Conservation & local programs

Managing genomic diversity and farm structure in the Leccese chicken using high-density SNP genotypes

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Abstract

The Leccese chicken is a relict Mediterranean local breed maintained in a small, fragmented metapopulation in Southern Italy. Its long-term survival depends on retaining genetic diversity while preventing uncoordinated drift across small-scale farms. We used high-density SNP genotypes to describe the genomic structure of the Leccese population, quantify diversity at farm level, and derive practical guidelines for conservation-oriented mating plans. Seventy-nine Leccese chickens (25 males and 54 females) from nine farms (FOSSA, ABBONDANZA, CARANI, CARPARELLI, SPADARO, MITRUGNO, CORVAGLIA, SOLACCIO and FRANCIOSO) were genotyped with the Affymetrix Axiom® 600K Chicken Genotyping Array; after quality control and filtering, 432,091 autosomal SNPs were retained. An LD-pruned subset of markers was used for PCA and ADMIXTURE analyses, whereas the full filtered dataset was used to estimate within-farm diversity, genomic inbreeding based on runs of homozygosity (FROH), pairwise kinship, and Weir & Cockerham's FST. A genomic kinship network was built from SNP-based relatedness (kinship > 0.01), and a composite conservation-priority index was calculated by combining farm-specific FST (uniqueness), expected heterozygosity (He), FROH, and sample size. Within-farm diversity was moderate across the metapopulation, with Ho and He generally between 0.25 and 0.33, and negative mean FIS values indicating an overall excess of heterozygotes. PCA and ADMIXTURE revealed clear subdivision among farms, with FOSSA as a highly differentiated nucleus and a cluster of more closely related farms (ABBONDANZA, CARPARELLI, SOLACCIO and MITRUGNO), while CARANI, SPADARO, CORVAGLIA and FRANCIOSO showed intermediate or mixed ancestry. Pairwise FST values confirmed this pattern, exceeding 0.20 for contrasts involving FOSSA and remaining below 0.03 among the most similar farms. The genomic kinship network comprised 79 nodes and 1,303 edges, with a mean kinship of 0.10 and a modularity of 0.42 for the two main communities identified by the Louvain algorithm. A few individuals showed high betweenness centrality and acted as bridges between otherwise weakly connected groups, whereas FOSSA birds formed a dense, internally cohesive but externally weakly connected cluster. The composite conservation-priority index ranked FOSSA, ABBONDANZA and CARANI among the top farms, reflecting the combination of uniqueness, diversity, and manageable inbreeding levels. Overall, high-density SNP data combined with network metrics and a simple conservation-priority index provide operational tools to design mating schemes that preserve unique genetic pools, maintain gene flow, and control inbreeding, improving the long-term viability of this endangered local chicken population.

Keywords: 2026

How to Cite:

Landi, V., Saleh, M., Rusco, G., Camarda, A. & De Palo, P., (2026) “Managing genomic diversity and farm structure in the Leccese chicken using high-density SNP genotypes”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2295102. doi: https://doi.org/10.31274/wcgalp.24330

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