Genome-wide association studies of beef cow terrain-use traits using Bayesian multiple-SNP regression
Autor: | Paul J. Meiman, Courtney F. Pierce, Derek W. Bailey, R. M. Enns, Milt Thomas, Larry D. Howery, W.F. Mandeville, Angela Cánovas, Scott E Speidel, S.J. Coleman, Juan F. Medrano |
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Rok vydání: | 2020 |
Předmět: |
0301 basic medicine
Candidate gene General Veterinary 0402 animal and dairy science Single-nucleotide polymorphism Genome-wide association study 04 agricultural and veterinary sciences Beef cattle Quantitative trait locus Biology 040201 dairy & animal science 03 medical and health sciences 030104 developmental biology Evolutionary biology Grazing Oxygen homeostasis Animal Science and Zoology human activities Genetic association |
Zdroj: | Livestock Science. 232:103900 |
ISSN: | 1871-1413 |
DOI: | 10.1016/j.livsci.2019.103900 |
Popis: | 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. |
Databáze: | OpenAIRE |
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