Natural and artificial selection for more than 9000 years have led to a variety of domestic pig breeds. Accurate identification of pig breeds is important for breed conservation, sustainable breeding, pork traceability, and local resource registration. We evaluated the performance of four selectors and six classifiers for breed identification using a wide range of pig breeds (N = 91). The internal cross-validation and external independent testing showed that partial least squares regression (PLSR) was the most effective selector and partial least squares-discriminant analysis (PLS-DA) was the most powerful classifier for breed identification among many breeds. Five-fold cross-validation indicated that using PLSR as the selector and PLS-DA as the classifier to discriminate 91 pig breeds yielded 98.4% accuracy with only 3K single nucleotide polymorphisms (SNPs). We also constructed a reference dataset with 124 pig breeds and used it to develop the web tool iDIGs ( http://alphaindex.zju.edu.cn/iDIGs_en/ ) as a comprehensive application for global pig breed identification. iDIGs allows users to (1) identify pig breeds without a reference population and (2) design small panels to discriminate several specific pig breeds. In this study, we proved that breed identification among a wide range of pig breeds is feasible and we developed a web tool for such pig breed identification.

中文翻译：

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用于全球猪品种鉴定的网络工具

9000 多年的自然和人工选择造就了多种家猪品种。猪品种的准确鉴定对于品种保护、可持续育种、猪肉溯源和地方资源登记具有重要意义。我们使用广泛的猪品种 (N = 91) 评估了四个选择器和六个分类器的品种识别性能。内部交叉验证和外部独立测试表明，偏最小二乘回归（PLSR）是最有效的选择器，偏最小二乘判别分析（PLS-DA）是众多品种中最强大的品种识别分类器。五折交叉验证表明，使用 PLSR 作为选择器和 PLS-DA 作为分类器来区分 91 个猪品种，结果为 98。仅 3K 单核苷酸多态性 (SNP) 的准确度为 4%。我们还构建了一个包含 124 个猪品种的参考数据集，并使用它开发了网络工具 iDIGs ( http://alphaindex.zju.edu.cn/iDIGs_en/ ) 作为全球猪品种鉴定的综合应用程序。iDIGs 允许用户 (1) 在没有参考种群的情况下识别猪品种，以及 (2) 设计小面板来区分几种特定的猪品种。在这项研究中，我们证明了在广泛的猪品种之间进行品种鉴定是可行的，并且我们开发了一个用于此类猪品种鉴定的网络工具。iDIGs 允许用户 (1) 在没有参考种群的情况下识别猪品种，以及 (2) 设计小面板来区分几种特定的猪品种。在这项研究中，我们证明了在广泛的猪品种之间进行品种鉴定是可行的，并且我们开发了一个用于此类猪品种鉴定的网络工具。iDIGs 允许用户 (1) 在没有参考种群的情况下识别猪品种，以及 (2) 设计小面板来区分几种特定的猪品种。在这项研究中，我们证明了在广泛的猪品种之间进行品种鉴定是可行的，并且我们开发了一个用于此类猪品种鉴定的网络工具。