Genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Swiss Large White pigs

Abstract

BackgroundThe improvement of protein efficiency (PE) is a key factor for a sustainable pig production as nitrogen excretion contributes substantially to environmental pollution. Protein efficiency has been shown to be clearly heritable and genetically correlated with some performance traits, such as feed conversion ratio (FCR) and average daily feed intake (ADFI). The study aimed to identify genomic regions associated with these traits through genome-wide association studies (GWAS) and regional heritability mapping (RHM) using imputed whole genome sequence variants for more than 1,000 Swiss Large White pigs.ResultsThe genomic-based heritability estimates using ∼15 million SNPs were moderate, ranging from 0.33 to 0.47. Using GWAS, no significant SNPs were found at the genome-wide Bonferroni and false- discovery rate (FDR) thresholds for any of the traits, with the exception of ADFI, where 52 significant SNPs were found on chromosome 1 at the FDR threshold. No region was found to be significant at the Bonferroni threshold using RHM. Regional heritability mapping found two suggestive regions for PE on chromosomes 2 and 9 located between 31 and 32Mb and between 2 and 3Mb, respectively, one suggestive region for ADG on chromosome 5 between 104 and 105Mb, and four suggestive regions for ADFI on chromosomes 1 (270-271Mb, 272-273Mb and 273-274Mb) and 14 (133- 134Mb).ConclusionsOur study identified suggestive regions for PE and the performance traits with RHM, except for FCR. However, the apparent difficulty in detecting significant regions probably reflects the relatively small sample size used in this study rather than a lack of true associations with PE. The finding of this study helps to understand the polygenicity of PE and may help in the design of breeding for protein-efficient pigs in a genomic prediction.