Whole-Genome Resequencing-Based Selection-Signal and Association Analyses Prioritize Candidate Genes and Haplotypes...

Area of Science:

• Genomics
• Animal Genetics
• Veterinary Science

Background:

• Porcine Reproductive and Respiratory Syndrome (PRRS) causes significant economic losses in the swine industry.
• Conventional PRRS control methods are limited by viral variability and host genetic complexity.
• Genomic approaches are vital for identifying host genetic factors for PRRS resistance and breeding disease-resistant swine.

Purpose of the Study:

• To identify host genetic factors associated with PRRS resistance using genomic analysis.
• To provide genetic insights for developing PRRS-resistant pig breeds.

Main Methods:

• Genome-wide selection-signal analysis and Genome-Wide Association Studies (GWAS) were performed on 133 pigs.
• Two-stage phenotypic screening based on post-immunization and post-infection profiles was utilized.
• Public PRRSV-related transcriptomic datasets were analyzed for gene expression evidence.

Main Results:

• 12 highly differentiated genomic regions and 11 candidate genes (e.g., NFXL1, NIPAL1) were identified.
• NFXL1 showed consistent association signals after genomic data adjustment.
• NIPAL1 and PYGM gene expression increased in PRRSV-infected porcine alveolar macrophages.
• A specific haplotype in the NFXL1 region on chromosome 8 was more frequent in PRRS-resistant pigs.

Conclusions:

• The study identified candidate genes and genomic regions associated with PRRS resistance.
• NFXL1, NIPAL1, and PYGM are promising candidates for further investigation in PRRS resistance breeding.
• Findings provide valuable genetic information for developing PRRS-resistant swine populations.