Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium
Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium
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DOI：
10.1111/j.1439-0388.2010.00862.x
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发表时间：
2010-10-01
影响因子：
2.6
通讯作者：
Rieder, S.
中科院分区：
文献类型：
--
作者：
Flury, C.;Tapio, M.;Rieder, S.
P>有效种群规模是评估牲畜种群遗传多样性及其随时间发展的重要参数。如果没有谱系信息，连锁不平衡（LD）分析可能为估计有效种群规模提供另一种视角。在这项研究中，使用 Illumina BovineSNP50 珠芯片对 128 只瑞士 Eringer 品种个体进行了基因分型。我们将 LD 分析的 bin 大小设置为 50 kb，假设近端单核苷酸多态性 (SNP) 对的 LD 反映遥远的育种历史，而远端 SNP 对的 LD 将反映近端历史。基因组不同区域的重组率各不相同。使用物理距离作为遗传距离的近似值（例如设置 1 Mb = 0.01 Morgan）导致基于 LD 的对 50 代以上有效种群规模的估计出现向上偏差，而对近期历史的估计不受影响。对有限样本量的修正并没有对这些结果产生实质性影响。基于 LD 的实际有效种群规模估计为 87-149 只，而基于谱系的有效种群规模为 321 只。出于保护目的，需要了解近期历史（< 50 代），假设恒定重组率的近似值似乎就足够了。
P>Effective population size is an important parameter for the assessment of genetic diversity within a livestock population and its development over time. If pedigree information is not available, linkage disequilibrium (LD) analysis might offer an alternative perspective for the estimation of effective population size. In this study, 128 individuals of the Swiss Eringer breed were genotyped using the Illumina BovineSNP50 beadchip. We set bin size at 50 kb for LD analysis, assuming that LD for proximal single nucleotide polymorphism (SNP)-pairs reflects distant breeding history while LD from distal SNP-pairs would reflect near history. Recombination rates varied among different regions of the genome. The use of physical distances as an approximation of genetic distances (e.g. setting 1 Mb = 0.01 Morgan) led to an upward bias in LD-based estimates of effective population size for generations beyond 50, while estimates for recent history were unaffected. Correction for restricted sample size did not substantially affect these results. LD-based actual effective population size was estimated in the range of 87-149, whereas pedigree-based effective population size resulted in 321 individuals. For conservation purposes, requiring knowledge of recent history (< 50 generations), approximation assuming constant recombination rate seemed adequate.