Deciphering the Genetic Basis of Sugar Cane (Saccharum spontaneum L) Root System and Related Traits under Nitrogen Stress through the Integration of Genome-Wide Association Studies and RNA-seq

Nitrogen (N) is an essential element for plant growth and development. Identifying functional gene loci associated with nitrogen absorption and utilization in sugar cane can facilitate the development of nutrient-efficient sugar cane varieties. In this study, sugar cane seedlings were subjected to normal and low nitrogen stress treatments within a hydroponic system for the identification of candidate genes related to six root-associated traits using a diversity population of 297 accessions. A total of 262 single nucleotide polymorphisms were found to be significantly associated with the mutation, including 30 stable or pleiotropic loci. The integration of genome-wide association studies and differential gene analysis from RNA sequencing (RNA-seq) identified five key candidate genes. Overexpression of one of them, ScMYB-CC gene, in Arabidopsis significantly affected root growth and development. In summary, the findings of this study provide valuable genetic resources for the breeding of nitrogen-efficient sugar cane varieties.