New loci and neuronal pathways for resilience to heat stress in cattle

Abstract

While understanding the genetic basis of heat tolerance is crucial in the context of global warming's effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual's heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature-humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across 100 vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2, and GRIA4) and neuroactive ligand-receptor interaction functions for heat tolerance (NPFFR2, CALCR, and GHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.

Figure 1

Manhattan plot of p values obtained from combining single-trait GWAS results for milk yield slope traits.

Figure 2

QTL discovery on chromosome 14 at 0 to 1 Mb for heat tolerance milk (HTMYslope; A), fat (HTFYslope; B), and protein (HTPYslope; C) yield slope traits. The three panels represent the GWAS p values before conditional analysis (right panel), after conditioning slope traits on the lead SNP (highlighted in blue) defined as the most significant SNP (middle panel), and after conditioning slope traits on the intercept traits (left panel), respectively. The red horizontal dashed line is the GWAS cut-off of p < 1E–05. The strength of LD (r²) between the lead SNP (blue color) and all the other SNPs are color-coded accordingly.

Figure 3

Proportion of candidate causal variants for heat tolerance within different functional classes identified from (a) single-trait GWAS, (b) meta-analysis, and (c) meta-analysis of conditional GWAS results for slope traits. Values in brackets are the proportions of all variants used in the study (~ 15 million SNPs). Functional classes without values in brackets were represented by a small (< 1%) proportion of SNPs in the study dataset.

Figure 4

Enrichment of the candidate causal variants for heat tolerance across functional classes. The values in brackets are the number of variants within each class. The class “Other” includes variants with very small proportions of candidate variants (frameshift, stop-codon, splice variants, etc.).

Figure 5

Enriched Kyoto Encyclopedia of Gene and Genomes (KEGG) pathways obtained from candidate gene-list for slope traits detected at false discovery rate (FDR < 0.10). SS-slope genes–gene-list from single-trait GWAS; Meta-slope genes–gene-list from multi-trait meta-analysis of slope traits; All-slope genes–combined gene-list from single-trait and meta-analysis. Cells are color-coded according to the strength of the significance for each pathway. Values in brackets are the number of genes within each pathway.

Figure 6

Enriched Kyoto Encyclopedia of Gene and Genomes (KEGG) pathways obtained from our gene-list for single-trait GWAS analysis of slope traits. HTMYslope (heat tolerance milk yield slope); HTFYslope (heat tolerance fat yield slope); and HTPYslope (heat tolerance protein yield slope). Cells are color-coded according to the strength of the significance for each pathway. Values in brackets are the number of genes within each pathway.

Figure 7

QTL discovery for heat tolerance milk (HTMYslope) and protein (HTPYslope) yield slope traits around the NPFFR2 gene in bovine chromosome 6.