Sugarcane Grassy Shoot Research Articles

First Report of a 'Candidatus Phytoplasma sacchari'-Related Strain Associated with Yellowing and Decline of Silver Bluestem in Texas, U.S.A.

Silver bluestem [Bothriochloa laguroides (DC.) Herter] is a warm-season grass native to Texas. This perennial grass plays a crucial role in maintaining ecological balance and supporting wildlife in the region. In September 2022, while investigating the ecological impact of invasive grass species on a grassland located near Pipe Creek (TX), B. laguroides plants were observed showing symptoms that included yellowing of the blades and occasionally brown discoloration of the midveins and stems (Fig. S1). Disease incidence was estimated as 2% of silver bluestem plants in the 2 hectares surveyed. To investigate the possibility of a phytoplasma association with the symptoms, four symptomatic and four asymptomatic leaf samples were collected for further study. Total DNA was extracted from leaf midribs using a DNeasy Plant Mini Kit (Qiagen). The DNA extracts were tested using a phytoplasma-specific quantitative PCR assay (Hodgetts et al. 2009), which identified two out of the four symptomatic B. laguroides samples as positive for phytoplasmas. A semi-nested PCR assay for amplification of the 16S rRNA gene fragment was then performed on these samples with primers P1/16S-SR followed by P1A/16S-SR (Deng, and Hiruki 1991; Lee et al. 2004), and two additional housekeeping genes (tuf and secA) were amplified as previously described (Makarova et al. 2012; Hodgetts et al. 2008; Bekele et al. 2011). All amplicons of the expected size, 1.5 kb (16S rRNA), 0.4 kb (tuf) and 0.6 kb (secA), were purified and bi-directionally sequenced using primers from each gene second round PCR amplification. Analysis of the sequences derived from the three gene fragments revealed no variation between the two plant samples and confirmed they originated from a phytoplasma, termed strain TXSB-2 (Texas Silver Bluestem). Sequences from a single B. laguroides plant DNA extract were deposited in GenBank with accession numbers OR711913 (16S rRNA), OR709687 (tuf) and OR709688 (secA). A BLAST search of the 16S rRNA gene sequence from TXSB-2 against the NCBI nucleotide database, showed 99.58% sequence identity with an unclassified phytoplasma clone 139-1 from a leafhopper collected in Australia (MW281491) (Fig. S2). The partial nucleotide sequence of the tuf and secA genes showed 90.60% and 89.78% similarity, respectively, to the corresponding genes in 'Ca. P. sacchari' strain SCWL1 (CP115156) associated with sugarcane in China. The iPhyClassifier, an interactive online tool for phytoplasma identification and classification (Zhao et al. 2009), was used to determine the 'Candidatus Phytoplasma' species affiliation and group/subgroup classification status of this phytoplasma strain. The result showed that the TXSB-2 16S rDNA shared 98.94% sequence identity with that of the 'Ca. P. sacchari' reference strain (GenBank accession: MN889545), indicating TXSB-2 is a 'Ca. P. sacchari'-related strain. The result from virtual restriction fragment length polymorphism (RFLP) analysis of the 16S rDNA F2nR2 fragment revealed that TXSB-2 possessed a collective RFLP pattern that is distinct from the reference patterns of all established phytoplasma ribosomal subgroups and is proposed as the representative strain of a new subgroup designated as 16SrXI-H. 'Candidatus Phytoplasma sacchari' has been reported associated with sugarcane grassy shoot disease, which is considered among the most damaging diseases of sugarcane across parts of Southeast Asia and India (Kirdat et al. 2021). The same phytoplasma was recently confirmed infecting sorghum in India (Nithya et al. 2024). To our knowledge, this is the first report of a 'Ca. P. sacchari'-related strain infecting B. laguroides in the United States. Moreover, B. laguroides is a new host for strains related to 'Ca. P. sacchari'. Further investigation is required to elucidate the prevalence of this disease in the area, its natural vectors, and the potential consequences arising from this novel phytoplasma strain within its ecosystem in Texas.

A Fractional Order Approach in the Eco-epidemiological Model of Sugarcane Grassy Shoot Disease Using Controls

A Fractional Order Approach in the Eco-epidemiological Model of Sugarcane Grassy Shoot Disease Using Controls

Micro structuring and host tissue patterning of sugarcane grassy shoot phytoplasma through scanning electron microscopy

Micro structuring and host tissue patterning of sugarcane grassy shoot phytoplasma through scanning electron microscopy

Natural infection of Ca. Phytoplasma sacchari causing sugarcane grassy shoot disease in Sorghum bicolor

Natural infection of Ca. Phytoplasma sacchari causing sugarcane grassy shoot disease in Sorghum bicolor

Complete genome sequence of "Candidatus Phytoplasma sacchari" obtained using a filter-based DNA enrichment method and Nanopore sequencing.

