Park Sunchung, Zhang Dapeng, Ali Gul Shad
Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States.
Subtropical Horticulture Research Station, United States Department of Agriculture, Agriculture Research Service, Miami, FL, United States.
Front Plant Sci. 2024 Jan 4;14:1337736. doi: 10.3389/fpls.2023.1337736. eCollection 2023.
The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the germplasm into five clusters, corresponding to and . An assignment test, based on the five species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., '', 'unknown', and 'hybrid'). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor-joining clustering analysis. Analysis of Molecular Variance revealed that within-species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement.
位于佛罗里达州迈阿密的美国农业部农业研究局所保存的世界甘蔗及相关禾本科植物种质库，是世界上最大的甘蔗种质资源库之一。然而，该种质库中甘蔗属种质的遗传完整性尚未得到充分分析。在本研究中，我们使用单剂量SNP面板对901份甘蔗种质进行基因分型，这些种质代表了6个甘蔗物种及各种杂交种。我们的分析发现该种质库中克隆标签错误率很高。具体而言，我们鉴定出86组重复样本，其特征是具有相同的SNP基因型，涵盖211份种质（占总克隆数的23%），而135组，共471个克隆（占总数的52%）表现出近乎相同的基因型。此外，还检测到27个同名组，它们共享相同的克隆名称但SNP基因型不同。群体结构的层次分析将甘蔗种质划分为五个簇，对应于不同的物种。基于这五个物种的分配测试能够纠正141例错误标记的物种归属和不准确信息。此外，我们还澄清了298个具有模糊护照记录（如“ ”、“未知”和“杂交种”）的克隆的物种归属和亲本关系。主坐标分析和邻接聚类分析进一步支持了这五个物种的群体结构和遗传多样性。分子方差分析表明，种内遗传变异占总分子方差的85%，其余15%归因于种间遗传变异。本研究开发的单剂量SNP标记为全球甘蔗种质的鉴定提供了一个强大的工具。这些发现对甘蔗基因库管理、种质交换和作物遗传改良具有重要意义。
