Molecular characterization and genetic diversity of sugarcane phytoplasmas and their natural reservoirs

Abstract

During survey of sugarcane fields across 11 major sugarcane growing states of India, Presence of phytoplasmas was confirmed in 82 SCGS and 4 SCLY symptomatic sugarcane samples by nested PCR assays using phytoplasma 16S rRNA gene specific universal primer pairs. Association of 16SrXIB and 16SrXIF subgroups of phytoplasmas was confirmed with 79 and 3 SCGS symptomatic samples, respectively through sequence comparison and in silico RFLP analysis. However, association of 16SrIB subgroup phytoplasma was confirmed with SCLY symptomatic samples from Haryana and Uttar Pradesh. Fifteen different weed species grown in and around sugarcane fields showing phytoplasma suspected symptoms of little leaf, leaf yellows, chlorotic leaves, witches broom symptoms, were assessed for their role as alternative hosts and source of secondary spread of phytoplasmas in nature. Out of 9 phytoplasma positive weed species, six Cynodon dactylon, Digitaria ciliaris, Eleusine indica, Dicanthium annulatum, Cannabis sativa and Digitaria sanguinalis belonged to 16SrXIVA subgroup, two Parthenium hysterophorus and Oplismenus burmannii belonged to 16SrIID subgroup whereas Phalaris minor belonged to 16SrIB subgroup. Association of C. sativa with 16SrXIVA subgroup, P. hysterophorus and O. burmannii with 16SrIID and P. minor with 16SrIB subgroup are the new reports. Leafhopper species feeding in sugarcane fields were studied for their role in natural transmission of sugarcane phytoplasmas. Leafhopper species Cofana unimaculata, Maiestas portica and Exitianus indicus confirmed associated with 16SrXIB subgroup phytoplasma whereas E. indicus was also confirmed as a host of 16SrXIVA subgroup phytoplasma in natural condition. Besides 16S rRNA gene, secA gene was also evaluated for its potentiality to identify and characterize phytoplasmas. Hence, the present study also confirmed the utility of secA gene sequence in identification and characterization of phytoplasmas belonging to 16SrXIB subgroup. newline newline newline