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High-density genomic characterization of native Croatian sheep breeds

Citation

Drzaic, Ivana et al. (2022), High-density genomic characterization of native Croatian sheep breeds, Dryad, Dataset, https://doi.org/10.5061/dryad.pg4f4qrsn

Abstract

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 > 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.

Methods

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.

Usage Notes

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).

Funding

Hrvatska Zaklada za Znanost, Award: IP-2018-01-8708

National Natural Science Foundation of China, Award: 31661143014

National Natural Science Foundation of China, Award: 31825024

National Natural Science Foundation of China, Award: 31972527

National Natural Science Foundation of China, Award: 31660651

National Natural Science Foundation of China, Award: 31760661