Integration of non-additive genome-wide association study with a multi-tissue transcriptome analysis of growth and carcass traits in Duroc pigs

Chen Wei; Haonan Zeng; Zhanming Zhong; Xiaodian Cai; Jingyan Teng; Yuqiang Liu; Yunxiang Zhao; Xibo Wu; Jiaqi Li; Zhe Zhang

doi:10.1016/j.animal.2023.100817

Integration of non-additive genome-wide association study with a multi-tissue transcriptome analysis of growth and carcass traits in Duroc pigs

Animal. 2023 Jun;17(6):100817. doi: 10.1016/j.animal.2023.100817. Epub 2023 Apr 17.

Authors

Chen Wei¹, Haonan Zeng¹, Zhanming Zhong¹, Xiaodian Cai¹, Jingyan Teng¹, Yuqiang Liu¹, Yunxiang Zhao², Xibo Wu³, Jiaqi Li¹, Zhe Zhang⁴

Affiliations

¹ National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China.
² School of Life Science and Engineering, Foshan University, Foshan 528225, PR China.
³ Guangxi Guiken Yongxin Animal Husbandry Group Co. Ltd, Nanning 530000, PR China.
⁴ National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China. Electronic address: zhezhang@scau.edu.cn.

PMID: 37196577
DOI: 10.1016/j.animal.2023.100817

Abstract

Growth and carcass traits are of economic importance in the pig production, which affect pork quality and profitability of finishing pig production. This study used whole-genome and transcriptome sequencing technologies to identify potential candidate genes affecting growth and carcass traits in Duroc pigs. The medium (50-60 k) single nucleotide polymorphism (SNP) arrays of 4 154 Duroc pigs from three populations were imputed to whole-genome sequence data, yielding 10 463 227 markers on 18 autosomes. The dominance heritabilities estimated for growth and carcass traits ranged from 0.000 ± 0.041 to 0.161 ± 0.054. Using non-additive genome-wide association study (GWAS), we identified 80 dominance quantitative trait loci for growth and carcass traits at genome-wide significance (false discovery rate < 5%), 15 of which were also detected in our additive GWAS. After fine mapping, 31 candidate genes for dominance GWAS were annotated, and 8 of them were highlighted that have been previously reported to be associated with growth and development (e.g. SNX14, RELN and ENPP2), autosomal recessive diseases (e.g. AMPH, SNX14, RELN and CACNB4) and immune response (e.g. UNC93B1 and PPM1D). By integrating the lead SNPs with RNA-seq data of 34 pig tissues from the Pig Genotype-Tissue Expression project (https://piggtex.farmgtex.org/), we found that the rs691128548, rs333063869, and rs1110730611 have significantly dominant effects for the expression of SNX14, AMPH and UNC93B1 genes in tissues related to growth and development for pig, respectively. Finally, the identified candidate genes were significantly enriched for biological processes involved in the cell and organ development, lipids catabolic process and phosphatidylinositol 3-kinase signalling (P < 0.05). These results provide new molecular markers for meat production and quality selection of pig as well as basis for deciphering the genetic mechanisms of growth and carcass traits.

Keywords: Candidate genes; Dominance quantitative trait loci; Fine mapping; Imputed whole-genome sequence data; Transcriptome sequence data.

MeSH terms

Animals
Biological Phenomena*
Gene Expression Profiling / veterinary
Genome-Wide Association Study* / veterinary
Genotype
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Swine / genetics