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Not AvailableYellowing of leaf midrib, its extending to adjoining lamina and necrosis of discoloured tissues from the tip portion are the common yellow leaf (YL) symptoms observed in tropical climatic conditions in India. As symptoms of this disease vary among the varieties, the progress of these symptoms was studied in Coimbatore from disease free status in the plant, using a newly devised YL 0-5 disease severity scale. Progress of recovery of symptoms in symptomatic leaves was monitored with a 0-4 symptom severity scale for four seasons. Detailed observations with ten symptomatic varieties have very clearly indicated a clear variation in symptom expression among them. First symptoms were recorded in leaf 1 and 2 in few plants of the cvs CoPant 84211 and B38192. Apart from yellow discoloration of midrib, reddish discoloration, pinkish midrib and laminar discoloration were recorded in cvs B38192, Co 86010 and Co 85019, respectively. Progress of laminar discoloration on both sides parallel to the midrib varied from ~0.5 to 3.0 cm in different varieties. Apart from severe laminar discoloration progressive leaf drying from the tip region along the midrib towards leaf base and bunching of leaves in the crown were identified as the severe form of disease in sugarcane varieties. For such leaf drying with characteristic pattern of ‘V’ or ‘Y’ shape and in a bunchy top, leaf yellowing was recorded up to -7th leaf and drying was recorded up to -1st leaf in severe YL-affected variety B38192. Progressive increase in disease symptom was noticed in most of the varieties till nine months after planting and later a fluctuation in disease expression was noticed among the varieties. Subsequently decrease of yellowing was observed leaving behind the dried laminar region at the tip. The correlation and regression analyses with meteorological parameters established that ~ 50 % of variability in disease severity grades is explained by minimum temperature and relative humidity in the afternoon. This study on the disease symptomology has clearly revealed variation in YL symptom expressions among the varieties and impact of prevailing weather factors on the fluctuation of disease expressions.Not Availabl

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Not AvailableThe Potyviridae family is one of the largest and economically most significant families of plant viruses, owing to their effects on crops globally. Sugarcane streak mosaic virus (SCSMV), a member of the genus Poacevirus, of this family, an important viral pathogen affects the sugarcane production in India. The genome has a single open reading frame that is translated in to a large polypeptide and consequently cleaved into functional proteins. This virus causes mosaic of sugarcane along with the Sugarcane mosaic virus (SCMV) which is a serious disease causing varietal degeneration reported from India in 1999 and later has been reported from geographically different Asian countries. The coding region for P1 peptidase is located at the very beginning of the viral genome of the family Potyviridae. P1 was thought of as serine peptidase with RNA-binding activity and with possible influence in cell-to-cell viral spreading. In order to unveil its mechanism of evolution we initiated the study by characterizing 10 P1 gene of Indian isolates and the sequences were compared with previously reported SCSMV isolates from different countries. Comparison of all of the sequenced virus isolates revealed a high level of diversity in the P1 gene (83–98% nt sequence identity; 87–100% aa sequence identity), and the Indian isolates were found to be the most divergent (up to 9% variation at the amino acid level). Phylogenetic analysis revealed clustering of 17 SCSMV isolates into two groups. Group I included isolates from India (except SCSMV-TPT) and Pakistan, and group II consisted of isolates from Japan, Indonesia, Thailand and SCSMV-TPT. The results obtained from phylogenetic study were further supported with the SNPs (single nucleotide polymorphism), INDELs (insertion and deletion) and evolutionary distance analysis. A significant proportion of recombination sites were found at the N terminal region of P1 gene of Indian isolates. Analysis of selection pressure indicated that the P1 gene of Indian SCSMV isolates is under strong negative selection. It is likely that recombination, along with strong negative selection, enhances the speed of elimination of lethal mutations in the P1 gene of Indian SCSMV isolates.Not Availabl

