Integrated analysis of genome-wide association studies and 3D epigenomic characteristics reveal the BMP2 gene regulating loin muscle depth in Yorkshire pigs

Abstract

The loin muscle depth (LMD) is positively correlated with lean meat content and can therefore be used to estimate the lean meat content of pigs. The loin muscle depth is a quantitative trait that is influenced by whole-genome distributed polygenes. To identify the possible candidate genes and mutations impacting the LMD, we used genome-wide association study (GWAS), which is commonly used to identify candidate genomic regions associated with complex growth traits, to mapping the genomic regions. As over 90% of the identified variants have been localized to non-coding regions of the pig genome and their functions in phenotype regulation are poorly understood, we further combined 3D epigenomics to understand the mechanism of genetic variants regulating LMD. In combination with different types of data and analyses, we identified a 10 kb quantitative trait locus (QTL) on chromosome 17 that was significantly associated with LMD. We identified the BMP2 gene as a major candidate gene, and SNP rs1111440035 and rs321846600 were identified as likely candidate mutations affecting the LMD. Our study is unique in its attempt to identify candidate genetic variants by integrating GWAS and 3D epigenomics in pigs.

Quanshun Mei

Postdoctoral researcher

My research interests include applying genomic selection and machine learning in animal breeding.