Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS national plant germplasm system collection using single-dose SNP markers

Authors: Park, Sunchung - Sun; Zhang, Dapeng; Ali, Gul - Shad

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/15/2023
Publication Date: 1/4/2024
Citation: Park, S., Zhang, D., Ali, G.S. 2024. Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS national plant germplasm system collection using single-dose SNP markers. Frontiers in Plant Science. 14.Article 1337736. https://doi.org/10.3389/fpls.2023.1337736.
DOI: https://doi.org/10.3389/fpls.2023.1337736

Interpretive Summary: The USDA National Plant Germplasm System maintains one of the world largest collection of sugarcane and related grasses at the Subtropical Horticulture Research Station, Miami, Florida. This collection is used by researchers and breeders in the U.S.A. and throughout the world for developing improved sugarcane varieties and for conducting genetic, genomic, botanical, agronomic and molecular biology studies. This collection needs maintenance, safety, health and genetic and improved modern germplasm management methods. Towards this goal, in this study the entire germplasm collection was genetically characterized using molecular markers, which has resulted in better management, characterization, distribution of this collection. The findings reported in this study have facilitated planning and conducting experiments aimed at identifying genes and application of latest genomic and phenomic technologies for developing high-yielding sugarcane varieties with high sucrose content.

Technical Abstract: The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, Florida, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum 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 Saccharum 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 Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum 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., ‘Saccharum spp’, ‘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.