Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (Ovis canadensis canadensis)

被引:1
|
作者
Deakin, Samuel [1 ]
Coltman, David W. [1 ,2 ]
机构
[1] Univ Alberta, Dept Biol Sci, Edmonton, AB, Canada
[2] Univ Western Ontario, Dept Biol, London, ON, Canada
来源
PEERJ | 2024年 / 12卷
基金
加拿大自然科学与工程研究理事会;
关键词
Ungulate; Genetic; Sheep; SNP; Tecan; Allegro; Genomic; Bighorn; Development; SPET; GENETIC-STRUCTURE; PATTERNS; PACKAGE; FORMAT; CELL; DNA;
D O I
10.7717/peerj.16946
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, highdensity, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped similar to 45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.
引用
收藏
页数:20
相关论文
共 35 条