Detection of sugarcane grassy shoot phytoplasma infecting sugarcane in India and its phylogenetic relationships to closely related phytoplasmas

In several sugarcane-growing areas of India, sugarcane plants showing typical symptoms of sugarcane grassy shoot (SCGS) disease as well as non-symptomatic sugarcane plants and sugarcane with non-specific yellowing and stunting symptoms were examined for phytoplasmal infections by means of polymerase chain reaction (PCR) technology, using primers directed to phytoplasma ribosomal DNA (rDNA) sequences. From all field-collected, symptomatic sugarcane plants and those with non-specific symptoms as well as from most the non-symptomatic plants, detectable PCR products were obtained through the highly sensitive nested-PCR assays. Also, the phylogenetic relationships of SCGS phytoplasma strains including those whose rDNA sequences were determined in this study, to each other and to other closely related phytoplasmas, at both 16S rRNA gene and 16S/23S rDNA spacer region sequence levels were examined. The SCGS phytoplasma is a member of the rice yellow dwarf (RYD) phytoplasma group or 16SrXI group, and proved very closely related to the sugarcane with leaf (SCWL) agent. More distantly related to the SCGS agent, are sorghum grassy shoot (SGS), Bermuda grass white leaf (BGWL) (=‘Candidatus Phytoplasma cynodontis’) and RYD (= ‘Candidatus Phytoplasma oryzae’) phytoplasmas. The extensive survey of phytoplasmal infections in sugarcane plants in India as well as analysis of phylogenetic relationships of SCGS phytoplasma strains to each other and to other closely related phytoplasmas, at both 16S rRNA gene and 16S/23S rDNA spacer region sequence levels, had previously not been known.