Sugarcane Yellow Leaf Virus Genotypes Research Articles

Potential targets for evaluation of sugarcane yellow leaf virus resistance in sugarcane cultivars: in silico sugarcane miRNA and target network prediction

The Sugarcane yellow leaf virus (SCYLV) is associated with sugarcane yellow leaf disease (SCYLD) and is considered to be the most economically deleterious emerging pathogen that represents a potential threat and danger to sugarcane cultivation in China. Over the last two decades, high genetic diversity in the SCYLV genotypes was observed worldwide, with a greater chance of YLD incidence for sugarcane injury. SCYLV infection has significantly damaged its economic traits and is responsible for substantial losses in biomass production in sugarcane cultivars. This study aims to identify and analyse sugarcane microRNAs (miRNAs) as therapeutic targets against SCYLV using plant miRNA prediction tools. Mature sugarcane miRNAs are retrieved and are used for hybridisation of the SCYLV. A total of seven common sugarcane miRNAs were selected based on consensus genomic positions. The biologically significant, top ranked ssp-miR528 was consensually predicted to have a potentially unique hybridisation site at nucleotide position 4162 for targeting the ORF5 of the SCYLV genome; this was predicted by all the algorithms used in this study. Then, the miRNA–mRNA regulatory network was generated using the Circos algorithm, which was used to predict novel targets. There are no acceptable commercial SCYLV-resistant sugarcane varieties available at present. Therefore, the predicted biological data offer valuable evidence for the generation of SCYLV-resistant sugarcane plants.

A survey of causal agents associated with sugarcane yellowing in Northeast Brazil

The etiological agents of the yellow leaf syndrome (YLS) are the Sugarcane yellow leaf virus (ScYLV), and phytoplasmas of different groups. Due to a lack of knowledge on the occurrence of YLS and the importance of sugarcane to Brazil, the aims of this study were to assess the occurrence and distribution of the pathogens associated with YLS in sugarcane cultivation areas in three states of Northeast Brazil. For this purpose, 101 sugarcane samples with symptoms of YLS were collected in 2018 crop cycle. ScYLV and a new phytoplasma were detected by RT-PCR and nested PCR, respectively. The identity of virus- and phytoplasma-positive samples was confirmed by Sanger sequencing, and these sequences were used in subsequent phylogenetic studies. Both pathogens were present in all sampled regions. ScYLV and the phytoplasma were detected in 40.4% and 62.2% of the samples, respectively. Mixed infections were found in 33.5% of the samples. Phylogenetic analysis showed that the ScYLV isolates identified were most closely related to ScYLV genotypes REU, PER, HAW, CHN2 and BRA. The phytoplasma 16S rDNA gene nucleotide sequences shared 99.0% identity with sequences of the 16SrVII phytoplasmas from Argentina and Brazil. This is the first report of the presence of a member of the 16SrVII phytoplasma group in association with sugarcane leaf yellowing in the world. These findings are important to raise awareness among sugarcane producers on the impact of pathogens causing YLS in Northeast Brazil.

Phylogenetic and recombination analysis of sorghum isolates of Sugarcane yellow leaf virus

Recombination has played an important role in evolution and genetic diversity of Sugarcane yellow leaf virus (SCYLV) isolates sequenced to date. This study found that three newly sequenced SCYLV sorghum isolates from the USA underwent intraspecies recombination. No statistical significance on probable progeny–parent relationships involving SCYLV sorghum isolates were found in possible interspecies recombination with 18 members of the Luteoviridae family. Sorghum isolates deposited in the GenBank database under accession numbers KT960995, KT960996 and KT960997 were phylogenetically closely related to SCYLV genotypes IND, CUB and CHN1, all members of phylogroup II. Networked relationships among the sorghum isolates showed that numerous incompatibilities occurred in the sequences. These conflicting signals were probably due to recombination, especially in KT960997, which was heavily impacted by recombination. The KT960997 accession was positioned on a distinct branch compared to other members of phylogroup II, suggesting that it has probably emerged as a new genotype. Future studies on molecular evolution may reveal further insights into the adaptation capacity of these SCYLV lineages to new environments.

