Identifying pleiotropic genes for backfat thickness and semen traits in pigs using GWAS summary data

Area of Science:

• Animal Genetics
• Reproductive Biology
• Quantitative Genetics

Background:

• Backfat thickness (BFT_100) is crucial for pig carcass quality.
• Semen quality (SEMVOL, SPMOT) is vital for boar reproductive efficiency.
• The genetic relationship between fat deposition and semen traits is poorly understood.

Purpose of the Study:

• To identify genes pleiotropically affecting BFT_100, SEMVOL, and SPMOT in pigs.
• To explore the genetic correlations and networks between these traits.
• To investigate the causal genetic associations between BFT_100 and semen quality.

Main Methods:

• Applied the PLACO method for pleiotropic gene discovery.
• Utilized Pearson correlation and Cochran's Q test for effect consistency.
• Constructed protein-protein interaction networks using STRING database.
• Employed Generalized Summary-data-based Mendelian Randomization (GSMR) for association analysis.

Main Results:

• Identified 99 significant pleiotropic genes (FDR < 0.05), with seven affecting all three traits.
• Observed positive correlations in 57.5% and negative correlations in 42.5% of gene-trait associations.
• Discovered gene networks enriched in energy metabolism and immune pathways.
• GSMR showed BFT_100 positively affects SEMVOL (P=1.545×10⁻⁷) and negatively affects SPMOT (P=0.0138).

Conclusions:

• Established complex genetic links between pig fat deposition and semen traits.
• Highlighted key pleiotropic genes and potential molecular mechanisms.
• Provided insights for molecular breeding and genetic improvement in pigs.
• Suggests adiposity influences reproductive performance through identified genetic pathways.