birth weight and size in zebu cattle (Bos primigenius indicus).

PLAG1 and NCAPG‐LCORL in livestock

“…Utsunomiya et al . (2013) detected association of the PLAG1 region with birth weight in Nellore ( Bos indicus ), although they did not show whether the PLAG1 allele is segregated in the population. Recent human GWAS using tens of thousands of people identified several loci for birth weight (Horikoshi et al .…”

Single nucleotide variant detection in Jaffrabadi buffalo (Bubalus bubalis) using high-throughput targeted sequencing

“…Clearly, the identification of variation in livestock genomes that predisposes to health and productivity with less reliance on hormones, antibiotics and pesticides will be a major step in meeting this global challenge (Womack 2005). In recent times, many such studies (Georges 2007;Jiang et al 2010;Bolormaa et al 2011;Utsunomiya et al 2013) have been carried out to identify genetic differences in the form of molecular markers, such as single nucleotide polymorphisms (SNPs) responsible for or associated with variations in phenotypic trait, particularly those of economic importance. Understanding this genetic basis of phenotypes generally requires genotyping thousands of gene-targeted loci, genome wide.…”

Alternative parameterizations of relatedness in whole genome association analysis of pre-weaning traits of Nelore-Angus calves

“…Seven associated markers were within the bp limits of the XK, Kell blood group subunit-related family, member 4 ( XKR4 ), and another was upstream > 25 kb of this gene (Table S1). A significant association of a SNP within this gene with birth weight was also detected in Nelore cattle (Utsunomiya et al , 2013); this was one of five total associations detected in that study, as those researchers applied Bonferroni corrections to p-values for the 434,020 loci evaluated. Detected marker-subcutaneous rump fat associations were reported for markers in and around XKR4 in Brahman and Brahman-influenced cattle (Bolormaa et al , 2011; Porto Neto et al , 2012), and this was considered a candidate gene based on marker-trait associations for average daily gain, average daily feed intake, and residual feed intake in Bos taurus cattle (Lindholm-Perry et al , 2012).…”