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

• Published in: BMC genomics Vol. 23; no. 1; pp. 1 - 517
• Main Authors: Smith, Johanna L, Wilson, Miranda L, Nilson, Sara M, Rowan, Troy N, Schnabel, Robert D, Decker, Jared E, Seabury, Christopher M
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 16-07-2022; BioMed Central; BMC
• Subjects: Analysis; Beef; Beef cattle; Birth weight; Cattle; Dairy cattle; Diseases; Efficiency; Environmental stress; Feed efficiency; Feeds; Gene polymorphism; Genetic aspects; Genome-wide association studies; Genomes; Genomics; Genotype & phenotype; Genotype-by-environment interaction; Genotype-environment interactions; Growth; Growth traits; GWAA; Heritability; Metabolism; Methods; Milk production; Nervous system; Nucleotides; Polygenic inheritance; Polymorphism; QTL; Quantitative genetics; Quantitative trait loci; Red Angus; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Vasodilation; Weaning; United States; United States > US
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-022-08667-6

Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled a dataset consisting of 15,815 Red Angus beef cattle distributed across the continental U.S. and a union set of 836,118 imputed SNPs to conduct genome-wide association analyses (GWAA) for growth traits using univariate linear mixed models (LMM); including birth weight, weaning weight, and yearling weight. Genomic relationship matrix heritability estimates were produced for all growth traits, and genotype-by-environment (GxE) interactions were investigated. Moderate to high heritabilities with small standard errors were estimated for birth weight (0.51 [+ or -] 0.01), weaning weight (0.25 [+ or -] 0.01), and yearling weight (0.42 [+ or -] 0.01). GWAA revealed 12 pleiotropic QTL (BTA6, BTA14, BTA20) influencing Red Angus birth weight, weaning weight, and yearling weight which met a nominal significance threshold (P [less than or equai to] 1e-05) for polygenic traits using 836K imputed SNPs. Moreover, positional candidate genes associated with Red Angus growth traits in this study (i.e., LCORL, LOC782905, NCAPG, HERC6, FAM184B, SLIT2, MMRN1, KCNIP4, CCSER1, GRID2, ARRDC3, PLAG1, IMPAD1, NSMAF, PENK, LOC112449660, MOS, SH3PXD2B, STC2, CPEB4) were also previously associated with feed efficiency, growth, and carcass traits in beef cattle. Collectively, 14 significant GxE interactions were also detected, but were less consistent among the investigated traits at a nominal significance threshold (P [less than or equai to] 1e-05); with one pleiotropic GxE interaction detected on BTA28 (24 Mb) for Red Angus weaning weight and yearling weight. Sixteen well-supported QTL regions detected from the GWAA and GxE GWAA for growth traits (birth weight, weaning weight, yearling weight) in U.S. Red Angus cattle were found to be pleiotropic. Twelve of these pleiotropic QTL were also identified in previous studies focusing on feed efficiency and growth traits in multiple beef breeds and/or their composites. In agreement with other beef cattle GxE studies our results implicate the role of vasodilation, metabolism, and the nervous system in the genetic sensitivity to environmental stress.