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Abstract
Simple SummaryA major problem in the swine meat industry is significant weight loss due to pigs overheating. Our approach to solving this problem is breeding swine based on their ability to survive in high temperatures. We determined in this study that genetically there is a difference between the most successful animal in hot conditions and the most successful animal in cooler conditions. This can be applied to selection of breeding animals for swine companies. Additionally, we found a few genes that may be related to this heat resistance, but more studies need to be completed to validate this finding.The purpose of this study was to perform a genome-wide association study to determine the genomic regions associated with heat stress tolerance in swine. Phenotypic information on carcass weight was available for 227,043 individuals from commercial farms in North Carolina and Missouri, U.S. Individuals were from a commercial cross of a Duroc sire and a dam resulting from a Landrace and Large White cross. Genotypic information was available for 8232 animals with 33,581 SNPs. The pedigree file contained a total of 553,448 animals. A threshold of 78 on the Temperature Humidity Index (THI) was used to signify heat stress. A two-trait analysis was used with the phenotypes heat stress (Trait One) and non-heat stress (Trait Two). Variance components were calculated via AIREML and breeding values were calculated using single step GBLUP (ssGBLUP). The heritability for Traits One and Two were calculated at 0.25 and 0.20, respectively, and the genetic correlation was calculated as 0.63. Validation was calculated for 163 genotyped sires with progeny in the last generation. The benchmark was the GEBV with complete data, and the accuracy was determined as the correlation between the GEBV of the reduced and complete data for the validation sires. Weighted ssGBLUP did not increase the accuracies. Both methods showed a maximum accuracy of 0.32 for Trait One and 0.54 for Trait Two. Manhattan Plots for Trait One, Trait Two, and the difference between the two were created from the results of the two-trait analysis. Windows explaining more than 0.8% of the genetic variance were isolated. Chromosomes 1 and 14 showed peaks in the difference between the two traits. The genetic correlation suggests a different mechanism for Hot Carcass Weight under heat stress. The GWAS results show that both traits are highly polygenic, with only a few genomic regions explaining more than 1% of variance.
Highlights
Heat stress is a problem for almost all livestock producers around the world
This indicates the polygenic nature of heat stress traits as it has been shown in previous studies that Quadratic weighting will only improve accuracy when there are only a few major Quantitative Trait Loci (QTL) or genes affecting a trait [30]
There was quick convergence in accuracy as Single Nucleotide Polymorphisms (SNPs) weights varied using Nonlinear “A” weighting methods. This result was shown by Fragomeni et al where it was concluded that Nonlinear “A” weighting showed a stability in accuracy in complex traits [6]
Summary
Heat stress is a problem for almost all livestock producers around the world. swine are disproportionately sensitive to high temperatures because they are unable to sweat. In response to high temperatures, swine have been shown to experience weight loss due to reduced feed intake and physiological changes [1]. This weight loss has significant impacts on both breeding and finishing herds in the swine industry. Many breeding programs use purebred animals from nucleus farms, previous studies have demonstrated that crossbred animals have more significant impacts from heat stress [3]. Because of this difference in heat stress impact, selection programs based on data from purebred animals has proven ineffective [4]. An efficient alternative to this approach is to use data from commercial animals when developing a heat stress tolerance breeding program
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