Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle

Johanna L Smith; Miranda L Wilson; Sara M Nilson; Troy N Rowan; David L Oldeschulte; Robert D Schnabel; Jared E Decker; Christopher M Seabury

doi:10.1186/s12864-019-6231-y

Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle

BMC Genomics. 2019 Dec 4;20(1):926. doi: 10.1186/s12864-019-6231-y.

Authors

Johanna L Smith¹, Miranda L Wilson¹, Sara M Nilson², Troy N Rowan^{2

3}, David L Oldeschulte¹, Robert D Schnabel^{2

3

4}, Jared E Decker^{2

3

4}, Christopher M Seabury⁵

Affiliations

¹ Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA.
² Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.
³ Genetics Area Program, University of Missouri, Columbia, 65211, USA.
⁴ Informatics Institute, University of Missouri, Columbia, 65211, USA.
⁵ Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA. cseabury@cvm.tamu.edu.

Abstract

Background: Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated.

Results: GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36-0.37, SE = 0.02-0.06), WW (0.27-0.29, SE = 0.01), and YW (0.39-0.41, SE = 0.01-0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level (P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1, NCAPG, LCORL, ARRDC3, STC2). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold (P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05).

Conclusions: Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.

Keywords: GWAA; Gelbvieh; Genotype-by-environment interaction; Growth traits; QTL.

MeSH terms

Animals
Birth Weight / genetics*
Cattle
Gene-Environment Interaction
Genome-Wide Association Study / veterinary*
Oligonucleotide Array Sequence Analysis / veterinary*
Polymorphism, Single Nucleotide
Quantitative Trait Loci*
Quantitative Trait, Heritable
Species Specificity
Weaning