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Not AvailableSugarcane streak mosaic virus (SCSMV), a member of the genus Poacevirus is an important viral pathogen affecting sugarcane production in India. The P1 gene of ten Indian isolates was sequenced and compared with previously reported SCSMV isolates. Comparative sequence analysis revealed a high level of diversity in the P1 gene (83–98% nucleotide sequence identity; 87–100% amino acid sequence identity), and the Indian SCSMV isolates were found to be the most variable (up to 9% diversity at the amino acid level). Phylogenetic tree analysis showed clustering of 17 SCSMV isolates into two groups: group I included isolates from India (except SCSMV-TPT) and Pakistan, and group II consisted of isolates from Japan, Indonesia, Thailand and SCSMV-TPT. The results obtained from phylogenetic study were further supported by the different Insilco analysis viz. SNPS (single nucleotide polymorphism), INDELS (insertion and deletion) and evolutionary distance analysis. A significant proportion of recombination sites were observed at the N terminal region of P1 gene. Analysis of selection pressure indicated that the P1 gene of the Indian SCSMV isolates is under strong negative or purifying selection. It is likely that recombination identified in Indian SCSMV isolates, along with strong purifying selection, enhances the speed of elimination of deleterious mutations in the P1 gene. The evolutionary processes (recombination and selection pressure) together contributed to the observed genetic diversity and population structure of Indian SCSMV isolatesNot Availabl

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Not AvailableSugarcane streak mosaic virus (SCSMV), an unassigned member of the family Potyviridae is an important viral pathogen affecting sugarcane cultivation in India. The complete nucleotide sequence of a SCSMV isolate from India (SCSMV-IND) was determined. The linear, assembled, single stranded positive sense RNA genome of SCSMV-IND was 9786 nucleotides in length (excluding the poly (A) tail) and it comprises a large open reading frame encoding polyprotein of 3131 amino acid residues. The genome of SCSMV-IND shared high degree of sequence identity at nucleotide (93%) and amino acid (97%) levels with SCSMV-PAK and shared 81% and 94% nucleotide and amino acid identities respectively with all the three SCSMV isolates (SCSMV-JP1, -JP2 and -ID). Phylogenetic analysis of the complete genome sequences of SCSMV isolates revealed that they can be clustered into two groups: group I includes isolates from India (SCSMV-IND) and Pakistan (SCSMV-PAK), group II consists of isolates from Japan (SCSMV-JP1 and -JP2) and Indonesia (SCSMV-ID). SCSMV-IND and -AP isolates originating from the same geographical region (India) showed 18% divergence at nucleotide level within the highly conserved 3 half genome indicated existence of diversity among SCSMV isolates from India. Recombination analysis revealed one potentially significant intra-specific recombination in SCSMV-PAK. This work provided the first opportunity to establish the whole genome and polyprotein variability between SCSMV isolates from India and other Asian countries.Not Availabl

