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Sugarcane is the world’s most widely grown sugar crop accounts for almost 75% of world sugar production. Diseases are the major productivity constraints for sugarcane that considerably reduce yield and sugar recovery. Identification of disease resistance is an important and sustainable approach for disease management. More recently, Brazilian researchers have characterized the whole genome sequences of a commercial sugarcane cv SP80-3280 and mapped 373,869 genes or ninety nine percent of the total genome. Use of next- generation sequencing (NGS) techniques have facilitated the availability of complete genomic information of various sugarcane pathogens, have led to the understanding of organization of the disease resistance gene clusters for unraveling the genetic mechanism involved in developing new resistance strategies to manage sugarcane diseases. Genome wide association study (GWAS) reveal polymorphisms related with composite characters in the whole genome. In the omics era, whole genome sequencing of host and pathogens combined with the availability of bioinformatics tools for their analyses led to the emergence of GWAS, a potent method for identifying genomics region covering resistance loci in various plants. This review summarizes the literature generated during last the 10 years on GWAS in sugarcane related to disease resistance and along with novel single nucleotide polymorphism and quantitative trait loci’s hotspots identified for economically important diseases of sugarcane.

Dragon fruit (Hylocereus spp.) a member of the family Cactaceae, is widely cultivated throughout the world, includingspan style="font-family:'Times New Roman'; letter-spacing:0.05pt; color:#333333"India. During 2020-2021 crop growing season, mosaic symptoms were observed on the cladodes of dragon fruit plants (Purple Pink cultivar: 1-2% disease incidence) grown at a farmer's field of Telangana, India (Fig. S1 a). The symptomatic cladodes (n= 4), observed under leaf-dip electron microscopy (Zuchmaan and Zellnig, 2009) at Indian Agricultural Research Institute, New Delhi, revealed the presence of flexuous rod- shaped virus-like particles (Fig S1 b). Virus particles were of 580 x 13 nm size, corresponding to the genus Potexvirus. For further confirmation, the total RNA isolated from symptomatic cladodes using a NucleoSpin RNA Plant Mini kit (Macherey-Nagel). Subsequently, a reverse transcription polymerase chain reaction (RT-PCR) was performed using the PrimeScript 1st strand cDNA Synthesis Kit (Takara Bio). The cDNA was further amplified with the primers specific to coat protein (CP) gene of four different species of the genus Potexvirus known to infect members of Cactaceae family. Four sets of primers were used for detection, viz., Cactus virus X (CVX) (F, 5'-ATGTCTACTACTGGAGTCCA-3'; R, 5'-CTACTCAGGGCCTGGGAGAA-3'); Pitaya virus X (PiVX) (F, 5'-ATGGCTACTCAAACAGCACAA-3'; R, 5'-CTACTCTGGGGAGGGAAG-3'); Schlumbergera virus X (SchVX) (F, 5'-ATGTCGACCACTCCATCTTC-3'; R, 5'-TTATTCAGGGGATGGTAGTA-3') and Zygocactus virus X (ZyVX) (F, 5'-ATGTCTAACACTGCAGGAGT-3'; R, TCATTC GGGACCCGGTAGGA-3') (Duarte et al., 2008; Janssen et al., 2021; Parameswari et al., 2021), by following the PCR profile (Park et al., 2018). The species-specific primers of CVX, PiVX and SchVX did not amplify any amplicon, whereas the primers specific to ZyVX at nucleotide position 5841-6521 from complete CP gene have resulted in amplification of expected size (~680 base pairs) from all the samples. The gel-purified RT-PCR products were cloned into a pDrive cloning vector (Qiagen, Germany) and sequenced bi-directionally using Sanger sequencing. The resultant sequences (681 nt) of the CP gene showed 98% (nucleotide) and 100% (amino acid) sequence similarity with the CP gene sequence (Accession No: KY581590) of ZyVX. Hence, one representative sequence was deposited to the NCBI GenBank database as ZyVX-DPC isolate (Accession number- OK415019). The Neighbour Joining Phylogenetic Tree constructed using MEGA6 software (Tamura et al. 2013) showed grouping of Indian ZyVX-DPC isolate with the previously reported ZyVX isolates from Korea, Taiwan, China and Germany (Fig. S1c). These results confirmed the association of ZyVX with the symptomatic cladodes of dragon fruit plants collected from Telangana, India. Earlier studies revealed that ZyVX is a member of the genus Potexvirus known to infect dragon fruit plants from Brazil and China (Duarte et al., 2008). In India until now, anthracnose disease (Colletotrichum siamense) and CVX from Hylocereus spp. were reported (Abirami et al., 2019; Parameswari et al., 2021). To the best of our knowledge, this is the first report of ZyVX infection on dragon fruit in India. The draon fruit, being vegetatively propagated and with increasing cultivable area in India (Abirami et al, 2019), the present study gains significance. Further studies on mode of virus transmission, estimation of crop yield losses, host range studies and finding out source of resistance are essential.

