Extensive genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle

Abstract

We identify genotype-by-environment interactions (GxE) for birth, weaning and yearling weights (BW, WW, and YW, respectively) using ~835,000 SNPs in ~13,500 Simmental cattle by conducting: direct GxE genome-wide association analyses using continuous environmental variables (minimum, mean, maximum and mean dew point temperatures; elevation; precipitation; and minimum and maximum vapor pressure deficit), and in combination (U.S. ecoregions); and variance-heterogeneity genome-wide association (vGWA) analyses, indicative of interactions, using residuals adjusted for additive, dominance, and epistatic relationships.Genotype-by-environment interactions contributed to 10%, 4%, and 3% of the phenotypic variance of BW, WW, and YW, respectively. Genes were related to response to stimulus, nitrogen compound, gene expression, development and metabolic processes. Twenty-two vQTL (difference in variance between genotypes) were detected. Some vQTL were enriched with GxE effects while one vQTL was also a QTL (difference in the mean between genotypes). This study reveals the importance to investigate alternative approaches using genomic information to identify loci contributing to genetic control of complex traits. Further, we provide evidence for extensive GxE interactions in Simmental cattle.

Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

“…We expect that the many significant GPSM regions will be tagging allele frequency changes driven by selection. That said, we observe relatively few of the regions identified by GPSM overlap with major growth QTL identified using identical Gelbvieh and Simmental datasets 55,56 . Most of the major growth-related QTL still segregating in these breeds are effectively unchanged over the course of our sampled datasets.…”

“…"Retrograde endocannabinoid signaling", "dopaminergic synapse", "GABAergic synapse", and "serotonergic synapse" pathways are also significantly enriched by envGWAS candidate genes. Nearly all of these important neural signaling pathways are also enriched in a series of gene-by-environment interaction GWAS for birth weight, weaning weight, and yearling weight in Simmental cattle 56 . Taken together, these results suggest that pathways involved in neuron development and neurotransmission are essential components of local adaptation in cattle.…”

“…Previous work in cattle has identified loci that are involved in genotype-by-environment (GxE) interactions. GxE variants have different effects in different environments 55,56,176,177 . These approaches are different, but complementary to our envGWAS analysis.…”

Evaluation of Zoetis GeneMax Advantage genomic predictions in commercialBos taurusAngus cattle

“…While genetic predictions were never intended to predict the performance of a single individual, the average progeny performance is accurately predicted by the additive genetic merit of the parent. However, biological variation remains, including non-additive genetic effects and interactions (Smith et al, 2019; Braz et al, 2020) and especially Mendelian sampling (Cole and VanRaden, 2011) between full- or half-siblings. The increased adoption of genomic technologies in commercial cattle production has the opportunity to significantly increase long-term genetic gain through more accurate replacement animal selection.…”

Leveraging large scale beef cattle genomic data to identify the architecture of polygenic selection and local adaptation

“…Still, the genetic variants underlying GxE interactions are not well understood. Most GxE mapping studies in beef cattle have focused on identifying SNPs with significant growth trait-by-environment interactions [32,33], treating GxE as a quantitative genetic problem. It is also clear that despite the use of national genetic evaluations used to select sires, cattle populations are directly selecting for animals that produce well in their herd's environment.…”