Genetic variation and genome wide association study of cane traits in diverse sugarcane (Saccharum spp.) germplasm

Authors: ELATHER, SHAMSELDEEN - Oak Ridge Institute For Science And Education (ORISE); Destefano, Douglas; ABUASBEH, YASMEEN - Florida Sugar Cane League; SANDHU, HARDEV - Everglades Research And Education Center; Rouse, Matthew; Ali, Gul; Singh, Sukhwinder

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/19/2025
Publication Date: 10/30/2025
Citation: Elather, S., Destefano, D., Abuasbeh, Y., Sandhu, H.S., Rouse, M.N., Ali, G.S., Singh, S. 2025. Genetic variation and genome wide association study of cane traits in diverse sugarcane (Saccharum spp.) germplasm. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2025.1643469.
DOI: https://doi.org/10.3389/fpls.2025.1643469

Interpretive Summary: Sugarcane (Saccharum spp.) is a high-yielding perennial grass cultivated mainly for its sucrose-containing stalks. The stalks are utilized in the production of sugar and bioethanol. As a significant cash crop, sugarcane yields nearly 80% of the world's sugar and a total of 60% of biofuel production. The genus Saccharum consists of several species including S. officinarum, S. spontaneum, S. robustum, S. sinense, and S. barberi. Among them, S. officinarum is a high sugar containing species, while S. spontaneum has donated characters such as disease resistance and tolerance to a broad spectrum of environmental conditions The Cane Presentation System (CPS) measure the quality of sugarcane by ensuring that the harvested product meets the industrial standards required for sugar extraction. Single Nucleotide Polymorphisms (SNPs) have become the marker of choice for mapping and marker-assisted selection (MAS) in sugarcane breeding. This is because they are codominant, have a high frequency, lowering sequencing costs, and efficient SNP genotyping techniques are available Over the last few years, hundreds of genetic loci and single nucleotide polymorphisms (SNPs) related to important agronomic traits in sugarcane have been uncovered using different methods, such as quantitative trait loci (QTL) mapping, gene mapping, and genome-wide association studies (GWAS). The objective of this research was to investigate the genetic diversity of cane quality traits among diverse Saccharum species. Through genome wide association mapping, the study sought to identify alleles associated with high sucrose content, which would be valuable for future marker-assisted selection (MAS) research.

Technical Abstract: This comprehensive study aimed to screen a diverse collection of 397 Saccharum accessions, focusing on identifying the genetic foundations underlying key cane quality characteristics in sugarcane. The research also sought preliminary genome-wide association studies (GWAS) to pinpoint potential quantitative trait loci (QTLs) related to sugar and fiber content in this extensive germplasm. Utilizing the Cane Presentation System (CPS) for cane quality analysis, phenotypic investigations unveiled significant variation in essential traits such as Brix values, polarity, fiber content, and moisture levels across different Saccharum species. Notably, hybrid and Robustum genotypes demonstrated superior agronomic qualities, highlighting their potential for breeding programs. Correlation analysis between traits revealed non-significant relationships, suggesting that independent genetic control mechanisms govern them. The multifaceted approach (three GWAS models: the Generalized Linear Model - GLM), the Mixed Linear Model - MLM, and FarmCPU) identified significant marker-trait associations for key characteristics, including Brix, polarity, moisture, and fiber content. Population structure analysis classified the accessions into three distinct subpopulations, each exhibiting varying degrees of genetic diversity and differentiation. GWAS identified 40 statistically significant SNP markers dispersed across multiple chromosomes (2, 3, 4, 5, 6, 7 and 8). Among these, three markers (AX-171243917-4651; chr 6D, AX-171305424-5045; chr 7B, and AX-171305424-5356; chr7D), consistently correlated with brix content across all analytical models and associated with chromosomes 4, 6 and 7. Additionally, two markers (AX-171287224-1157; chr 2A and AX-171363600-3972; chr 5D) showed strong associations with fiber content. Marker AX-171243917-4651, on chromosome 6D, displayed pleiotropic effects, significantly linked to brix and polarity traits. These findings hold considerable promise for enhancing sugarcane breeding programs. By providing valuable genetic stocks for marker-assisted selection, the results can facilitate the development of cultivars with improved sugar content and processing quality traits, ultimately contributing to the efficiency and productivity of the sugarcane industry.