Pertoldi C, Purfield D C, Berg P, Jensen T H, Bach O S, Vingborg R, Kristensen T N
Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark Aalborg Zoo, Aalborg, Denmark
Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
J Anim Sci. 2014 Jun;92(6):2372-6. doi: 10.2527/jas.2013-7206. Epub 2014 Mar 26.
In this paper we present results from a genetic characterization of a herd of the Danish Jutland cattle breed named the Kortegaard herd (n = 135; 57 males and 78 females). The herd is genotyped on the Bovine HD BeadChip microarray with 697,548 evenly spaced SNP across the bovine genome. The aim of the study was to characterize the genetic profile of the Kortegaard herd, which has been closed for several generations, by quantifying the degree of genetic homogeneity within the herd and to compare its genetic profile to that of other cattle breeds. A total of 868 animals from the Angus, Belgian Blue, Charolais, Friesian, Hereford, Holstein, Holstein-Friesian crosses, Limousin, and Simmental breeds was used for genetic profile comparisons. The level of genetic variation within the breeds were quantified by the expected heterozygosity (H(E)), observed heterozygosity (H(O)), average minor allele frequency (MAF), the degree of polymorphism, and runs of homozygosity (ROH), which are contiguous lengths of homozygous genotypes of varying length. Interestingly, the Kortegaard herd had the lowest within-breed genetic variation (lowest H(E), H(O), and MAF), showed moderate levels of short ROH (<5 Mb), and had the highest mean long ROH (>5 Mb) compared to all the other breeds. This is possibly due to recent consanguineous matings, a strong founder effect, and a lack of gene flow from other herds and breeds. We further examined whether the observed genetic patterns in the Kortegaard herd can be used to design breeding strategies for the preservation of the genetic pool by focusing on a subset of SNP outside homozygote regions. By calculating the pairwise identical-by-state between all possible matings, we designed a breeding plan that maximized heterozygosity in the short term. The benefits and limitations of such a breeding strategy are discussed.
在本文中，我们展示了对一群名为科尔特加德牛群（n = 135；57头雄性和78头雌性）的丹麦日德兰牛品种进行基因特征分析的结果。该牛群在牛HD基因分型芯片上进行了基因分型，该芯片在牛基因组中均匀分布着697,548个单核苷酸多态性（SNP）。本研究的目的是通过量化牛群内的遗传同质性程度来描述已封闭几代的科尔特加德牛群的基因概况，并将其基因概况与其他牛品种进行比较。总共使用了来自安格斯、比利时蓝牛、夏洛莱、弗里西亚、赫里福德、荷斯坦、荷斯坦 - 弗里西亚杂交牛、利木赞和西门塔尔品种的868头动物进行基因概况比较。通过预期杂合度（H(E)）、观察杂合度（H(O)）、平均次要等位基因频率（MAF）、多态性程度和纯合子连续片段（ROH，即不同长度的纯合基因型的连续长度）来量化品种内的遗传变异水平。有趣的是，与所有其他品种相比，科尔特加德牛群具有最低的品种内遗传变异（最低的H(E)、H(O)和MAF），显示出中等水平的短ROH（<5 Mb），并且具有最高的平均长ROH（>5 Mb）。这可能是由于近期的近亲交配、强烈的奠基者效应以及缺乏来自其他牛群和品种的基因流动。我们进一步研究了科尔特加德牛群中观察到的遗传模式是否可用于通过关注纯合子区域外的SNP子集来设计保护基因库的育种策略。通过计算所有可能交配之间的成对状态相同性，我们设计了一个在短期内使杂合度最大化的育种计划。讨论了这种育种策略的优点和局限性。
