Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133 Iran ; Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, PB 76169-133 Iran.
Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133 Iran.
J Anim Sci Technol. 2015 Dec 24;57:47. doi: 10.1186/s40781-015-0080-2. eCollection 2015.
Knowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data.
A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the r(2) criterion were computed by grouping all syntenic SNP pairwises for inter-marker distances from 0 Kb up to 1 Mb using three distance sets. Average r(2) above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations.
A wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.
不同群体之间的连锁不平衡（LD）水平的知识可用于检测遗传多样性，并研究群体规模的历史变化。新测序技术提供的大量 SNP 为广泛研究牛品种中的 LD 模式提供了机会。本研究的目的是利用高密度 SNP 基因分型数据比较伊朗牛品种之间的连锁不平衡程度。
总共 70 个样本，代表 7 个伊朗本土牛品种，对 777962 个 SNP 进行了基因分型。基于 r(2)标准，通过对所有同线 SNP 对进行分组，计算了不同标记间距离为 0 Kb 至 1 Mb 的 LD 平均值，使用了三个距离集。对于 Sistani 和 Kermani，距离小于 30 Kb 的 r(2)平均值大于 0.3，对于 Najdi、Taleshi、Kurdi 和 Sarabi，距离为 20 Kb，对于 Mazandarani，距离为 10 Kb。伊朗牛品种之间的 LD 水平差异很大，在较长距离上，研究品种之间的 LD 程度差异更明显。与其他品种相比，Mazandarani 品种的 LD 水平较低，表明该品种的祖先群体规模较大。在 3 Kb 距离后，Kermani 品种的 LD 衰减速度比其他品种都要慢。在更大的距离（>100 Kb）上，Kurdi 和 Sarabi 品种的 LD 衰减速度较慢，表明这些群体在更近的几代中经历了更为剧烈的种群衰退。
伊朗牛品种之间的 LD 水平反映了广泛的遗传多样性和不同的历史背景。在不同的牛种群中，较短的距离（小于 10 Kb）观察到更多的 LD 波动。尽管存在样本量的影响，但本研究中发现的高 LD 水平与伊朗牛品种的近交和种群衰退是一致的。
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