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Not AvailableSugarcane grassy shoot (SCGS) caused by SCGS-phytoplasma is an important disease of sugarcane reported widely in many sugarcane growing countries in Asian region. The disease was recorded more than 60 years before in India and currently occurs in all the sugarcane growing states. Almost all the varieties under cultivation are susceptible to the disease and the disease continues to cause severe economic losses in the country. Vegetative propagation i.e. planting of disease infected setts facilitates disease introduction in the field. However, subsequent ratoon crops exhibit severe incidences of the disease and it is one of the causes for poor cane yield in ratoons in sugarcane. Further different insects were reported as vectors and they facilitate transmission of this pathogen in the field. The disease is known to exhibit different phenotypic symptoms depending on the host genotype, location and environment. Usually production of excessive grassy tillers affects production of number of millable canes in the affected crop. Apart from excess tillers production, varying intensities of leaf chlorosis in severe symptomatic plants often coincides with physiological disorders which makes complications in early diagnosis of the disease. In view of that several diagnostic methods like ELISA and immunofluorescent techniques were developed in the past. Further, because of the limitations and lack of sensitivity in serological methods, PCR based assays were standardized for the precise diagnosis of the disease. At ICAR-SBI, indexing of sugarcane seedlings raised through tissue culture for SCGS-phytoplasma is being taken up and the service is extended to the tissue culture production units in the country to produce healthy planting materials. Apart from heat therapy to inactivate phytoplasma in infected setts, tissue culture combined with molecular diagnosis serves as a viable strategy to manage the disease in the country. Since the disease expresses in various forms under field conditions, detailed investigations were carried out on variability in SCGS phytoplasmas at molecular level. Sequence analyses of rDNA and RFLP with different restriction endonucleases were performed to elucidate the genetic relationship among the phytoplasmas and between other related phytoplasmal groups. Although there were significant variations in phenotypic expression of SCGS phytoplasmas on sugarcane, we could not establish any genotypic variation among the pathogenic isolates in rDNA region. Among the other reported SCGS phytoplasmas it shared sequence similarity ranging from 99.7% to 94.3%. The new SCGS phytoplasmas showed 99.6% similarity with other phytoplasmas infecting sugarcane such as SCWL and 97.8% with SCYL. Despite with significant phenotypic variations in symptom expressions16S rRNA, 16S-23S rRNA SR and 23S rRNA sequencing and the restriction mapping of the amplicons did not show any genotypic variations among them and further characterization of the phytoplasma genome is necessaryNot Availabl

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Not AvailableThe HC-Pro gene which is located upstream of the P1 region is the silencing suppressor protein among the Potyviridae family. It is known to be involved in the RNA silencing mechanism by interacting with host proteins yet to be studied. Twelve HC-Pro (Helper component proteinase) isolates of Indian SCSMV of 1410bp was characterized and compared with the available database isolates like Pakistan, Indonesia and Japan. The overall nucleotide and protein level identity was 75-95% and 88-100% respectively. High level of variation was observed among the isolates. The phylogenetic analysis clustered Indian and Pakistan isolates into one group, whereas Japanese and Indonesian in the other group. Potential recombination event detected in the isolates using non-parametric methods showed parental and the recombinant sequences. However, the isolates lacked the conserved motifs associated with aphid transmission at its N-Terminal region and suppression of RNA silencing at the central region. Also the zinc finger motif responsible for RNA silencing activity was found in the P1 region and not in HC-Pro as like other viruses in the Potyviridae family, when the complete genome sequence of SCSMV was characterized. P1 gene of 10 Indian SCSMV isolates were sequenced and compared with five other isolates reported worldwide for their phylogenetic survey of recombination events revealed a similar pattern like HC-Pro. The sequence lengths of the P1 genes of different SCSMV isolates are similar (1074 nucleotide) and each encoding a protein of 358 amino acids. Comparative sequence analysis of 10 Indian P1 isolates revealed 86-98% nucleotide sequence identity among themselves and 83-91% identity to the other SCSMV isolates like Pakistan, Japan and Indonesia. The ratio of non-synonymous to synonymous polymorphic sites is found to be negative in selection to purge the deleterious mutations in the coding sites. Since P1 is the first protein to be produced upon translation of the viral RNA, its further study will shed new lights to understand the mechanism of host viral interaction.Not Availabl

