Estimation of Effective Population Size in the Sapsaree: A Korean Native Dog (Canis familiaris)
Estimation of Effective Population Size in the Sapsaree: A Korean Native Dog (Canis familiaris)
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DOI：
10.5713/ajas.2012.12048
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发表时间：
2012-08-01
期刊：
影响因子：
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通讯作者：
Kim, J. J.
中科院分区：
文献类型：
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作者：
Alam, M.;Han, K. I.;Kim, J. J.
有效种群大小（N-e）是了解动物种群结构和遗传变异的重要指标。本研究的目的是使用近交率信息和基因组数据来估计Sapsaree犬的N-e，所述近交率信息和基因组数据分别来自系谱和Illumina CanineSNP 20（20 K）和CanineHD（170 K）微珠芯片。使用三个SNP组，即Sap 134（20 K）、Sap 60（170 K）和Sap 183（来自20 K和170 K的组合组）分别对134、60和183个动物样品进行基因分型。大约5到13代前，基于近亲繁殖率的N-e估计值范围为16到51。通过使用SNP基因型，两种方法被应用于N-e估计，即使用距离的简单期望的成对r（2）值和假设有限群体大小的具有各自距离的非线性回归下的r（2）值。使用Sap 134、Sap 60和Sap 183组中位于5 Mb内的SNP对，跨代的平均成对N-e估计值分别为1，486、1，025和1，293。在非线性回归方法下，各样本组的平均N-e估计值分别为1，601、528和1，129。此外，在第5、20和50代前，过去N-e的点估计值分别在64至75、245至286和573至646之间，表明在过去几代中N-e显著减少。这些结果表明，通过应用基因组选择或其他育种策略来增加N-E，以保持遗传变异并避免Sapsaree种群未来的瓶颈，从而最大限度地减少近亲繁殖的强烈必要性。
Effective population size (N-e) is an important measure to understand population structure and genetic variability in animal species. The objective of this study was to estimate N-e in Sapsaree dogs using the information of rate of inbreeding and genomic data that were obtained from pedigree and the Illumina CanineSNP20 (20K) and CanineHD (170K) beadchips, respectively. Three SNP panels, i.e. Sap134 (20K), Sap60 (170K), and Sap183 (the combined panel from the 20K and 170K), were used to genotype 134, 60, and 183 animal samples, respectively. The N-e estimates based on inbreeding rate ranged from 16 to 51 about five to 13 generations ago. With the use of SNP genotypes, two methods were applied for N-e estimation, i.e. pair-wise r(2) values using a simple expectation of distance and r(2) values under a non-linear regression with respective distances assuming a finite population size. The average pair-wise N-e estimates across generations using the pairs of SNPs that were located within 5 Mb in the Sap 134, Sap60, and Sap 183 panels, were 1,486, 1,025 and 1,293, respectively. Under the non-linear regression method, the average N-e estimates were 1,601, 528, and 1,129 for the respective panels. Also, the point estimates of past N-e at 5, 20, and 50 generations ago ranged between 64 to 75, 245 to 286, and 573 to 646, respectively, indicating a significant N-e reduction in the last several generations. These results suggest a strong necessity for minimizing inbreeding through the application of genomic selection or other breeding strategies to increase N-e, so as to maintain genetic variation and to avoid future bottlenecks in the Sapsaree population.