Andorf Carson M, Ross-Ibarra Jeffrey, Seetharam Arun S, Hufford Matthew B, Woodhouse Margaret R
USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.
Department of Computer Science, Iowa State University, Ames, IA 50011, USA.
G3 (Bethesda). 2025 Feb 5;15(2). doi: 10.1093/g3journal/jkae281.
Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0's broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.
获取和分析玉米核苷酸多样性的工作在范围上差异很大，但这些工作中使用的参考基因组版本和软件算法的差异阻碍了比较，而且这些数据通常无法在易于使用的可视化平台中获取，以便快速访问和分析。为了解决这些问题，玉米遗传学和基因组学数据库与玉米研究人员合作，通过针对B73参考基因组第5版的标准化变异检测流程，提供来自1498个自交系、传统品种和大刍草的不同数据集的变异数据。对输出结果进行了映射质量、完整性和连锁不平衡方面的筛选，并根据相对于B73 RefGen_v5基因注释的变异效应进行注释。玉米遗传学数据库还更新了一个网络工具SNPversity 2.0，以根据感兴趣的基因组位置和种质筛选、可视化和下载基因型集，并添加了外部数据集以展示SNPversity 2.0的广泛用途。随着更多重测序数据的获得，玉米遗传学数据库计划每年更新这些资源，并计划将范围扩大到所有公开可用的序列数据。