Phytoplasmas are phloem-limited plant pathogens, such as sugarcane white leaf (SCWL) phytoplasma, which are responsible for heavy economic losses to the sugarcane industry. Characterization of phytoplasmas has been limited because they cannot be cultured in vitro. However, with the advent of genome sequencing, different aspects of phytoplasmas are being investigated. In this study, we developed a DNA enrichment method for sugarcane white leaf (SCWL) phytoplasma, evaluated the effect of DNA enrichment via Illumina sequencing technologies, and utilized Illumina and Nanopore sequencing technologies to obtain the complete genome sequence of the "Candidatus Phytoplasma sacchari" isolate SCWL1 that is associated with sugarcane white leaf in China. Illumina sequencing analysis elucidated that only 1.21% of the sequencing reads from total leaf DNA were mapped to the SCWL1 genome, whereas 40.97% of the sequencing reads from the enriched DNA were mapped to the SCWL1 genome. The genome of isolate SCWL1 consists of a 538,951 bp and 2976 bp long circular chromosome and plasmid, respectively. We identified 459 protein-encoding genes, 2 complete 5S-23S-16S rRNA gene operons, 27 tRNA genes, and an incomplete potential mobile unit (PMU) in the circular chromosome. Phylogenetic analyses and average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values based on the sequenced genome revealed that SCWL phytoplasma and sugarcane grassy shoot (SCGS) phytoplasma belonged to the same phytoplasma species. This study provides a genomic DNA enrichment method for phytoplasma sequencing. Moreover, we report the first complete genome of a "Ca. Phytoplasma sacchari" isolate, thus contributing to future studies on the evolutionary relationships and pathogenic mechanisms of "Ca. Phytoplasma sacchari" isolates.

Studies on yield and quality of sugarcane affected by mixed infection of sugarcane grassy shoot and sugarcane yellow leaf diseases

Studies on yield and quality of sugarcane affected by mixed infection of sugarcane grassy shoot and sugarcane yellow leaf diseases

Production of sugarcane grassy shoot disease free setts by using hot water treatment

Production of sugarcane grassy shoot disease free setts by using hot water treatment

Sugarcane grassy shoot phytoplasma (grassy shoot of sugarcane)

Sugarcane grassy shoot phytoplasma (grassy shoot of sugarcane)

Our understanding about phytoplasma research scenario in India

Since the first report of existence of phytoplasma disease in 1874 in India, now more than 172 plant species are reported to be the host of ten different groups of phytoplasmas. The phytoplasma diseases are well documented from all parts of the country and aster yellows group (16SrI) is the most prevalent and widespread group followed by 16SrII, 16SrVI, 16SrXI and 16SrXIV groups. Sesame phyllody, brinjal little leaf, sugarcane grassy shoot, sandal spike, coconut root wilt, areca nut yellow leaf and many ornamentals and vegetables maladies are the major phytoplasma threats in India causing serious economic losses every year. Nearly a dozen of leafhopper and planthopper species have been identified as natural vectors and more than 40 weed species have been identified as natural reservoirs of different phytoplasma strains. A large number of new phytoplasma strains on several crops have been characterized in India during last decade, which revealed that phytoplasmas are more diverse than the earlier thought. Very recently two draft genome sequences of 16SrXI (sugarcane grassy shoot) and 16SrXIV (Bermudagrass white leaf disease) have been submitted from India which open-ups the possibilities of studies on functional genomics. Mixed infections of phytoplasmas and viruses have also emerged as serious problems in several crops and are responsible for more synergistic losses. Nested PCR assays have been routinely employed to detect phytoplasma strains in symptomatic plants and insect vectors by utilizing 16S rRNA, 16Sr-23S rRNA spacer region and several multilocus gene specific primers. However, new developed isothermal amplifications methods (LAMP and RPAs) for sensitive and quick detection of phytoplasmas need to be explored for easier identification of phytoplasma strains. Multiplex PCR system has also been developed to detect the phytoplasma utilizing nested PCR primers and multilocus gene specific primers in one PCR cycle. Very little attempt has been made to study metabolic interaction in phytoplasma hosts and insects in India. However, some efforts in last decade has been made to elucidate the host responses at biochemical, genomics, proteomics and metabolomic levels for understanding the host–pathogen interactions but still more concentrated efforts need to be explored that will help to formulate strategies for controlling phytoplasma diseases. Presently the suggested effective management practices in India are: pruning infected portions, growing resistant varieties, heat therapy, use of tertracycline, control of insect vectors and natural host reservoirs. However, none of them have completely proved successful. Future approach on epidemiology, resistance, host-pathogen-insect interaction, full genome sequencing of major phytoplasma strains and RNA interference needs to be focussed in India for a better understanding and management of these peculiar microbial pathogens.

