Association mapping of sugar related traits in sugarcane (Saccharum spp.)

Sucrose content is a highly desirable traits in sugarcane. Increasing sugar yield is an important objective of sugarcane breeding programs worldwide. Candidate gene association mapping could be a better alternative to identify molecular markers associated with desirable traits in sugarcane. In the first study, marker-trait associations (MTAs) were evaluated for four sugar-related traits, total soluble solids (Brix), sucrose content (Pol), commercial cane sugar (CCS), and Fiber on 160 sugarcane accessions using intron length polymorphisms (ILPs). ILPs were developed from candidate genes involving in sucrose metabolism using in-house transcriptomic and proteomic data. From the gene-based markers, 112 ILP markers from 88 genes yielded 249 alleles, with an average of 2.22 alleles per locus. The polymorphism information content (PIC) ranged from 0.11 to 0.37, with an average of 0.30. A STRUCTURE analysis revealed two subpopulations. Using the Fixed and random model Circulating Probability Unification (FarmCPU) model, a total of 12 significant (P < 0.01) marker-traits associations were identified for all sugar-related traits. After multiple comparisons adjustments, the plant U-box marker was strongly associated with Brix, explaining 7.73% of the phenotypic variance. The second study, 109 candidate genes obtained from the starch and sucrose metabolism pathway, cDNA microarrays, transcriptome and proteome were used to identify single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) in 120 sugarcane accessions using multiplex PCR targeted amplicon sequencing. After filtering, 170 SNPs and 68 InDels from 38 genes was used for candidate gene association mapping with sugar-related traits. FarmPCU model also showed a better effect to reduce the false positives than the other models. When multiple comparisons adjustments were performed, favorable alleles of the candidate genes involved in signaling and transcriptional regulation were associated with CCS and Fiber, and explaining 12.21 and 10.83% of the phenotypic variance, respectively. Knowledge gained from this study may contribute towards marker-assisted selection in sugarcane breeding.