Dragon fruit (Hylocereus spp.) is an important fruit crop for its high nutrition and profitability grown in India and many other countries. Dragon fruit stem samples exhibiting chlorosis and mottling symptoms, collected from Sangareddy district of Telangana, India revealed a flexuous rod-shaped virus with a length of ~ 600 nm in electron microscopic examination. The RT-PCR based detection of Cactus virus X using specific primers resulted in the production of ~ 900 bp amplicons covering the full length triple gene block protein 3 and coat protein regions. Further, cloning and sequence information of the ~ 900 bp amplicon revealed the presence of Cactus virus X (CVX) in dragon fruit. To our knowledge, this is the first record of CVX causing particular disease in dragon fruit from India.

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.

The mining industry acts as a catalyst for the growth of other core industries. This paper shows how India’s mineral production helps our Industrial development and by inference the overall economic development. To elucidate the importance of mineral production on industrial development, regression analysis was made. From the analysis, the researcher got the result of all mineral production explains about 99% variation in Industrial production.

Among 10 proteins encoded by Papaya ringspot virus (PRSV), only coat protein (CP) has been studied extensively from mainly the papaya-originated isolates i.e. PRSV-P. In this study, besides CP, the helper component proteinase (HC-pro) and nuclear inclusion protein-a (NIa-pro) coding regions from 19 PRSV-P and -W isolates originating from different geo-climatic locations and hosts were analyzed. Unlike CP, both HC-pro and NIa-pro did not reveal the variability in their length. HC-pro and NIa-pro sequences revealed less than 10% deduced amino acid (daa) diversity worldwide, the CP was found highly variable (up to 20% daa diversity). Highest variability in CP sequence was noticed among the cucurbit-originating PRSV-P Indian isolates, especially from Warm semi-arid climate, which was attributed to a large number of aa insertions/deletions. However, papaya-originating PRSV-P isolates from the Oceanic climate were less variable (up to 5% daa diversity). In NIa-pro, besides already known host/pathotype-specific switching of aa Lys/Asp27, switching of Lys27 → Arg27 and Asp27 → Glu27 was identified within P and W pathotypes. Additionally, a novel aa switching from Ser/Met134 → Thr134 between P and W pathotypes respectively was identified. The phylogeny of PRSV isolates was largely based on the geo-climatic locations and hosts. Through recombination detection analysis, three recombinant isolates were detected based on both NIa-pro and CP sequences, which possessed cucurbit-originated PRSV (either -P or -W) isolates as one of their parents (either major or minor.) Patterns of codon usage among the three protein coding sequences generated further revealed that the CP gene is under maximum selection pressure (with six sites) followed by NIa-pro gene (with one site). This investigation shows that the genetic recombination between the isolates originating from different hosts and geo-climatic locations as well as mutations are the significant mechanisms playing their role in generating diverse populations of PRSV.

Sugarcane mosaic virus (SCMV) one of the causative viruses of mosaic disease in sugarcane occurs in sugarcane growing countries worldwide. India is the second largest sugarcane producing country and genome of SCMV from India has not been characterized so far. Hence detailed studies were carried out to characterize the virus isolates based on its complete genome. Comparative genome analyses of five new isolates were performed with previously reported SCMV full genome sequences of isolates infecting sugarcane, maize, sorghum and Canna. Sequence identity matrix and phylogenetic analyses clearly represented that Indian isolates are closely related to sugarcane infecting isolates reported from Australia, Argentina, China and Iran and they diverged as a separate subgroup from other reported maize infecting isolates from Mexico, China, Ohio, Spain, Germany, Iran, Ethiopia, Kenya and Eucador. Selection pressure analysis clearly depicted the predomination of strong purifying selection throughout the viral genome, and strongest in CI and HC-Pro gene. Evidence for few positively selected sites was identified in all the cistrons except in 6 K1 and Nib rep. Among the genomic region, CI gene has exhibited comparatively more recombination hotspots followed by HC-Pro unlike other reported isolates. As the cultivation of sugarcane first originated in India, our results from the recombination events strongly suggest that Indian SCMV populations contribute for the emergence of upcoming new recombinant SCMV isolates not only within the sugarcane isolates but also with maize infecting isolates of SCMV in other countries irrespective of geographic origin and host type.

