Analysis of polygenic selection in purebred and crossbred pig genomes using generation proxy selection mapping

Area of Science:

• Population genetics
• Quantitative genetics
• Animal breeding

Background:

• Artificial selection on quantitative traits alters allele frequencies at numerous genetic loci in livestock.
• Understanding the genetic basis of phenotypic diversity is key for swine breeding programs.
• Polygenic selection, driven by breeding values and selection indices, shapes livestock genomes over time.

Purpose of the Study:

• To apply generation proxy selection mapping (GPSM) to identify loci under artificial selection in commercial pig populations.
• To assess the efficacy and accuracy of GPSM in detecting selected loci over a five-to-ten-year period.
• To compare selected loci across different pig populations to infer shared selection objectives and genetic architectures.

Main Methods:

• Utilized genome-wide association analysis of single nucleotide polymorphism (SNP) genotypes in four large pig populations.
• Applied GPSM to SNP data (38,294-46,458 markers) for birth date to detect selection signals.
• Conducted gene-drop simulations to validate GPSM performance and estimate error rates.

Main Results:

• GPSM identified 49 to 854 loci under selection across various population subsets.
• Pooling data across populations increased the number of significant associations, with several loci identified in multiple populations.
• Gene-drop simulations confirmed negligible false-positive rates (<0.02%), demonstrating GPSM's ability to distinguish selection from genetic drift.

Conclusions:

• Generation proxy selection mapping (GPSM) is a validated and accurate method for detecting selected loci in commercial pig populations.
• Results indicate concurrent selection objectives and shared genetic architectures across different swine populations.
• The identified loci are significant for improving traits relevant to swine production.