In silico genome-wide discovery and characterization of SSRs and SNPs in powdery mildew disease resistant and susceptible cultivated and wild Helianthus species

In silico approach was applied for the discovery and characterization of SSRs and SNP markers. RNA sequencing was applied to generate large scale genome-wide transcripts associated with powdery mildew disease of sunflower ( Helianthus annuus L. ). The sunflower materials from which the transcripts were generated comprised one susceptible (PS 2023B), two cultivated resistant accessions (TX16R, ID 25) and three wild species ( H. praecox [1823], H. niveus [1452], and H. debilis [DEB-689]). For the susceptible and resistant accessions, control (no infection) and pooled (with infection) samples were created based on which the transcripts were developed. A total of 123,058 SSRs were discovered from the assembled transcriptome of each accession. Out of this total obtained SSRs, 112,326 were classified as perfect and 10,732 as compound SSRs. The percent contribution of compound SSRs in susceptible and in all the tolerant accessions ranged from 8.51 to 9.15%. There was no prominent or significant difference in the number of SSR motifs, comparing the susceptible and resistant accessions tested. A significantly higher CG motif was observed in the susceptible accessions than in the resistant accessions. We, therefore, speculate that the CG motif might play a vital role in the susceptibility of sunflower to powdery mildew disease. Similarly, the percentage of GC motif was found to be significantly higher in the resistant accessions. It is likely that the GC motifs might be involved in the induction of resistance to powdery mildew in sunflower plants. Trinucleotide motif based predictions resulted in significantly higher levels of the following amino acids in the susceptible accession: Ile, Lys, Met, Phe, Pro, Thr and Val. It is presumed that these amino acids might be involved in the vulnerability to the powdery mildew disease in 2023B. In total 35,390 Single Nucleotide Polymorphisms (SNPs) loci were identified that were distributed on all 17 linkage groups with the average resolution of 443.2 Kb/SNP. Linkage group 10 had the highest localized SNPs (3631) with an average of 576 Kb/ SNP and 7 had least (781) with average of 441 Kb/ SNP. Most of the SNPs identified were observed to be transition mutations with mainly A/G type substitutions. The discovered markers will prove useful after wet laboratory studies for screening and marker assisted breeding for powdery mildew resistance in sunflower.