Identification of new candidate genes affecting drip loss in pigs based on genomics and transcriptomics data

Area of Science:

• Animal Genetics
• Molecular Biology
• Meat Science

Background:

• Drip loss (DL) is a critical indicator of pork muscle quality.
• Identifying genetic factors influencing DL is essential for breeding programs aimed at enhancing meat quality.

Purpose of the Study:

• To identify quantitative trait loci (QTL) and candidate genes associated with drip loss (DL) in Chinese Suhuai pigs.
• To pinpoint novel genes influencing DL through integrated genomic and transcriptomic analyses.

Main Methods:

• Genotyping of Chinese Suhuai pigs using the Neogen GGP Porcine 80K SNP array.
• Imputation of SNP data to whole-genome sequence (iWGS) followed by genome-wide association studies (GWAS).
• RNA sequencing (RNA-seq) and quantitative trait transcriptome (QTT) analysis to identify differentially expressed genes (DEGs) linked to DL.

Main Results:

• Significant SNPs associated with DL were detected on SSC4, SSC13, and SSC14, identifying 3 new QTL regions.
• 37 candidate genes were identified via GWAS, including AACS, CRB4, and OXSM.
• Integration of GWAS, RNA-seq, and QTT analyses pinpointed 9 novel candidate genes for DL, such as GALNT15, TBC1D1, and PPARGC1A.

Conclusions:

• Newly identified QTL regions and candidate genes provide a basis for understanding the genetic architecture of DL in pigs.
• The identified genes (e.g., GALNT15, TBC1D1, PPARGC1A) are potential targets for marker-assisted or genomic selection to improve pork meat quality.
• This study lays the groundwork for enhancing meat quality traits in pig breeding programs.