The genetic structure and selective sweep analysis of meat pigeon breeds raised in Hainan using whole genome resequencing technology

To investigate the genetic relationships and domestication status of Hainan meat pigeon populations, whole-genome sequencing was performed on 70 individuals across seven breeds: Shiqi (SQ), Silver King (SK), Shenwang (SW), Dabao (DB), Tianxiang No.1 (TX), Hybrid King (HK), and White Carneau (WC), with each breed represented by 10 individuals (5 males and 5 females). From 824 Gb of high-quality sequencing data, we identified 13,347,452 high-confidence single nucleotide polymorphisms (SNPs). Population structure analysis revealed divergent genetic clustering: WC, DB, TX, and HK individuals demonstrated extensive genomic admixture, while SK, SQ, and SW breeds formed distinct clusters with minimal interbreed genetic exchange. Selective sweep analysis highlighted genes under strong positive selection (TAFA2, FNDC3B, TFAP2B, PDCL3, EPC1 and LHX2). Functional annotation linked TAFA2 to accelerated growth in SK pigeons through muscle development modulation. The genes FNDC3B and TFAP2B were associated with fat deposition capacity in SQ pigeons. Concurrently, PDCL3, NEK6, LHX2, and EPC1 were implicated in SW pigeons' large body size and superior production traits. This study provides the first genomic compendium for Hainan meat pigeons, delineating their genetic diversity, adaptive evolution, and domestication patterns. The identified selection signatures establish a foundation for precision breeding strategies targeting growth, reproduction, and climate resilience in commercial pigeon production.