Genome-wide association study of sucrose content and stem diameter in sugarcane (Saccharum spp.)

• Sucrose content and stem diameter of 292 sugarcane germplasm resources were determined. • Through genome-wide association analysis, a total of 46 SNPs were found to be associated with phenotypic traits. • Twenty-six candidate genes related to the traits were identified. Increasing the sucrose content of sugarcane, a major sugar crop, is a breeding objective. However, the complex genetic background of sugarcane affects development of sugarcane hybrids. In this study, we sequenced 292 sugarcane germplasm accessions and identified 2,542,965 single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). We performed a genome-wide association analysis of two important sugarcane traits—sucrose content and stem diameter. Both traits conform to a normal distribution and exhibit typical characteristics of quantitative traits. Population structure analysis revealed Four subpopulations with an average genetic distance of 0.236 were identified. Genome-wide association analysis of the sucrose content revealed 27 SNPs. After annotating genes at or near significant loci, 17 candidate genes were screened. For stem diameter, genome-wide association analysis revealed 19 SNPs, from which 9 candidate genes were identified. These results improve our understanding of genetic mechanisms affecting sucrose content in sugarcane, and identify important genetic resources to accelerate breeding of new sugarcane varieties with high sucrose content.