DT-PICS：一种用于拟南芥种质资源鉴定的高效且具有成本效益的 SNP 选择方法,International Journal of Molecular Sciences

当前位置： X-MOL 学术 › Int. J. Mol. Sci. › 论文详情

Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)

DT-PICS：一种用于拟南芥种质资源鉴定的高效且具有成本效益的 SNP 选择方法
International Journal of Molecular Sciences ( IF 4.9 ) Pub Date : 2023-05-14 , DOI: 10.3390/ijms24108742
Liwen Xiong ₁ , Zirong Li ₁ , Weihua Li ₁ , Lanzhi Li ₁

Affiliation

种质鉴定对于植物育种和保护至关重要。在这项研究中，我们开发了一种新方法 DT-PICS，用于在种质资源鉴定中高效且经济地选择 SNP。该方法基于决策树概念，可以根据整体高 PIC 值递归划分数据集，而不是考虑单个 SNP 特征，从而有效地选择信息最丰富的 SNP 进行种质鉴定。该方法减少了 SNP 选择的冗余，提高了选择过程的效率和自动化程度。DT-PICS在训练和测试数据集上均表现出显着优势，在独立预测上表现出良好的性能，验证了其有效性。从 749 中提取了 13 个简化的 SNP 集，1135个拟南芥品种重测序数据集中的636个SNP，共包括769个DT-PICS SNP，平均每组59个SNP。每个简化的 SNP 集可以区分 1135 个拟南芥品种。模拟表明，使用两个简化的 SNP 集的组合进行识别可以有效地提高独立验证中的容错性。在测试数据集中，确定了两个可能被错误标记的品种（ICE169 和 Star-8）。对于68个同名品种，识别准确率达到94.97%，平均共享标记仅30个；对于12个不同名称的品种，待测种质可以与其他1,134个品种有效区分，同时将极其相似的品种（Col-0）归为一类，反映了它们的实际遗传相关性。

"点击查看英文标题和摘要"

DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis

Germplasm identification is essential for plant breeding and conservation. In this study, we developed a new method, DT-PICS, for efficient and cost-effective SNP selection in germplasm identification. The method, based on the decision tree concept, could efficiently select the most informative SNPs for germplasm identification by recursively partitioning the dataset based on their overall high PIC values, instead of considering individual SNP features. This method reduces redundancy in SNP selection and enhances the efficiency and automation of the selection process. DT-PICS demonstrated significant advantages in both the training and testing datasets and exhibited good performance on independent prediction, which validates its effectiveness. Thirteen simplified SNP sets were extracted from 749,636 SNPs in 1135 Arabidopsis varieties resequencing datasets, including a total of 769 DT-PICS SNPs, with an average of 59 SNPs per set. Each simplified SNP set could distinguish between the 1135 Arabidopsis varieties. Simulations demonstrated that using a combination of two simplified SNP sets for identification can effectively increase the fault tolerance in independent validation. In the testing dataset, two potentially mislabeled varieties (ICE169 and Star-8) were identified. For 68 same-named varieties, the identification process achieved 94.97% accuracy and only 30 shared markers on average; for 12 different-named varieties, the germplasm to be tested could be effectively distinguished from 1,134 other varieties while grouping extremely similar varieties (Col-0) together, reflecting their actual genetic relatedness. The results suggest that the DT-PICS provides an efficient and accurate approach to SNP selection in germplasm identification and management, offering strong support for future plant breeding and conservation efforts.

更新日期：2023-05-14

点击分享查看原文

点击收藏

公开下载

阅读更多本刊新发论文