Integrated GWAS and eQTL Colocalization Identified Candidate Genes for Growth Traits in Pigs

Growth traits, as core economic indicators in pig breeding, are closely associated with production costs, rearing duration, and final carcass quality and have thus consistently been a major focus of genetic improvement. This study aimed to identify candidate genes affecting Age to 120 kg live weight (AGE120), Backfat thickness at 120 kg (BF120), and Loin muscle depth at 120 kg (LMD120) in pigs. Ear tissue samples were collected from 3364 healthy adult pigs (including 558 boars and 2805 sows) from three breeds: Large White, Landrace, and Duroc. Genotyping was performed using an 80 K functional site array, and quality-controlled SNP (Single-Nucleotide Polymorphism) loci were subjected to genotype imputation, resulting in 15,447,611 loci obtained. Genome-wide association studies (GWASs) for Age to 120 kg live weight, Back fat thickness at 120 kg, and Loin muscle depth at 120 kg were conducted using a mixed linear model in Genome-wide Complex Trait Analysis (GCTA). Genes located within 500 kb upstream and downstream of significant GWAS loci were extracted using the biomaRt package in R. Furthermore, colocalization analysis was performed using expression Quantitative Trait Locus (eQTL) data of 34 tissues from the PigGTEx database to identify genes that share the same causal variant as the GWAS signals. Through integrated GWAS and eQTL colocalization analysis, in addition to five previously reported genes associated with pig growth traits (TAF11, ZC3HAV1L, ANKS1A, USP20, and TBC1D1), a set of novel, high-confidence candidate genes was identified: ZNF215, UBE2Z, HOXB7, SARDH, ADAMTSL2, ATP6V0A4, RPL10A, PGM2, and RELL1. These findings enrich our understanding of the genetic architecture underlying growth traits in pigs at heavy body weights and provide an important foundation for subsequent functional validation and molecular breeding applications.