Genotyping of Sugarcane Yellow Leaf Virus in Commercial Cultivars and the Cuban Germplasm Collection

Sugarcane yellow leaf disease caused by Sugarcane yellow leaf virus (SCYLV) was spread over the world through infected germplasm. This study was conducted in order to determine the presence of SCYLV in commercial fields and germplasm collection and study the genetic diversity of the virus in Cuba. Leaf samples were collected from commercial cultivars in eight provinces and the Cuban germplasm collection in Matanzas province. The diagnosis of SCYLV was performed using tissue-blot immunoassay and reverse transcription polymerase chain reaction (RT-PCR). Our results revealed the widespread incidence of SCYLV in commercial sugarcane plantations in Cuba. The coat protein sequence analyses of SCYLV isolates under study confirmed the presence of BRA-PER, CUB and REU genotypes. The REU genotype is reported first time in Cuba. Coinfections of SCYLV genotypes (BRA-PER + CUB, BRA-PER + REU and CUB + REU) were also reported. The most predominating SCYLV genotypes reported in Cuba were identified as CUB and BRA-PER.

Prevalence of Sugarcane yellow leaf virus in Sugarcane-Producing Regions in Kenya Revealed by Reverse-Transcription Loop-Mediated Isothermal Amplification Method

Yellow leaf (YL) is a disease of sugarcane that is currently widespread throughout most American and Asian sugarcane-producing countries. However, its actual distribution in Africa remains largely unknown. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to facilitate and improve the detection of Sugarcane yellow leaf virus (SCYLV), the causal agent of YL. The RT-LAMP assay was found to be comparable with or superior to conventional RT-polymerase chain reaction (PCR) for the detection of SCYLV genotypes CUB and BRA in infected sugarcane 'C132-81' and 'SP71-6163', respectively. Additionally, 68 sugarcane samples that tested negative by RT-PCR were found positive by RT-LAMP, whereas the RT-LAMP assay failed to detect SCYLV in only 5 samples that tested positive by RT-PCR. Combining RT-PCR and RT-LAMP data enabled the detection of SCYLV in 86 of 183 Kenyan sugarcane plants, indicating high SCYLV prevalence throughout the country (ranging from 36 to 64% in individual counties). Seminested PCR assays were developed that enabled the amplification of a fragment encompassing the capsid protein coding region gene and its flanking 5' and 3' genomic regions. Sequences of this fragment for four Kenyan SCYLV isolates indicated that they shared 99.2 to 99.6% pairwise identity with one another and clearly clustered phylogenetically with SCYLV-BRA genotype isolates. To our knowledge, this is the first report of SCYLV in Kenya.

Biology and management of sugarcane yellow leaf virus: an historical overview.

Sugarcane yellow leaf virus (SCYLV) is one of the most widespread viruses causing disease in sugarcane worldwide. The virus has been responsible for drastic economic losses in most sugarcane-growing regions and remains a major concern for sugarcane breeders. Infection with SCYLV results in intense yellowing of the midrib, which extends to the leaf blade, followed by tissue necrosis from the leaf tip towards the leaf base. Such symptomatic leaves are usually characterized by increased respiration, reduced photosynthesis, a change in the ratio of hexose to sucrose, and an increase in starch content. SCYLV infection affects carbon assimilation and metabolism in sugarcane, resulting in stunted plants in severe cases. SCYLV is mainly propagated by planting cuttings from infected stalks. Phylogenetic analysis has confirmed the worldwide distribution of at least eight SCYLV genotypes (BRA, CHN1, CHN3, CUB, HAW, IND, PER, and REU). Evidence of recombination has been found in the SCYLV genome, which contains potential recombination signals in ORF1/2 and ORF5. This shows that recombination plays an important role in the evolution of SCYLV.

