Identification and validation of simple sequence repeats markers in Tilletia indica and compatibility assay of monosporidial lines

Tilletia indica is a floret infecting fungal pathogen of wheat inciting Karnal bunt disease of wheat. Simple sequence repeats are widely used to uncover the population structures in fungi. In present study, a total of 5,772 simple sequence repeat loci were identified in the T . indica genome. In silico analysis, forty microsatellite markers were used to genotype of 20 T. indica isolates collected from north-western plains zone of India. Among SSRs, tri-nucleotide was most abundant (42%), followed by di-nucleotide (28%), mono-nucleotide (23%), tetra-nucleotide (3%), hexa-nucleotide (3%) and penta-nucleotide (1%). In PCR analysis, 130 alleles were amplified in 20 isolates of T . indica using 40 SSR markers. The polymorphic information value content (PIC) values ranged from 0.20 to 0.81 with an average of 0.51. The maximum PIC (0.81) was obtained for TiSSR34 marker. 18 SSR markers were highly informative (PIC ≥ 0.5), 15 SSRs were moderately informative (0.5 > PIC