# Genome-Wide Association Study Identifies Candidate Genes for Body Size Traits in Wanyue Black Pigs

## TL;DR

This study identifies genetic markers linked to body size in Wanyue Black pigs, aiding in breeding improvements and pork supply stability.

## Contribution

The study identifies novel candidate genes and genomic regions influencing body size traits in Wanyue Black pigs through GWAS, TWAS, and PheWAS.

## Key findings

- Four genome-wide significant loci (rs343276492 and rs321308815 among them) were identified as associated with body size traits.
- Expression of PTH2R was significantly linked to pituitary-related traits.
- Selection signals enriched in circadian rhythm and MAPK pathways were found to influence growth and adaptability.

## Abstract

This study focuses on the body size traits such as body length and chest girth of the Wanyue Black Pig, aiming to explore its genetic basis to assist in breed improvement. The study involved genotyping and phenotype data collection from 139 sows. Using various genetic analysis methods, multiple genetic loci and candidate genes related to body size were identified, and selection signals associated with growth and adaptability were also detected. These findings reveal the genetic regulatory mechanisms underlying the body size traits of the Wanyue Black Pig and provide practical molecular markers. These markers can help improve the breeding efficiency of this local pig breed and are of significant importance for ensuring pork supply and promoting the development of the pig industry.

This study aimed to elucidate the genetic basis of body-size-related traits in Wanyue Black pigs, including body length, chest circumference, forearm circumference, and hip circumference. Phenotypic data were collected from 139 four-month-old female pigs, and genotyping was performed using a 50K SNP array. After stringent quality control and genotype imputation, approximately 4,697,453 high-quality autosomal variants were retained for subsequent genome-wide association study (GWAS), transcriptome-wide association study (TWAS), and phenome-wide association study (PheWAS). The GWAS identified four genome-wide significant loci, including rs343276492 and rs321308815. TWAS results revealed that the expression level of PTH2R was significantly associated with pituitary-related traits. In addition, selection signal analysis identified multiple genomic regions related to growth, development, and environmental adaptability, which were significantly enriched in pathways such as circadian rhythm regulation and the MAPK signaling pathway. These pathways play critical roles in growth regulation and adaptive evolution in Wanyue Black pigs. Collectively, this study provides valuable candidate genes and potential molecular markers for the genetic improvement and breeding of Wanyue Black pigs.