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

Increasing the sucrose content of sugarcane, a major sugar crop, is a key 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 study (GWAS) for two important sugarcane traits: sucrose content and stem diameter. Both traits followed a normal distribution and showed typical characteristics of quantitative traits. Population structure analysis revealed four subpopulations with an average genetic distance of 0.236. GWAS of the sucrose content detected 27 SNPs. After annotating genes at or near significant loci, 17 candidate genes were screened. For stem diameter, GWAS 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.