DOI: 10.5061/dryad.pg4f4qrsn
title: High-density genomic characterization of native Croatian sheep breeds

description: A recent comprehensive genomic analysis based on 50K SNP profiles has
 shown that the regional Balkan sheep populations have considerable genetic
 overlap but are distinctly different from surrounding breeds. All eight
 Croatian sheep breeds were represented by a small number of individuals
 per breed. Here, we genotyped 220 individuals representing the native
 Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep,
 Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka,
 Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip
 (606,006 SNPs). In addition, we included publicly available Balkan
 Pramenka and other Mediterranean sheep breeds. Our analyses revealed the
 complex population structure of Croatian sheep breeds and their origin and
 geographic barriers (island versus mainland). Migration patterns confirmed
 the historical establishment of breeds and the pathways of gene flow.
 Inbreeding coefficients (FROH &gt; 2 Mb) between sheep populations
 ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in
 Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik
 sheep. The estimated effective population size ranged from 61 to 1039 for
 Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding
 levels and lower effective population size indicate the need for improved
 conservation management to maintain genetic diversity in some breeds. Our
 results will contribute to breeding and conservation strategies of native
 Croatian sheep breeds.
description: For this study, blood or
 tissue samples were randomly collected from 101 female and 100 male sheep
 located on 104 family farms representing 20 Cres Island Sheep, 20 Krk
 Island Sheep, 20 Rab Island Sheep, 20 Lika Pramenka, 25 Istrian Sheep, 26
 Dubrovnik sheep, 26 Dalmatian Pramenka, 45 Pag Island
 Sheep. Samples were
 genotyped using the Ovine Infinium HD BeadChip (Illumina, San Diego, CA,
 United States) by Gene Seek, Neogen Genomics (Neogene Europe Ltd,
 Scotland, UK). Genotypes were mapped to the Oar4.0 map. Quality control
 and filtering of SNPs were obtained using SNP & Variation Suite
 v8.7.0 (Golden Helix, Inc., Bozeman, MT, www.goldenhelix.com. Genotypes were mapped to the Oar4.0 map. Quality control and filtering of SNPs were obtained using SNP & Variation Suite v8.7.0 (Golden Helix, Inc., Bozeman, MT, www.goldenhelix.com). The accuracy and efficiency of SNP genotyping were assessed by applying a cut-off value of 0.7 for the Illumina GenCall score and 0.4 for the Illumina GenTrain score. All SNPs with more than 10% missing genotypes and individuals with more than 5% missing genotypes were removed. SNPs without position or SNPs that had been assigned to sex chromosomes or mitochondrial genome were also excluded.
description: The genotypes are in standard plink binary format. 
 Many softwares support this type of data, but the main software
 is PLINK 1.9 (Purcell, S. et al. (2007) PLINK: a toolset for whole-genome
 association and population-based linkage analysis. American Journal of
 Human Genetics, 81).