Genetic diversity, population structure and selective sweeps in Italian Leccese chickens

Italy hosts a rich heritage of poultry genetic resources, leading to the development of several unique native chicken breeds. Among them, the Leccese (LEC) chicken breed requires urgent genetic characterization to support conservation, development, and sustainable use. This study assessed the genetic diversity and population structure of the LEC chicken breed using the 600 K Affymetrix SNP array, comparing it with 25 Italian indigenous breeds and four commercial lines. In addition, selection signatures were explored through runs of homozygosity and integrated haplotype score analyses. The observed heterozygosity, expected heterozygosity, and minor allele frequency in LEC were 0.343, 0.358, and 0.268, respectively. The inbreeding coefficient based on observed versus expected homozygosity was 0.044, and the inbreeding coefficient based on runs of homozygosity was 0.189. Population structure analyses revealed clear genetic differentiation between the LEC and other Italian chicken breeds. Selective sweep analyses (runs of homozygosity and integrated haplotype score) identified candidate genomic regions harboring genes related to growth (GBE1, CYFIP1, NIPA2, BBOX1), bone development (PHEX), disease resistance (ROBO2, TLR7, EIF3M), and environmental adaptation (ANO5, CCDC34, HSF4, SPON1). These findings provide novel insights into the genetic background of the LEC, supporting breed identification, conservation planning, and the design of sustainable breeding programs. The identified candidate genes within selective sweep regions may serve as markers for future selection to enhance productive traits and adaptation in the LEC chicken breed.