Genomic regions and biological mechanisms underlying climatic resilience traits derived from automatically-recorded vaginal temperature in lactating sows under heat stress conditions

Abstract

Climate change poses a growing threat to the livestock industry, impacting animal productivity, animal welfare, and farm management practices. Thus, enhancing livestock climatic resilience (CR) is becoming a key priority in various breeding programs. CR can be defined as the ability of an animal to be minimally affected or rapidly return to euthermia under thermally stressful conditions. The primary study objectives were to perform genome-wide association studies for 12 CR indicators derived from variability in longitudinal vaginal temperature in lactating sows under heat stress conditions. A total of 31 single nucleotide polymorphisms (SNPs) located on nine chromosomes were considered as significantly associated with nine CR indicators based on different thresholds. Among them, only two SNPs were simultaneously identified for different CR indicators, SSC6:16,449,770 bp and SSC7:39,254,889 bp. These results highlighted the polygenic nature of CR indicators with small effects distributed across different chromosomes. Furthermore, we identified 434 positional genes associated with CR. Key candidate genes include SLC3A2, STX5, POLR2G, and GANAB, which were previously related to heat stress responses, protein folding, and cholesterol metabolism. Furthermore, the enriched KEGG pathways and Gene Ontology (GO) terms associated with these candidate genes are linked to stress responses, immune and inflammatory responses, neural system, and DNA damage and repair. The most enriched quantitative trait loci are related to "Meat and Carcass", followed by "Production", "Reproduction", "Health", and "Exterior (conformation and appearance)" traits. Multiple genomic regions were identified associated with different CR indicators, which reveals that CR is a highly polygenic trait with small effect sizes distributed across the genome. Many heat tolerance or HS related genes in our study, such as HSP90AB1, DMGDH, and HOMER1, have been identified. The complexity of CR encompasses a range of adaptive responses, from behavioral to cellular. These results highlight the possibility of selecting more heat-tolerant individuals based on the identified SNP for CR indicators.

Keywords: climate resilience; genome-wide association studies; genomic regions; heat stress; livestock breeding.

FIGURE 1

Quantile-quantile plots (QQ-plot) and lambda values for the climatic resilience indicators evaluated¹. ¹Indicators: LnVar(Ave), log-transformed variance of the deviations between each observation and the average values from moving windows that contains six continuous observations with 10-mins interval in between; Autocor (Ave): Lag-1 autocorrelation of the deviations between the average values from moving windows that contains six continuous observations with 10-mins interval in between; Skew (Ave): skewness of the deviations between each observation and the average values from moving windows that contains six continuous observations with 10-mins interval in between; LnVar(Med): log-transformed variance of the deviations between the median values from moving windows that contains six continuous observations with 10-mins interval in between; Autocor (Med): Lag-1 autocorrelation of the deviations between the median values from moving windows that contains six continuous observations with 10-mins interval in between; Skew (Med): skewness of the deviations between each observation and the median values from moving windows that contains six continuous observations with 10-mins interval in between; Nor_avevar: normalized average T_V multiplies the normalized T_V variance; Nor_medvar: normalized median T_V multiplies the normalized T_V variance; HSU_A: sum of T_V values above the HS threshold during the whole data collection period; HSU_B: sum of T_V values below the HS threshold during the whole data collection period; HSD: The length of time during which the body temperature remained above the HS threshold value for each collection day; Max_Tv: The highest T_V of each measurement day.