Loop-mediated isothermal amplification (LAMP) is a rapid, highly specific and reliable technique, which is widely incorporated in the field for diagnosis of pathogens at their early stage of infection. In present study, RT-LAMP assay was developed successfully to detect Sugarcane yellow leaf virus (SCYLV) causing yellow leaf disease in sugarcane and compared with conventional reverse transcription-polymerase chain reaction (RT-PCR) and quantitative real-time polymerase chain reaction (qRT-PCR) to assess its sensitivity. RT-LAMP was able to detect the SCYLV up to a limit of 10 pg (picogram), while RT-PCR assays were able to detect this virus up to 100 pg only. The sensitivity of the RT-LAMP method was tenfold higher than that of conventional RT-PCR assay. This study revealed high sensitivity of RT-LAMP in detecting SCYLV in Indian sugarcane cultivars.

Sugarcane, an important field crop, is cultivated under tropical and subtropical regions around the world. Fusarium sacchari causing wilt, is a stalk disease, inflicting severe damage to the crop in India and other countries. Similarly, pokkah boeng (PB) a foliar disease caused by different species of Fusarium also infects the crop throughout the world. In India, both the diseases occur in different states in various sugarcane varieties. Although both diseases occur independently in the field, we recorded that they occur together in a plant. Hence, a detailed investigation was conducted to characterize different Fusarium isolates from wilt- and PB-affected sugarcane varieties by sequencing TEF1-α gene. Gene sequencing of 48 isolates revealed that 44 were of F. sacchari and the remaining four belonged to F. proliferatum. Of the four F. proliferatum, three were associated with PB and one with wilt. Almost all the 41 wilt-associated isolates belonged to F. sacchari. Investigation carried out to identify Fusarium isolates from the plants exhibiting both the wilt and the PB in two varieties Co 0238 and MS 901 revealed that only F. sacchari caused wilt and PB symptoms in both. Further, several varieties showed progressive disease severity through different phases of PB and that resulted in wilt development. The results clearly established for the first time that the same fungal pathogen systematically infects sugarcane plant and exhibits both the diseases.

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.

The family Luteoviridae comprises of three genera Luteovirus, Enamovirus and Polerovirus, of which, only two genera Luteovirus and Polerovirus are known in India. Though luteovirus and polerovirus infects many crops throughout the world, only a few have been documented in India. Luteoviruses were reported in field crops like barley (barley yellow dwarf virus) and chickpea (chickpea stunt virus), while polerovirus was recorded from potato, jute (potato leaf roll virus [PLRV]) sugarcane (sugarcane yellow leaf virus [SCYLV]) and cotton (cotton leaf roll dwarf virus) crops from India. SCYLV and PLRV are the most important poleroviruses as they are of serious constraints in all the sugarcane and potato growing states of India. SCYLV infection causes 39–43% reductions in plant growth and 30–34% loss in yield in sugarcane. The virus is mainly transmitted through infected seed canes. The secondary spread of the virus in the field is by the aphid vectors. PLRV is reported to cause 50–60% yield losses in potato crop and this virus is tuber borne and transmitted mainly by aphid vectors in a circulative non-propagative manner. The complete genome sequences SCYLV and PLRV isolates from sugarcane and potato are available from India. This book chapter deals with an uptodate information available on distribution, biological properties, identification, serological relationships, genetic diversity and transmission of the luteoviruses and poleroviruses reported on different crops from India.

In India, potyvirus infection is common in Solanaceae, Cucurbitaceae, Poaceae and Leguminosae families. Economically important crops like potato, tomato, papaya, banana, sugarcane and pepper are affected by potyviruses as one of the major production constraints. There are as many as 39 different potyviruses recorded in India of which the virus species Potato virus Y, Papaya ringspot virus, Sugarcane mosaic virus and Banana bract mosaic virus are economically more significant. An up-to-date information on the occurrence, biology, serology and molecular biology of the potyviruses that has been investigated in India is presented in this chapter.

