Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy.
Anim Genet. 2014 Apr;45(2):304-7. doi: 10.1111/age.12121. Epub 2014 Jan 21.
The European rabbit (Oryctolagus cuniculus) is a domesticated species with one of the broadest ranges of economic and scientific applications and fields of investigation. Rabbit genome information and assembly are available (oryCun2.0), but so far few studies have investigated its variability, and massive discovery of polymorphisms has not been published yet for this species. Here, we sequenced two reduced representation libraries (RRLs) to identify single nucleotide polymorphisms (SNPs) in the rabbit genome. Genomic DNA of 10 rabbits belonging to different breeds was pooled and digested with two restriction enzymes (HaeIII and RsaI) to create two RRLs which were sequenced using the Ion Torrent Personal Genome Machine. The two RRLs produced 2 917 879 and 4 046 871 reads, for a total of 280.51 Mb (248.49 Mb with quality >20) and 417.28 Mb (360.89 Mb with quality >20) respectively of sequenced DNA. About 90% and 91% respectively of the obtained reads were mapped on the rabbit genome, covering a total of 15.82% of the oryCun2.0 genome version. The mapping and ad hoc filtering procedures allowed to reliably call 62 491 SNPs. SNPs in a few genomic regions were validated by Sanger sequencing. The Variant Effect Predictor Web tool was used to map SNPs on the current version of the rabbit genome. The obtained results will be useful for many applied and basic research programs for this species and will contribute to the development of cost-effective solutions for high-throughput SNP genotyping in the rabbit.
欧洲兔（Oryctolagus cuniculus）是一种经过驯化的物种，其经济和科学应用范围广泛，研究领域众多。兔基因组信息和组装已经可用（oryCun2.0），但迄今为止，对其变异性的研究很少，而且尚未为该物种发表大规模发现多态性的研究。在这里，我们通过两种简化基因组文库（RRL）测序来鉴定兔基因组中的单核苷酸多态性（SNP）。10 只不同品种的兔的基因组 DNA 被混合，并使用两种限制酶（HaeIII 和 RsaI）消化以创建两种 RRL，然后使用 Ion Torrent Personal Genome Machine 对其进行测序。两种 RRL 共产生了 2 917 879 和 4 046 871 条reads，总测序长度分别为 280.51 Mb（质量>20 的 248.49 Mb）和 417.28 Mb（质量>20 的 360.89 Mb）。分别约有 90%和 91%的获得的reads可以映射到兔基因组上，总共覆盖了 oryCun2.0 基因组版本的 15.82%。映射和专门的过滤程序可以可靠地调用 62 491 个 SNPs。少数基因组区域的 SNPs 通过 Sanger 测序进行了验证。Variant Effect Predictor Web 工具用于将 SNPs 映射到兔的当前基因组版本上。所得结果将对该物种的许多应用和基础研究计划有用，并有助于开发用于兔高通量 SNP 基因分型的经济高效解决方案。