Survey, Symptomatology and Incidence of Sugarcane Phytoplasma in Uttar Pradesh, India

Sugarcane grassy shoot diseases (SCGS) caused by phytoplasma is one of the major sugarcane diseases which is responsible for qualitative and quantitative losses. An extensive survey of 13 districts of central, western and eastern Uttar Pradesh were done during 2013-2017 crops session. The disease incidence were varied from 1-63% and the maximum incidence was recorded in western U P followed by eastern and central UP. Total twenty four varieties were observed during survey and the most prominent symptoms were white leaf, and stunting. The present study indicate the wide occurrence of SCGS in almost all the commercial sugarcane varieties grown in various part of UP.

'Candidatus Phytoplasma sacchari', a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease.

Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with 'Ca. Phytoplasma cynodontis' strain BGWL-C1 followed by 97.65 % similarity with 'Ca. P. oryzae' strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to 'Ca. P. cynodontis', were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22. Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon 'Candidatus Phytoplasma sacchari' is proposed.

Phytoplasmal diseases in India and its management

Phytoplasmas are phloem-limited pleomorphic bacteria which lacks the cell wall, mainly transmitted through leafhoppers but also by plant propagation materials and seeds. In India evidences showed that phytoplasma have been found associated with 129 plant species including Cereals, vegetables, fruits, trees, ornamental, sugarcane, grasses and weeds which is increasing at alarming rate. Sesame phyllody, brinjal little leaf, sugarcane grassy shoot, sandal spike, coconut root wilt, areca nut yellow leaf and many diseases in ornamental plants which causes the most severe economic losses in India. In earlier days, very few phytoplasma diseases were identified in India merely based on the bright-field, fluorescence, electron microscope observations, tetracycline treatment and to a lesser extent by serological assays. Recently detection of phytoplasma based on molecular methods including nested PCR assays are efficiently carried out and on that basis several plant species are reported to have phytoplasma infections. Identified phytoplasmas are related to ‘Candidatus Phytoplasma asteris’, ‘Ca. P. pruni’, ‘Ca. P. ziziphi’, ‘Ca. P. trifolii’, ‘Ca. P. solani’, ‘Ca. P. cynodontis’, ‘Ca. P. oryzae’, ‘Ca. P. phoenicium’, ‘Ca. P. australasia’ and ‘Ca. P. pini’. At present the suggested effective management practices in India includes growing resistant varieties, control of insect vectors, weed species as alternative hosts and use of healthy planting materials. It is moreover essential to understand the molecular basis of phytoplasma-vector interaction and other factors involved in disease development in order to reduce the outbreak of phytoplasma. In this chapter, we have discussed overall progress on phytoplasma disease on plant species in India in terms of detection, transmission and management of phytoplasma.

Mixed Infection of Sugarcane Yellow Leaf Virus and Grassy Shoot Phytoplasma in Yellow Leaf Affected Indian Sugarcane Cultivars.

Sugarcane is an important sugar crop contributes more than 80% of world sugar production. Mosaic, leaf fleck, and yellow leaf (YL) are the major viral diseases affecting sugarcane, amongst YL occurrence is widely reported in all the sugarcane growing countries. It is caused by Sugarcane yellow leaf virus (SCYLV) and detailed works were done on complete genome characterization, transmission, and management. However, in countries like Egypt, South Africa, Cuba, Mauritius and Hawaii, the disease was reported to the cause of sugarcane yellow leaf phytoplasma (SCYP) and/or SCYLV as single/combined infections. Hence, we have investigated in detail to identify the exact Candidatus phytoplasma taxon associated in Indian cultivars affected with YL. The sequencing results and the restriction fragment length polymorphism pattern of the PCR products using the universal phytoplasma primers confirmed presence of sugarcane grassy shoot (SCGS) phytoplasma (16SrXI group) in the YL-affected plants. Mixed infection of SCYLV and SCGS phytoplasma was estimated as 32.8% in YL affected plants. Evolutionary genetic relationship between SCYP and SCGS phytoplasma representatively taken from different countries showed that SCYP from South Africa and Cuba were diverged from others and had a highest similarity with SCGS phytoplasma. Although we wanted to identify SCYP from YL affected Indian sugarcane cultivars, the study clearly indicated a clear absence of SCYP in YL affected plants and we found SCYLV as the primary cause for the disease.

Draft Genome Sequences of Two Phytoplasma Strains Associated with Sugarcane Grassy Shoot (SCGS) and Bermuda Grass White Leaf (BGWL) Diseases

We performed whole-genome sequencing of two phytoplasmas associated with sugarcane grassy shoot (SCGS) and Bermuda grass white leaf diseases. These are the first draft genomes of SCGS phytoplasma (strain SCGS) and 'Candidatus Phytoplasma cynodontis' (strain LW01) and may help to delineate these phytoplasmas at a finer taxonomic level.

