Identification of a novel QTL for lean meat percentage using imputed genotypes

Area of Science:

• Animal Genetics
• Quantitative Genetics
• Livestock Production

Background:

• Lean meat percentage is crucial for the economic viability and sustainability of pig farming.
• Identifying genetic factors influencing leanness can improve breeding efficiency.
• Crossbred pigs are commonly used in commercial production, making them relevant models.

Purpose of the Study:

• To conduct a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) associated with lean meat percentage in crossbred pigs.
• To prioritize candidate genes and single nucleotide polymorphisms (SNPs) within identified QTL regions.
• To investigate the role of specific genetic variants, such as mutations, in regulating porcine leanness.

Main Methods:

• Genome-wide association study (GWAS) was performed on 850 Duroc × (Landrace × Yorkshire) crossbred pigs.
• Imputed variants were analyzed to predict their effects on lean meat percentage.
• The PigGTEx database was utilized to identify molecular QTL and prioritize candidate genes and SNPs within QTL regions.

Main Results:

• Quantitative trait loci (QTL) associated with lean meat percentage were identified on swine chromosomes (SSC) 3 and 18.
• Candidate genes and SNPs within these QTL regions were prioritized based on predicted effects and molecular QTL data.
• A nonsense mutation in the ZC3HAV1L gene located on SSC18 was found to have a direct and significant effect on lean meat percentage.

Conclusions:

• The study successfully identified genetic regions associated with lean meat percentage in pigs.
• A specific nonsense mutation in ZC3HAV1L on SSC18 is a key genetic factor influencing porcine leanness.
• These findings provide valuable genetic information for improving lean meat percentage in pig breeding programs, contributing to industry sustainability.