Genetic diversity of phytoplasmas associated with sugarcane grassyshoot and leaf yellows diseases in India

Phytoplasma infection drastically damages the growth of sugarcane crops affecting their commercial value. Sugarcane grassy shoot (SCGS) and sugarcane leaf yellows (SCLY) are the major diseases of sugarcane associated with the phytoplasma presence. During the survey of sugarcane fields across eleven major sugarcane growing states of India viz., Uttarakhand, Uttar Pradesh, Tamil Nadu, Andhra Pradesh, Karnataka, Maharashtra, Punjab, Bihar, Chhattisgarh, Haryana and Assam from the year 2013 to 2015, symptoms including profuse tillering, internode shortening, stunted growth, chlorotic leaves midrib and lamina yellowing were recorded in 48 commercial sugarcane varieties. Out of a total 109 sugarcane leaf samples collected, the phytoplasma presence was confirmed in 82 SCGS and 4 SCLY symptomatic samples by nested PCR assays using the phytoplasma 16S rRNA gene-specific universal primer pairs, P1/P7 and R16F2n/R16R2. Association of 16SrXI-B (in 79 samples) and a 16SrXI-F (in 3 samples) subgroups of phytoplasmas was detected. The presence of 16SrI-B subgroup was confirmed in only 4 SCLY symptomatic samples from Haryana and Uttar Pradesh. Besides the 16S rRNA gene, the secA gene was also used to detect sugarcane phytoplasmas presence in SCGS and SCLY symptomatic samples. The secA gene sequences also confirmed the finding of 16S rRNA gene-based classification results.