Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA.
Department of Biological Sciences, Kuwait University, Safat, Kuwait.
Sci Rep. 2018 May 4;8(1):7024. doi: 10.1038/s41598-018-25438-0.
The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array's genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50-1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.
高通量 SNP 基因分型技术的发展提高了包括猫在内的许多物种的简单和复杂性状的遗传分析。本文使用了超过 2000 个猫样本的数据集（迄今为止规模最大的数据集），描述了 Illumina Infinium iSelect DNA 阵列 62897 个猫 SNP 的特性，该数据集代表了 41 个猫品种、一个随机繁殖的群体和四个野生猫科物种。评估了该阵列基因型的准确性和效率及其在进行基于群体的分析中的应用。平均标记距离在整个阵列上为 37741 Kb，在整个数据集中，只有 1%（625 个）标记显示出较差的基因分型，只有 0.35%（221 个）显示孟德尔错误。标记多态性在猫品种之间存在差异，所有家猫的平均次要等位基因频率（MAF）为 0.21。群体结构分析证实了猫品种从西向东的结构连续性。家猫的全基因组连锁不平衡范围为 50-1500 Kb，欧洲野猫（Felis silvestris silvestris）为 750 Kb。在不同的遗传模式、选择和群体大小下，研究了该阵列在性状关联映射中的应用。高效的阵列设计和猫基因型数据集继续推进对猫品种的理解，并将支持猫品种和种群的单基因健康研究。
