Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed.

Mojca Simčič,Doris Seichter,Dragomir Kompan,Anamarija Smetko,Gregor Gorjanc,Johann Sölkner,Ivica Medugorac,Axel Janke

doi:10.1371/journal.pone.0123253

Mojca Simčič, Doris Seichter + Show 6 more

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https://doi.org/10.1371/journal.pone.0123253

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Abstract

The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.

Highlights

After domestication in the near east cattle became widespread in Europe along the Danubian and Mediterranean route [1]
To create a subset of the most unrelated purebred Cika animals required for phylogenetic analyses we removed highly related animals, and animals that had exceptionally high relationship coefficient (2 SD above average) compared to the animals from other breeds
At the beginning of the construction of the reduced dataset we excluded 24 admixed animals based on the known pedigree, which contained more than 12.5% of foreign genes

Summary

Introduction

After domestication in the near east cattle became widespread in Europe along the Danubian and Mediterranean route [1]. The primary loss of genetic diversity within these species is due to progressive upgrading and replacement of local strains with the imported germplasm of highly selected breeds instead of laborious and slow improvement of local populations based on the local agricultural infrastructure (e.g., [3]). The genetic homogenization of livestock is a special form of biotic homogenization which is considered as one of the most prominent forms of the biotic impoverishment worldwide. This process could even endanger the long-term success of species (populations) that are seemingly the ‘winners’ in the homogenization process [6]

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