Sugarcane 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 in silico 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 isolates.

A DETAILED DESCRIPTION OF Co 12029 (KARAN 13): A NEW MIDLATE SUGARCANE VARIETY RELEASED FOR COMMERCIAL CULTIVATION IN NORTH WEST ZONE OF INDIA

Sugarcane streak mosaic virus (SCSMV), a member of the genus Poacevirus, 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 9,786 nucleotides in length (excluding the poly (A) tail) and encoded a polyprotein of 3,131 amino acid residues. The genome of SCSMV-IND shared high degree of sequence identity with SCSMV-PAK (93 % at nucleotide and 97 % at amino acid), and shared only 81 % nucleotide and 94 % amino acid identities with all the four SCSMV isolates (SCSMV-JP1, -JP2, -ID, and -THA). Phylogenetic tree analysis of the complete genome sequences of SCSMV isolates revealed that they can be clustered into two groups. SCSMV-IND and -AP isolates showed 18 % (nucleotide) divergence within the highly conserved 3' partial genome, suggesting a high level of genetic diversity among the Indian SCSMV isolates.

Yellow leaf (YL) caused by Sugarcane yellow leaf virus (SCYLV) has become a serious constraint for sugarcane production in different countries. Worldwide seven genotypes have been reported, with five based on complete and two based on partial genome characterization. We have previously reported the occurrence of three different SCYLV genotypes in India based on their partial genome sequences. A further four SCYLV isolates from sugarcane from Coimbatore (in India) were characterized after complete genome sequencing (~ 5,875 nt). 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 ORF1. However, the difference was found to be least in ORF5. 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. Phylogenetic analyses showed a separate lineage for IND isolates. Evidence of recombination was found in ORF1 to ORF5 with the maximum number of sites occurring in ORF2. The high incidence of SCYLV recombination suggests that recombination plays an important role in SCYLV evolution.

Sugarcane streak mosaic virus (SCSMV), a member of the family Potyviridae, is an important viral pathogen affecting sugarcane production in India. The variability in the nucleotide (nt) and amino acid (aa) sequences of helper component proteinase (HC-Pro) of SCSMV isolates from India was investigated and compared with those of previously published virus isolates from different Asian countries. Comparison of all of the sequenced virus isolates revealed a high level of diversity in the HC-Pro gene (72-97% nt sequence identity; 83-99% aa sequence identity), and the Indian isolates were found to be the most divergent (up to 12% variation at the amino acid level). Phylogenetic analysis revealed clustering of 16 SCSMV isolates into two groups. Group I included isolates from India and Pakistan, and group II consisted of isolates from Japan and Indonesia. Recombination analysis revealed nine potentially significant recombination events, and putative recombination sites were identified throughout the HC-Pro gene. Analysis of selection pressure indicated that the HC-Pro gene of SCSMV is under strong negative selection. It is likely that recombination, along with strong negative selection, enhances the speed of elimination of deleterious mutations in the HC-Pro gene.

Papaya ringspot virus (PRSV) has a single-stranded RNA genome and causes severe economic losses both in cucurbits and papaya worldwide. The extent to which the genome of PRSV is shaped by recombination provides an understanding of the molecular evolution of PRSV and helps in studying features such as host specificity, geographic distribution, and its emergence as new epidemics. The PRSV-P-Indian isolate was completely sequenced and compared with 14 other isolates reported from the rest of the world for their phylogenetic survey of recombination events. Cistron-by-cistron sequence comparison and phylogenetic analysis based on full-genome polyprotein showed two distinct groupings of Asian and American isolates, although PRSV-P and W-India clustered along with the American isolates. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene. A significant proportion of recombination hotspots was found in the P1 gene, followed by P3, cylindrical inclusion (CI), and helper component proteinase (HcPro). Correlations between the presence of recombination sites, geographic distribution, and phylogenetic relationship provide an opportunity to establish the molecular evolution and geographic route of PRSV.

