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

Abstract

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.

Genetic Diversity of Sugarcane Grassy Shoot (SCGS)-Phytoplasmas Causing Grassy Shoot Disease in India

“…The phylogenetic relationships of SCGS phytoplasma strains to each other and to the most related phytoplasmas were examined, by sequencing both 16S rRNA gene and 16S/23S rRNA spacer region (SR, Rao et al 2008). The phylogenetic relationships of SCGS phytoplasma isolates among themselves and related phytoplasmas based on 16S rRNA gene sequences showed 100% identity/no variation among 16S rRNA gene sequences of 18 isolates.…”

Disease Scenario and Management of Major Sugarcane Diseases in India

“…SCGS and SCWL phytoplasmas shared a 16S rDNA sequence similarity which varied from of 97.5 to 98.8%. Of the phytoplasmas that cluster in other phylogenetic groups, those most closely related to SCGS phytoplasma are the BGWL (='Candidatus Phytoplasma cynodontis') and brachiaria grass white leaf (BraWL) agents, which share 97.3 and 97.1% 16S rDNA sequence similarity, respectively (Rao et al 2008). Nasare et al (2007) have analysed 198 sugarcane plant samples exhibiting grassy shoot symptoms in India tested positive for phytoplasma through PCR amplification of 16S rRNA gene and 16S-23S rRNA SR using primers specific for phytoplasmas and concluded that the sequence homology in the present SCGS-causing phytoplasma in India is more than 99%, and their homology with SCWL and BGWL is from 98 to 99%.…”

“…Nasare et al (2007) have analysed 198 sugarcane plant samples exhibiting grassy shoot symptoms in India tested positive for phytoplasma through PCR amplification of 16S rRNA gene and 16S-23S rRNA SR using primers specific for phytoplasmas and concluded that the sequence homology in the present SCGS-causing phytoplasma in India is more than 99%, and their homology with SCWL and BGWL is from 98 to 99%. Therefore, it can be concluded that SCGS, SCWL, SGS, and BGWL belong to the same species-level taxa (Rao et al 2008). In another study, the phylogenetic relationships of SCGS phytoplasma strains to each other and to the most related phytoplasmas were examined, by sequencing both 16S rRNA gene and 16S/23S rRNA spacer region.…”

Screening of Sugarcane Cultivars Against Colletotrichum Falcatum Causing Red Rot Disease and Its Control With Different Fungicides Under Laboratory Conditions

“…The major reason of common of red rot disease in Pakistan is due to cultivation of susceptible Sugarcane varieties that difficult to incorporate the new sugarcane cultivars with developed agronomic features and resistance to biotic and abiotic stresses (Zamir et al, 2012). Red rot of sugarcane may infect developed stems of cane, leaf mid ribs which results in considerable damages in sugar quality (Rao et al, 2008). The pathogen is setts-borne and inactive mycelia existing in the bud scales are responsible for post-germination and contaminate the freshly developing shoots of cane (Viswanathan and Rao, 2011).…”