Recovery of Native Genetic Background in Admixed Populations Using Haplotypes, Phenotypes, and Pedigree Information – Using Cika Cattle as a Case Breed

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.

Conservation of a domestic metapopulation structured into related and partly admixed strains

“…The here designed and applied composite test combines six metrics that each provide distinct information components about past admixture events and offers an objective, statistically valid and powerful tool for the detection of admixed outliers. The composite statistic (Filzmoser et al., ) as well as the six single metrics rely on well‐established, broadly applied methods (UAR, Yang et al., ; Nearest Neighbour Graph, Steinig et al., ; and spA, Simčič et al., and this study) and were additionally confirmed by their consistency with historical records of local strains ().…”

“…The here implemented methods and the use of multi‐allelic markers have the potential to reduce the ascertainment bias of the SNP array (Auton et al., ; Boyko et al., ; Lohmueller, Bustamante, & Clark, ; Simčič et al., ). Furthermore, they allowed us to demonstrate how to benefit from the allelic diversity of multi‐allelic markers as better indicators of future adaptation value (Caballero & Rodriguez‐Ramilo, ; Vilas et al., ).…”

“…To reduce ascertainment bias, similar to the study of Simčič et al. (), haplotype blocks that spanned less than 150 kb and contained four SNPs with an intermarker distance of less than 50 kb were defined. The use of 4‐SNP blocks with a maximum size of less than 150 kb presents a compromise between the maximum number of markers and the minimum recombination probability within the blocks.…”

“…Furthermore, to infer population structure, a heuristic method (Veit‐Kensch, Medugorac, Jedrzejewski, Bunevich, & Foerster, ) was applied and the D PS matrix was visualized in a two‐dimensional graph (2DD). This unsupervised clustering approach (Simčič et al., ) aimed to allocate individuals into clusters without prior knowledge of subpopulation or sample origin. Second, to investigate population structure based on SNP genotypes, the program admixture 1.23 (Alexander, Novembre, & Lange, ), which adopts the likelihood model implemented in the structure program (Falush, Stephens, & Pritchard, ; Pritchard, Stephens, & Donnely, ) but runs considerably faster, was used.…”

“…The genetic diversity of cattle, which are the most important domestic animal species in terms of global output of animal‐source foods, is under gradual depletion (FAO, ). Similar to other domesticated animal species, this process is primarily due to continuous replacement by crossing well adapted, scarcely selected and heterogeneous local populations with small numbers of highly selected and currently competitive cosmopolitan breeds (e.g., Simčič et al., ). This process is directly related to the genetic homogenization of domesticated species (Taberlet et al., ) and could be seen as a special form of biotic homogenization, which is considered one of the most prominent forms of the biotic impoverishment worldwide (Olden, LeRoy, Douglas, Douglas, & Fausch, ).…”