Grassy shoot: The destructive disease of sugarcane

Sugarcane is one of the important commercial cash crops grown widely for sugar production. Red rot, smut, wilt, grassy shoot and yellow leaf are the major diseases of sugarcane worldwide; however the sugarcane grassy shoot (SCGS) is considered the most destructive one due to the associated total loss of millable canes production. Although the crop is cultivated in tropical and sub-tropical regions across the globe, widespread occurrence of the disease is mostly reported only from South and South East Asian countries. The disease was first reported in India in 1949. Based on its symptomatology, it is known as grassy shoot in India, Pakistan, and white leaf in Thailand, Vietnam, Myanmar, China and known by both names in Sri Lanka. The past seven decades witnessed several research advancements in symptomatology recognition, diagnosis and management of this disease. The nested PCR based diagnostic approach initiatives taken during 1990s followed by the in silico virtual RFLP analyses development in the period of 2007–2009 revolutionized the molecular characterization of the pathogen based on the variability analyses which resulted in the description of reports of many phytoplasma strains infecting sugarcane. Several phloem sap feeding leafhoppers such as Deltocephalus vulgaris, Cofana unimaculata, Exitianus indicus and Maiestas portica in India, Matsumuratettix hiroglyphicus and Yamatotettix flavovittatus in Thailand and D. menoni in Sri Lanka were reported as insect vectors during the last ten years. The recent use of next generation sequencing technologies helped to sequence whole genome of the SCGS phytoplasma. Currently, heat therapy and pathogen elimination through meristem tissue culture based seedling production are the only available management techniques to prevent the disease spread into new areas. Despite the fast pace of research in pathogen detection and genomics, the research on disease management under field conditions still remain grey and pose challenges to sugarcane pathologists.

Emerging incidence and diversity analysis of sugarcane grassy shoot phytoplasma in western Uttar Pradesh, India

Emerging incidence and diversity analysis of sugarcane grassy shoot phytoplasma in western Uttar Pradesh, India

First Report of Sugarcane Grassy Shoot Phytoplasma (16SrXI) Associated with Little Leaf Disease of Chrysopogon zizanioides from India

First Report of Sugarcane Grassy Shoot Phytoplasma (16SrXI) Associated with Little Leaf Disease of <i>Chrysopogon zizanioides</i> from India

Immunological detection of the Weligama coconut leaf wilt disease associated phytoplasma: Development and validation of a polyclonal antibody based indirect ELISA.

Weligama coconut leaf wilt disease (WCLWD) causes heavy losses in the coconut cultivations of southern Sri Lanka. The in-house developed and validated indirect ELISA was based on specific polyclonal antibodies raised in female New Zealand White rabbits, against partially purified WCLWD associated phytoplasma. This ELISA has the potential to distinguish secA PCR confirmed, WCLWD associated phytoplasma positive palms from phytoplasma free palms at high accuracy (93%) and sensitivity (92.7%), but with marginal specificity (79%). The calculated ELISA cross reactivity index (CRI) values were low for sugarcane white leaf (7%) and sugarcane grassy shoot (8%) infected leaves, but with marked highCRIfor both Bermuda grass white leaf (69%) and areca nut yellow leaf (70%) infected leaves. SecA gene based phylogenetic relationships of the WCLWD associated phytoplasma with these other locally prevalent phytoplasma strains elucidated this immunological cross reactivity, which was further reiterated by virtual restriction fragment length polymorphism analysis. Based on scanning electron microscopy, this study provides additional visual evidence, for the presence of phytoplasmas in WCLWD infected tissues.

Incidence, symptomatology and transmission of sugarcane grassy shootdisease in Assam, India

A roving survey was conducted during 2015 and 2016 to study the incidence, symptomatology and transmission of sugarcane grassy shoot (SCGS) disease in the sugarcane growing areas of four districts of Assam, viz. Biswanath, Golaghat, Sonitpur, and Nagoan. Major symptoms observed in the fields were the production of narrow and chlorotic leaves ranging from pale yellow to completely white color, the development of chlorotic streaks in leaves, unproductive tiller proliferation and the bushy appearance of the infected stool, with thin and non millable canes with short internodes. The average disease incidence ranged from 10-22%. The transmission of the disease was attempted by different methods. Out of five predominant leafhopper species (Cofana unimaculata, Exitianus indicus, Hishimonus phycitis, Nephotettix nigropictus, Orosius albicinctus) collected and identified from the sugarcane fields, in all the four districts, only E. indicus was successful in transmitting the SCGS disease. The disease was also transmitted by the setts collected from sugarcane grassy shoot symptomatic canes and by dodder.

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

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