Abstract
Goats play an important role in the livestock sector in Greece. The national herd consists mainly of two indigenous breeds, the Eghoria and Skopelos. Here, we report the population structure and genomic profiles of these two native goat breeds using Illumina’s Goat SNP50 BeadChip. Moreover, we present a panel of candidate markers acquired using different genetic models for breed discrimination. Quality control on the initial dataset resulted in 48,841 SNPs kept for downstream analysis. Principal component and admixture analyses were applied to assess population structure. The rate of inbreeding within breed was evaluated based on the distribution of runs of homozygosity in the genome and respective coefficients, the genomic relationship matrix, the patterns of linkage disequilibrium, and the historic effective population size. Results showed that both breeds exhibit high levels of genetic diversity. Level of inbreeding between the two breeds estimated by the Wright’s fixation index FST was low (Fst = 0.04362), indicating the existence of a weak genetic differentiation between them. In addition, grouping of farms according to their geographical locations was observed. This study presents for the first time a genome-based analysis on the genetic structure of the two indigenous Greek goat breeds and identifies markers that can be potentially exploited in future selective breeding programs for traceability purposes, targeted genetic improvement schemes and conservation strategies.
Highlights
The Greek national flock of goats is the largest in the European Union (E.U.), counting approximately 5 million heads [1]
From the breeds that clustered near Greek breeds, principal component analysis (PCA) revealed that Eghoria and Skopelos grouped closer to the Carpatian breed (CRP), as well as to Italian breeds, such as Garganica (GAR), Rossa Mediterranea (RME) and Jonica (JON)
Genetic diversity and population structure of autochthonous Greek goat breeds was assessed for the first time using the Goat SNP50 BeadChip
Summary
The Greek national flock of goats is the largest in the European Union (E.U.), counting approximately 5 million heads [1]. These animals are classified into a wide range of farming systems; from semi-extensive low-input, traditional farms to large, semi-intensive, high producing and investing farms [2]. Most herds are traditionally reared in mountainous, semi-. Genome-wide DNA SNP analysis of Greek goat breeds. Bioeconomy - DataBio (H2020 Grant Agreement No 732064, grant awarded to AA) and c) THRIVING LAND project, financed by the Trans Adriatic Pipeline (Grant Agreement HOR.044609, grant awarded to AA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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