Genomic regions associated with body weight, feed intake and methane emissions in Australian Merino sheep

Abstract

This study aimed to better understand the genetic architecture of traits related to feed efficiency and methane emissions through the identification of genomic regions, candidate genes and metabolic pathways associated with body weight (BW), feed intake (FI), and methane emissions (ME) in Australian Merino sheep. Phenotypic records were available for 1,211 animals for FI, 1,183 for ME, and 78,466 for BW. A total of 41,011 SNPs were imputed from multiple SNP chips to the Applied Biosystems™ Axiom™ Ovine Genotyping Array 50K. All individuals with FI and ME information were genotyped, along with 4,023 animals with BW data. Pedigree-based heritability estimates were 0.37, 0.31 and 0.40 for FI, ME and BW, respectively. SNP effects were estimated from genomic estimated breeding values (GEBVs) using a weighted single-step genome-wide association study (ssGWAS) with two approaches: (1) p-values of single SNP effect, and (2) the percentage of additive genetic variance explained by 200 kb windows, defined according to the population´s linkage disequilibrium. Only genomic regions explaining more than 0.5% of the additive genetic variance were considered. Several candidate genes were identified for FI and BW including MEF2A (FI), and DCAF16, FAM184B, NCAPG and IBSP (BW). No windows exceeded the variance threshold for ME. Using a Bonferroni-corrected significance threshold, the p-value-based ssGWAS identified significant associations only for BW. Functional enrichment analysis revealed seven Gene Ontology (GO) terms, and four Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with FI, and 28 GO terms associated with BW (p < 0.05). These results can contribute to a better understanding of biological mechanisms related to feed efficiency in sheep. The moderate heritability of ME indicates that genetic progress is still possible for this trait despite the lack of significant genomic regions.