Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed.
Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed.
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DOI：
10.1371/journal.pone.0123253
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Medugorac I
中科院分区：
文献类型：
--
作者：
Simčič M;Smetko A;Sölkner J;Seichter D;Gorjanc G;Kompan D;Medugorac I
本研究的目的是获得对 Cika 牛多样性参数、种群历史和混合程度的公正估计，Cika 牛代表了面临灭绝风险的当地混合品种，正在经历具有挑战性的保护计划。对 76 只 Cika 动物和来自 14 个参考群体的 531 只动物的全基因组单核苷酸多态性 (SNP) Illumina Bovine SNP50 阵列数据进行了遗传分析。为了获得公正的估计，我们使用跨越四个标记的短单倍型而不是单个 SNP，以避免 BovineSNP50 阵列的确定偏差。全基因组单倍型与部分谱系和类型性状分类相结合，显示出改善低混合度纯种动物鉴定的潜力。系统发育分析证明了 Cika 动物独特的遗传特性。由根 Neighbour-Net 呈现的遗传距离矩阵表明 Cika 和 Pinzgauer 之间存在长期而广泛的系统发育联系。通过混合分析进行的无监督聚类以及个体之间遗传距离的二维表示也表明 Cika 是一个独特的品种，尽管在外观上与 Pinzgauer 相似。被确定为最纯种的动物可以用作恢复当前混合种群的本地遗传背景的核心。结果表明，当地适应性强的品系从未经过集约化管理和分化为特定品种，表现出较大的单倍型多样性。他们建议，保护和恢复方法不完全依赖于寻找原始的本地遗传背景，而是依赖于识别和去除常见的渐渗单倍型，这种方法会更有效。这种方法的成功实施应基于将感兴趣品种的表型、谱系和全基因组单倍型数据与一系列参考品种数据相结合，这些参考品种可能对感兴趣品种的遗传组成有直接或间接的历史贡献。
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.
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影响因子：
9.8
作者：
Boyko AR;Quignon P;Li L;Schoenebeck JJ;Degenhardt JD;Lohmueller KE;Zhao K;Brisbin A;Parker HG;vonHoldt BM;Cargill M;Auton A;Reynolds A;Elkahloun AG;Castelhano M;Mosher DS;Sutter NB;Johnson GS;Novembre J;Hubisz MJ;Siepel A;Wayne RK;Bustamante CD;Ostrander EA
通讯作者：
Ostrander EA
影响因子：
64.8
作者：
BOWCOCK, AM;RUIZLINARES, A;CAVALLISFORZA, LL
通讯作者：
CAVALLISFORZA, LL
影响因子：
2.6
作者：
Cinkulov, M.;Popovski, Z.;Kantanen, J.
通讯作者：
Kantanen, J.
影响因子：
3.7
作者：
Gautier, Mathieu;Laloe, Denis;Moazami-Goudarzi, Katayoun
通讯作者：
Moazami-Goudarzi, Katayoun
影响因子：
2.4
作者：
Frkonja, A.;Gredler, B.;Soelkner, J.
通讯作者：
Soelkner, J.