TRAP and SRAP molecular marker based profiling of radiation induced mutants of sugarcane (Saccharum officinarum L.)

Genetic variability is the mainstay for crop improvement programmes which includes generation of mutational repository, their selection and study of associated genetic diversity. Molecular marker profiling using 57 markers, comprising of 27 TRAP and 30 SRAP markers was carried out to validate the extent of genetic variability in the gamma ray-induced sugarcane mutants. Collectively these markers produced 260 PCR amplicons among which 147 were polymorphic (56.54%). The TRAP marker based analysis showed that the mutants AKTS-01 and AKTS-16 were more diverse (GS = 94 and 92%, respectively) than rest of the mutants. The polymorphic information content (PIC) based on TRAP marker analysis ranged from 0.0 to 0.22 (average 0.11), while 11 combinations showed a PIC ≥ 0.17. The resolving power (Rp) of TRAP analysis ranged from 0.0 to 6.18 (average 1.70). However, the SRAP marker based analysis showed minimum diversity between parent cultivar CoC-671 and high sugar mutant AKTS-02 (GS > 99%), followed by fairly good divergence (GS = 96%) among the mutants AKTS-01, AKTS-08, AKTS-11, AKTS-19 and AKTS-20; along with maximum divergence (GS = 91%) was shown by AKTS-06, AKTS-13 and AKTS-16. The PIC values for SRAP marker based analysis ranged from 0.0 to 0.39 (average 0.10), while 9 combinations showed a PIC ≥ 0.17 with Rp values in the range of 0.0 to 3.45 (average 0.82). The low sugar check genotype had the least similarity with high sugar cultivar CoC-671 and its induced mutants (GS in range of 40 to 60%). Nucleotide sequencing and in silico analysis of two polymorphic amplicons generated using SRAP markers showed homology with chloroplastic ATP synthase CF1 alpha chain and gypsy-like retrotransposon element. In silico analysis revealed homology of the retrotransposon sequence with flanking regions of mobile elements in close vicinity to the serine hydroxy methyltransferase (SHMT) coding region. In summary, our results suggest, for the first time, the application of TRAP and SRAP based markers for the characterization of the mutant germplasm developed through radiation induced mutagenesis in sugarcane.