Characterisation of alleles of the sucrose phosphate synthase gene family in sugarcane and their association with sugar-related traits

Abstract

Sucrose phosphate synthase (SPS) is a key enzyme in the production of sucrose. Five SPS gene families have been identified in monocotyledonous plants including sugarcane. Using SPS family-specific primers to four of the five families (we had previously characterised the fifth gene family), an approximately 400-nt region was amplified from the parents of a sugarcane mapping population, namely the cultivar Q165 and a S. officinarum line IJ76-514. Alignment of the sequences from both parents suggested from one to three genes per SPS gene family, with variable numbers of alleles per gene. Single-dose (SD) single-nucleotide polymorphisms (SNPs) were identified in at least one allele from each SPS gene family and mapped in Q165. For gene families SPS I–IV, SNPs from different alleles in each gene family mapped to different linkage groups within the same homology group (HG), suggesting a single gene per gene family, or multiple genes at a single locus. These map locations were syntenic with SPS gene family locations in sorghum. Two SNPs from different alleles in gene family SPS V were mapped to two different HGs, suggesting two genes in this family; one of the map locations was syntenic with the location of SPS V in sorghum. QTL analysis for sugar-related traits was undertaken with the SD and double-dose SNP markers. SNPs from SPS gene family IV were strongly associated with sugar-related traits, while SNPs from other gene families were associated with agronomic traits, such as stalk weight, diameter, and number. This study provides insight into the evolution of this important polyploid crop as well as highlights the importance of this gene family to sugar production in sugarcane.