Molecular detection, genetic diversity and distribution of Sugarcane yellow leaf virus genotypes in China

A total of 332 sugarcane leaf samples were collected from seven provinces in China during 2010 to 2013. RT-PCR was performed using the YLS111/YLS462 primers to detect the causal pathogen Sugarcane yellow leaf virus (SCYLV) causing yellow leaf disease in sugarcane. The incidence of SCYLV infection ranged from 24 to 38 % depending on geographic areas. A new primer pair (P0-R3/P0-F2) was designed to prime the amplification of a 968-nucleotide (nt) fragment from SCYLV-positive samples. The fragment contained a partial 5′ untranslated region, the complete ORF0 encoding P0, and a partial ORF1. A phylogenetic analysis of 141 P0 fragment sequences (937 nt) worldwide showed that all SCYLV isolates were clustered into eight genotypes. The 107 SCYLV isolates collected in this study were classified into three genotypes (BRA, HAW, and CHN3), of which the BRA genotype (102/107) was the most prevalent and was detected in all evaluated locations. One isolate (1/107) of genotype HAW was found in Hainan province. Four isolates (4/107) of the genotype CHN3 were observed in Guangxi, Guizhou and Hainan provinces. These findings help understand the genotypic diversity and distribution of SCYLV isolates in China.

Complete genome characterization of Sugarcane yellow leaf virus from India: Evidence for RNA recombination

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.

Molecular characterization and phylogenetic analysis of Sugarcane yellow leaf virus isolates from China

Sugarcane yellow leaf virus (SCYLV) (genus Polerovirus, family Luteoviridae), the causal agent of sugarcane yellow leaf disease (YLD), was first detected in China in 2006. To assess the distribution of SCYLV in the major sugarcane-growing Chinese provinces, leaf samples from 22 sugarcane clones (Saccharum spp. hybrid) showing YLD symptoms were collected and analyzed for infection by the virus using reverse transcription PCR (RT-PCR), quantitative RT-PCR, and immunological assays. A complete genomic sequence (5,879 nt) of the Chinese SCYLV isolate CHN-FJ1 and partial genomic sequences (2,915 nt) of 13 other Chinese SCYLV isolates from this study were amplified, cloned, and sequenced. The genomic sequence of the CHN-FJ1 isolate was found to share a high identity (98.4-99.1 %) with those of the Brazilian (BRA) genotype isolates and a low identity (86.5-86.9 %) with those of the CHN1 and Cuban (CUB) genotype isolates. The genetic diversity of these 14 Chinese SCYLV isolates was assessed along with that of 29 SCYLV isolates of worldwide origin reported in the GenBank database, based on the full or partial genomic sequence. Phylogenetic analysis demonstrated that all the 14 Chinese SCYLV isolates clustered into one large group with the BRA genotype and 12 other reported SCYLV isolates. In addition, five reported Chinese SCYLV isolates were grouped with the Peruvian (PER), CHN1 and CUB genotypes. We therefore speculated that at least four SCYLV genotypes, BRA, PER, CHN1, and CUB, are associated with YLD in China. Interestingly, a 39-nt deletion was detected in the sequence of the CHN-GD3 isolate, in the middle of the ORF1 region adjacent to the overlap between ORF1 and ORF2. This location is known to be one of the recombination breakpoints in the Luteoviridae family.

Occurrence of Three Genotypes of Sugarcane Yellow Leaf Virus in a Variety Collection in Mauritius

Sugarcaneyellow leaf virus (SCYLV) is widely distributed in Mauritius, but so far the characterisation of genotypes of the virus has not been determined. RT-PCR primers were used to identify genetic diversity of the virus in a variety collection plot. Total nucleic acids were extracted from leaves of thirteen introduced varieties infected by SCYLV and a two-step RT-PCR was optimised for each of the three genotype-specific primer pairs CUB-F/CUB-R, REU-F/B-REV, and PER-F/PER-R tested. The presence of three SCYLV genotypes namely the BRA-PER, CUB and REU was confirmed in the germplasm collection. Genotype REU was observed in 10 varieties while 4 varieties were infected by genotype BRA-PER. Mixed infection with genotypes CUB and REU was observed in variety Co6304 while Q88 was co-infected by genotypes BRA-PER and REU. PCR fragments of 363 bp (BRA-PER), 452 bp (CUB) and 905 bp (REU) amplified from varieties PR67245, Co6304 and S17 were cloned and sequenced. Blast analysis of these three sequences showed high homologies with the corresponding genotype sequences from GenBank—100% similarity with isolate Taiwl (AJ491144, BRA genotype), and >99% similarity with isolates CUB-YL1 (AM083988) and REU-YL2 (AM072756) respectively. Recent screening of some local commercial cultivars revealed infection by REU and BRA-PER genotypes. Further intensive surveys are being carried out to assess the distribution of the three SCYLV genotypes in sugarcane fields in Mauritius.