Pathogenic Behaviour Pattern of Colletotrichum falcatum Isolates of Sugarcane in Sub-tropical India Red rot caused by Colletotrichum falcatum is the most serious disease of sugarcane affecting cane production in different states in India. Since the pathogenic variants very frequently emerge in the field we have assessed pathogenic variation in 12 C. falcatum isolates collected from subtropical India along with previously designated pathotypes on a set of 16 host differentials for the eight seasons. By and large, a variable virulence pattern in C. falcatum isolates was recorded on most of the host differentials. The results showed that the predominant sub-tropical pathotypes (CF09 and CF08) isolated from then the ruling cultivars CoS 767 and CoJ 64, respectively showed less virulence and the pathotype CF02 isolated from Co 7717 showed higher virulence over the period of time on the host differentials. The higher aggressiveness exhibited by CF02 over on the differentials such as Co1148, Co 975 and Khakai and known susceptible differentials Co 997, Co 62399, CoC 671, CoJ 64 and another variety Co 89003 clearly revealed higher virulence of CF11 pathotype. Even though the pathotype CF08 remained virulent on its host cultivar CoJ 64, it could not cause same type of virulence on the recently developed cultivars and it suggests that the pathotype no longer maintains its virulence once a popular cultivar CoJ 64 removed from the cultivation. Among the 11 new C. falcatum isolates evaluated, the isolate Cf8436 Karnal was found to be virulent and the differential CoS 8436 succumbed to this isolate only. Of the different CoJ 64 pathotypes, Cf64-I exhibited higher virulence and showed susceptible to intermediate reaction on different host differentials. This study suggests continuous evolution of red rot pathogen and its adaptation to the new host cultivars in subtropical India....

Papaya ringspot virus (PRSV), a definite member of the family Potyviridae and the genus Potyvirus [5], occurs worldwide and is a major constraint to papaya (Carica papaya) and cucurbits production throughout the tropical and subtropical regions [21]. The virus is readily vectored by aphids in a non-persistent manner [16]. The virus was first recorded from western India in 1958 [4] and since then it has spread to different geographical locations, limiting papaya and cucurbits production [1, 8, 9]. Prevalence of both papaya-infecting (Type P) and non-papaya-infecting (Type W) pathotypes has been recorded. The virus induces variety of symptoms on foliage, stem and fruit in papaya and cucurbits. PRSV has flexuous filamentous particles (760–800 nm 9 12 nm) with a single-stranded, positivesense RNA genome of approximately 10,000 nucleotides. Fifteen PRSV isolates belonging to different geographical locations have been completely sequenced. PRSV isolates from India have been characterized for coat protein only [1, 8, 9], and information on their complete genome sequences is lacking. In this study, complete genome sequences of pathotypes P and W from India and their sequence divergence, phylogenetic relationships and recombination with 15 other PRSV genomes have been determined to investigate their origin and host specificity. Preliminary results on pathotype P have been published [15]. PRSV isolates from symptomatic papaya (Carica papaya) (pathotype P) and spongegourd (Luffa aegyptiaca) (pathotype W) plants were collected from the Indian Agricultural Research Institute experimental farm in New Delhi and propagated in papaya (cv. Pusa Nanha) and pumpkin (Cucurbita pepo), respectively, in a glass house through sap inoculations using 0.1 M phosphate buffer, pH 7.2, containing 0.1% 2-mercaptoethanol and celite as an abrasive. The details of the PRSV genome sequences collected from GenBank (http://www.ncbi.nlm.nih.gov) are shown in Table 1. The analysis utilized the nucleotide and translated amino acid sequences of the whole genome or of individual cistrons. The complete genome sequence of PRSV RNA was generated with nine overlapping fragments using nine pairs of specific primers. Viral RNA was reverse transcribed and amplified using high-fidelity Taq DNA polymerase (New England Biolabs). Two clones of each of the nine amplified products (700–1,900 bp) were sequenced in both (30 and 50) directions with 100% identity in the overlapping regions. The sequences of overlapping cloned fragments that were generated were assembled manually using the BioEdit software version 5.09.04 [7]. Nucleotide and amino acid sequences representing the complete genomes of pathotypes P and W and their cistrons were aligned using CLUSTAL W [19]. A sequence similarity matrix between polyproteins and specific cistrons was calculated using the BioEdit software version 5.09.04 [7]. Recombination sites were identified using RDP [11], GENECONV [14], BOOTSCAN [12], MAXIMUM CHISQUARE [13], CHIMAERA [12] and SISTER SCAN [6], the non-parametric recombination detection methods implemented in RDP2 [12]. A multiple comparison corrected P-value cutoff 0.05 and default settings were used throughout, and only events detectable by two or more different methods were retained for further analysis. S. K. Mangrauthia Plant Pathology Section, Directorate of Rice Research, Hyderabad, India