GWAS & Selection signatures

Genomic scans for selection signatures in Local Spanish chicken breeds

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Abstract

Native Spanish chicken breeds are valuable genetic resources shaped by both natural and artificial selection. Detecting and contrasting selection signatures in these local populations versus commercial lines can highlight genomic regions underpinning local adaptation and production-relevant traits. This study aimed to identify selection sweeps in nine native Spanish breeds grouped into four geographical clusters and to compare them with commercial chickens from the Synergistic Plant and Animal Breeding project (SYNBREED). We analysed 154 individuals from nine Spanish breeds genotyped with the Axiom® 600K Array, including 114 birds from seven breeds (Andaluza Azul, Andaluza Británica, Andaluz Ceniza, Combatiente Español, Utrerana Franciscana; Canaria; Mallorquina) and 40 birds from two Catalonian breeds (Prat and Red Villafranquina, n=20 each) obtained from SYNBREED. Four commercial populations (Rhode Island Red, White Plymouth Rock, broiler dam line and White Leghorn; n=18-20 per line) genotyped with the same array were used for comparison. Within each geographical group, selection signatures were detected using runs of homozygosity (ROH) and the integrated haplotype score (iHS). Between-group sweeps were identified using standardized log-ratios of the integrated site-specific extended haplotype homozygosity (Rsb), cross-population extended haplotype homozygosity (XP-EHH) and the fixation index (FST). ROH- and iHS-based scans identified 51 and 131 putative selected regions harbouring 1,028 and 1,286 candidate genes, respectively. The between-population approaches detected 101 (Rsb), 119 (XP-EHH) and 32 (FST) regions under selection, containing 1,275, 1,041 and 213 genes, respectively. Ten genomic regions (322 genes) were consistently supported by at least three methods and included genes linked to growth and carcass traits (e.g., FBLN1, KLF12, VCL, ELOVL3, SIM1), immune response (e.g., TLR2, IL5RA, SGPL1), environmental adaptation (e.g., CAMK2G, TPK1, SLC7A7, CALB1) and morphological traits (e.g., EDNRB). Overall, 165 quantitative trait loci associated with economically important traits overlapped the candidate regions. These results provide robust evidence of selection signatures in native Spanish chickens and highlight genomic targets relevant to adaptation to local environments and traditional production systems, offering useful candidates for conservation planning and breeding strategies aimed at maintaining resilience and local adaptation.

Keywords: 2026

How to Cite:

Saleh, M., Martínez, A., Baquero, M., Pons, Á., Canales, A. & Landi, V., (2026) “Genomic scans for selection signatures in Local Spanish chicken breeds”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2295104. doi: https://doi.org/10.31274/wcgalp.24331

Rights: 1