Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, Wageningen, The Netherlands.
Anim Genet. 2011 Dec;42(6):613-20. doi: 10.1111/j.1365-2052.2011.02198.x. Epub 2011 Apr 25.
The objectives of this study were to develop breed-specific single nucleotide polymorphisms (SNPs) in five pig breeds sequenced with Illumina's Genome Analyzer and to investigate their usefulness for breed assignment purposes. DNA pools were prepared for Duroc, Landrace, Large White, Pietrain and Wild Boar. The total number of animals used for sequencing was 153. SNP discovery was performed by aligning the filtered reads against Build 7 of the pig genome. A total of 313,964 high confidence SNPs were identified and analysed for the presence of breed-specific SNPs (defined in this context as SNPs for which one of the alleles was detected in only one breed). There were 29,146 putative breed-specific SNPs identified, of which 4441 were included in the PorcineSNP60 beadchip. Upon re-examining the genotypes obtained using the beadchip, 193 SNPs were confirmed as being breed specific. These 193 SNPs were subsequently used to assign an additional 490 individuals from the same breeds, using the sequenced individuals as reference populations. In total, four breed assignment tests were performed. Results showed that for all methods tested 99% of the animals were correctly assigned, with an average probability of assignment of at least 99.2%, indicating the high utility of breed-specific markers for breed assignment and traceability. This study provides a blueprint for the way next-generation sequencing technologies can be used for the identification of breed-specific SNPs, as well as evidence that these SNPs may be a powerful tool for breed assignment and traceability of animal products to their breeds of origin.
本研究的目的是在五个经 Illumina 基因组分析仪测序的猪品种中开发品种特异性单核苷酸多态性（SNP），并研究其在品种鉴定中的应用。为杜洛克猪、长白猪、大白猪、皮特兰猪和野猪准备了 DNA 池。用于测序的动物总数为 153 头。通过将过滤后的reads 与猪基因组的 Build 7 进行比对，进行 SNP 发现。共鉴定出 313964 个高可信度 SNP，并对品种特异性 SNP（在此上下文中定义为一个等位基因仅在一个品种中检测到的 SNP）的存在进行了分析。共鉴定出 29146 个可能的品种特异性 SNP，其中 4441 个 SNP 包含在 PorcineSNP60 珠芯片中。在用珠芯片重新检查获得的基因型后，确认了 193 个 SNP 是品种特异性的。这 193 个 SNP 随后被用于以测序个体为参考群体，对来自相同品种的另外 490 个个体进行品种鉴定。总共进行了四次品种鉴定测试。结果表明，所有测试方法的动物均正确鉴定，平均鉴定概率至少为 99.2%，表明品种特异性标记在品种鉴定和可追溯性方面具有很高的应用价值。本研究为下一代测序技术用于鉴定品种特异性 SNP 提供了蓝图，并证明这些 SNP 可能是动物产品品种鉴定和可追溯性的有力工具。
