What conservation insights can we drag from genome-wide SNPs data in Italian small goat breeds?

Abstract

Italy is home to several indigenous goat breeds with great economic and cultural implications, but their genetic makeup remains largely unexplored. This study used the Illumina Goat SNP chip to genotype 142 samples from four Italian goat breeds: Capestrina, Fulva, Grigia Ciociara, and Bianca Monticellana. The genotypes were combined with genome-wide SNP data from 31 Italian breeds to evaluate the genetic profile of Lazio’s indigenous goats. After filtering, the dataset included 51,423 SNPs. Genetic structure and diversity were assessed using MDS, ADMIXTURE analysis and inbreeding coefficients. Focusing on the four Lazio breeds, we examined inbreeding levels (FROH), effective population size (Ne), gene exchange, and runs of homozygosity islands (ROHi). The Bianca appeared highly inbred, whereas Fulva, Capestrina, and Grigia showed heterozygosity levels comparable to other breeds. The increased sample sizes highlighted changes in genetic composition, indeed, ADMIXTURE analysis revealed genetic substructures within Bianca and Fulva. The Ne was found to be declining, with Bianca having the lowest Ne, indicating high susceptibility to inbreeding and genetic drift. The NetView analysis identified two interconnected genetic groups corresponding to: Bianca and Fulva. Key contributors to genetic structure, representing ancestral genotypes, were identified, providing targets for conservation. Moreover, ROH analysis pinpointed individuals with excessive ROH and long homozygosity stretches, particularly in Capestrina and Bianca, which could be limited from breeding to preserve genetic diversity. Finally, ROHi revealed genes linked to coat colour, disease resistance, and heat stress tolerance. These conclusions emphasise the importance of local breeds in maintaining biodiversity and enhancing breeding strategies.

Keywords

• single nucleotide polymorphisms
• local goat populations
• runs of homozygosity islands
• genome-wide diversity
• local breeds conservation