Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America.
Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America.
PLoS One. 2019 Feb 27;14(2):e0212171. doi: 10.1371/journal.pone.0212171. eCollection 2019.
Thirty-three autosomal short tandem repeat (STR) markers were used to evaluate genetic heterogeneity and diversity in 525 golden retrievers (GRs). This breed was selected because of its popularity and artificial selection for conformation vs. performance phenotypes. Seven additional STRs were used to evaluate the highly polymorphic dog leukocyte antigen (DLA) class I and class II regions. From 3 to 13 alleles were found at each of the 33 loci (mean 7) and the average effective alleles (Ne) was 3.34. The observed heterozygosity was 0.65 and the expected heterozygosity was 0.68. The resulting fixation index was 0.035 indicating that the population was randomly breeding. We found that modern GRs retain 46% of genomic diversity present in all canids and 21/175 (12%) and 20/90 (22%) of the known DLA class I and class II haplotypes, respectively. Selection for performance or conformation led to a narrowing of genomic and DLA diversity with conformation having a greater effect than performance. A comparison was made between coefficient of inbreeding (COI) determined from 10 or 12 generation pedigrees and DNA based internal relatedness values. A weak but significant correlation was observed between IR score and 10 or 12 generation COI (r = 0.38, p<0.0001 and r = 0.40, p<0.0001, respectively). IR values were higher in conformation than performance lines but only significant at p = 0.17. This was supported by 10 and 12 generation COI values that were significantly (p<0.0001) higher in conformation than performance lines. We demonstrate herein that a low density of STR markers can be utilized to study the genetic makeup of GRs.
33 个常染色体短串联重复（STR）标记用于评估 525 只金毛猎犬（GR）的遗传异质性和多样性。选择这个品种是因为它的受欢迎程度和人工选择的形态对表现型。另外使用了 7 个 STR 来评估高度多态性的犬白细胞抗原（DLA）I 类和 II 类区域。在 33 个基因座中的每个基因座中发现了 3 到 13 个等位基因（平均值为 7），平均有效等位基因（Ne）为 3.34。观察到的杂合度为 0.65，预期杂合度为 0.68。由此产生的固定指数为 0.035，表明该群体是随机繁殖的。我们发现，现代 GR 保留了所有犬科动物基因组多样性的 46%，以及已知 DLA I 类和 II 类单体型的 21/175（12%）和 20/90（22%）。对性能或形态的选择导致基因组和 DLA 多样性的缩小，形态的影响大于性能。比较了从 10 代或 12 代系谱确定的近交系数（COI）和基于 DNA 的内部相关性值。IR 评分与 10 代或 12 代 COI 之间存在弱但显著的相关性（r = 0.38，p<0.0001 和 r = 0.40，p<0.0001）。在形态比性能线上的 IR 值更高，但仅在 p = 0.17 时显著。这得到了 10 代和 12 代 COI 值的支持，形态比性能线的 COI 值显著更高（p<0.0001）。我们在此证明，低密度 STR 标记可以用于研究 GR 的遗传构成。
