Genome-wide association studies of beef cow terrain-use traits using Bayesian multiple-SNP regression

• Published in: Livestock science 2020-02, Vol.232, p.103900, Article 103900
• Main Authors: Pierce, C.F., Speidel, S.E., Coleman, S.J., Enns, R.M., Bailey, D.W., Medrano, J.F., Cánovas, A., Meiman, P.J., Howery, L.D., Mandeville, W.F., Thomas, M.G.
• Format: Article
• Language: English
• Subjects: Bayesian theory; beef; beef cows; bioinformatics; Cattle; computer software; feed conversion; forage; genetic variance; Genetics; genomics; genotype; GWAS; homeostasis; landscapes; marker-assisted selection; mountains; oxygen; phenotypic variation; probability; QTL; quality control; quantitative traits; rangelands; SNP; Terrain-use; topography; Western United States
• ISSN: 1871-1413; 1878-0490
• DOI: 10.1016/j.livsci.2019.103900

•Genome-wide association studies for 6 beef cow terrain-use traits.•19 QTL and 8 putative candidate genes were associated with terrain-use traits.•Results of this study suggest that terrain-use is a multi-dimensional, polygenic trait. Beef cattle grazing patterns are influenced by topography in that cattle generally select grazing sites near water while avoiding steep, rugged terrain; therefore, forage is often left ungrazed in the mountainous uplands whereas lowland riparian zones can be heavily grazed. Improving uniformity in beef cattle terrain-use provides opportunities to increase forage harvest and sustain sensitive ecosystems. Studies suggest that terrain-use by cattle may be improved using genomic selection as combinations of single nucleotide polymorphisms (SNP) explained approximately 35% of the phenotypic variation in terrain-use indices that combined slope, elevation, and distance traveled from water. The objective of this study was to perform genome-wide association studies (GWAS) for six terrain-use traits (slope, elevation, vertical climb, distance traveled from water, rolling index, and rough index) in which we explored single-SNP associations, surveyed the genome in consecutive, one mega-base windows and examined quantitative trait loci (QTL) and underlying positional and functional candidate genes using bioinformatic tools to identify possible pleiotropic effects with other traits. Global positioning system (GPS) collars were used to track terrain-use patterns for 330 beef cows across 14 rangeland operations located in the western U.S. and Illumina BovineHD and BovineSNP50 SNP arrays were used to collect genomic data. Genotype quality control was conducted using PLINK software and association analyses were performed using BOLT, implementing a BayesC model. Quantitative trait loci detection was based upon the posterior inclusion probability (PIP) for individual loci and the proportion of total genetic variance explained by individual genomic windows. Analyses revealed 19 QTL that have been previously associated with health and production traits in dairy and beef cattle as well as 8 positional putative candidate genes that function in oxygen homeostasis, feed efficiency, and growth. These results suggest that beef cattle terrain-use traits are polygenic and may be pleiotropic with other production traits.