Data from: Recovery of native genetic background in admixed Populations Using haplotypes, phenotypes, and pedigree information – using Cika cattle as a case breed

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.