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Not AvailableDetailed studies were carried out to characterize full genome of the virus and to establish genomic variation existing in Indian SCYLV population using six different sets of forward and reverse primers. We have characterized four SCYLV isolates infecting sugarcane cvs Co 86032, CoC 85061, CoV 92102 and B 38192 from India after complete genome sequencing. ORF 0 were compared between nt 200-770 (571 nt), ORF 1 between nt 200-1776 (1557 nt) and ORF 5 between nt 3579-4189 (610 nt) and their deduced amino acid sequences were also aligned. The new full length SCYLV nucleotide sequences (~ 5875 nt) were aligned along with those of five other available genotypes and all the sequences were trimmed to on equal length of 5616 nt on the basis of multiple sequence alignment to reduce errors with unequal length of sequences in identity matrix. Sequence analysis revealed that these isolates (SCYLV-IND) exhibited amino acid (aa) sequence differences of 29.2-31.8, 28.1-34.4 and 30.7-33.4% with REU, HAW-PER and BRA in partial ORF0 sequences, respectively. Similarly IND isolates have 21.4-23.7, 22.5-25.0 and 21.4-23.9% aa sequence differences with REU, HAW-PER and BRA, respectively in partial ORF 1. However, the difference was found to be least in ORF5 and it varied 3.0-6.0% and 3.0-6.9% with REU and HAW-PER/BRA sequences. A phylogram with other genotypes based on complete genomes showed that IND isolates shared 86.3- 86.6% with REU, 86.1-86.7% with BRA and 84.9-86.2% with the recently combined genotype of HAW-PER. The genotype reported from China, CHN1 shared a very close relationship with IND isolates with minimum differences of 4.3-5.3%, 4.8-5.8% and 2.5-3.0% in ORF0, 1 and 5 in aa sequences, respectively and 4.4-5.3% in complete nucleotide sequences.Not Availabl

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Not AvailableYellow leaf disease (YLD) caused by Sugarcane yellow leaf virus (SCYLV) is a recently recorded disease in India and is found wide spread throughout country. In popular varieties, the disease incidence varied from 0 to 75.0% and attained epidemic levels under field conditions. Detailed studies on the impact of YLD on sugarcane revealed that the virus infection significantly reduces various cane growth parameters, cane yield and juice quality. Sequence comparisons of the coat protein (CP) and movement protein (MP) of 22 SCYLV isolates from India and database sequences showed a significant variation between Indian isolates and the database sequences both at nt and aa level in the CP/MP coding regions. The significant variation in our isolates with the database isolates, even in the least variable region of the SCYLV genome showed that the population existing in India is different from rest of the world. Further, comparison of partial sequences encoding for ORF 1 and 2 revealed that YLD in sugarcane in India is caused atleast by three genotypes viz., CUB, IND and BRA-PER, of which a majority of the samples were found infected with Cuban genotype (CUB). The genotype IND was identified as a new genotype and this was found to have significant variation with the reported genotypes. We have identified specific primers from CP region of the virus and optimized RT-PCR conditions to diagnose the virus. This assay has been found efficient in detecting the virus in asymptomatic plants and tissue culture derived seedlings. Elimination of the virus through meristem culture has been demonstrated to purify the virus from the infected planting materials and this technique needs to be adopted to supply disease-free planting materials for effective management of the disease. Studies are also in progress to identify the YLD-resistant sources in sugarcane germplasm to initiate breeding for YLD-resistance in sugarcaneNot Availabl

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Not AvailableSugarcane yellow leaf virus (SCYLV) that causes yellow leaf disease (YLD) in sugarcane belongs to Polerovirus. The disease expression is commonly observed during 6 to 8 months stages of the crop and there is a need to diagnose the disease before the symptom appearance. We have standardized RT-PCR technique with a new set of primers to detect SCYLV in sugarcane in pre-symptomatic stages of YLD. During pre symptomatic stage 33 of the 44 varieties studied tested positive to SCYLV in RT-PCR. During eighth month stage all the 44 varieties have shown characteristic disease symptoms and except one all of them tested positive to the virus in RT-PCR. The two RT-PCR assays performed separately during pre- and post-symptom expression stages in 44 varieties clearly revealed that most of the varieties have detectable level of the virus in asymptomatic stage. Expression of disease symptoms and presence of the virus in all the varieties except one very clearly indicated the severe virus infection in the tested varieties. The studies also proved the diagnostic efficiency of the new set of primers to detect SCYLV in asymptomatic plants.Not Availabl