Molecular characterization of Hawaiian Sugarcane yellow leaf virus genotypes and their phylogenetic relationship to strains from other sugarcane-growing countries

Sugarcane yellow leaf virus (SCYLV) is the causal agent of the sugarcane disease Yellow leaf (YL), which was first reported in Hawaii. The presence of SCYLV was detected by tissue blot immunoassay and the Hawaiian sugarcane cultivars fell into susceptible cultivars (with SCYLV) and resistant cultivars (without SCYLV). RT-PCR showed recently that the resistant cultivars also contain the virus, however with a 100-fold lower virus titre than in the susceptible cultivars. SCYLV is present as whole genome (6 kb) or as two subgenomic sequences of 2.4 and 1.0 kb. Virus preparations from three Hawaiian cultivars (one resistant and two susceptible) were fully sequenced and the sequences were aligned to published, full and partial sequences. The phylograms corroborate previous findings that the so-called YLS-segment, which codes for the coat protein, shows the least genetic diversity, whereas the other sequence fragments A–D, representing the ORFs 0–5, expressed a two-fold higher diversity. The Hawaiian SCYLV-strains clustered together next to the Peru strain, apart from the BRA-strains and well apart from the REU-strains. We propose that the Hawaiian SCYLV should be considered as an independent group together with the Peru strain and known as HAW-PER. The sequences from the two susceptible cultivars had a deletion of 48 to 54 nt in ORF1, which codes for the gene silencing suppressor and a RNA-dependent RNA-polymerase. It is speculated that this deletion is important for the high proliferation rate of the virus in the susceptible plants.

Variation in virus populations and growth characteristics of two sugarcane cultivars naturally infected by Sugarcane yellow leaf virus in different geographical locations

Two sugarcane cultivars (R570 and SP71‐6163) naturally infected by Sugarcane yellow leaf virus (SCYLV) were each imported from several geographical locations into a sugarcane yellow leaf‐free environment (Montpellier, France). Plants were grown as plant cane for 5–6 months and the experiment was repeated for three consecutive years (2003–2005) in a greenhouse. Several sugarcane‐growth and disease characteristics were monitored to identify variation in pathogenicity of SCYLV. Depending on their geographical origin, sugarcane cvs R570 and SP71‐6163 were infected by SCYLV genotypes BRA‐PER or REU, or a mixture of the two. Severity of symptoms did not vary between plants of cv. R570, but variation in disease severity between plants of cv. SP71‐6163 from different geographical locations suggested the occurrence of pathogenic variants of SCYLV. For each sugarcane cultivar, differences in stalk length, number of stalk internodes, virus titre in the top visible dewlap leaf, and percentage of infection of leaf and stalk phloem vessels were also found between plants from different geographical origins. However, these differences were not always reproducible from one year to another, suggesting occurrence of different plant responses to SCYLV isolates under varying environmental conditions.

Variation in Infection Capacity and in Virulence Exists Between Genotypes of Sugarcane yellow leaf virus.

Two experiments, one in Guadeloupe and one in Réunion Island, were performed to transmit different genotypes of Sugarcane yellow leaf virus (SCYLV) to eight sugarcane cultivars differing in resistance to infection by the virus and to yellow leaf. Transmission was attempted from SCYLV-infected sugarcane plants or leaves to healthy tissue-cultured plantlets grown in vitro and with the aphid vector Melanaphis sacchari. After inoculation and elimination of insects with an insecticide, plantlets were transferred to Montpellier, France and grown in a greenhouse. Plants were tested for presence of SCYLV by tissue-blot immunoassay and reverse-transcription polymerase chain reaction after 5 to 6 months of growth. SCYLV genotypes BRA-PER, CUB, and REU were detected in 47, 62, and 39% of plants inoculated with these genotypes in Guadeloupe, respectively. SCYLV genotypes BRA-PER and REU and a mixed infection of genotypes BRA-PER and REU were detected in 56, 33, and 42% of plants inoculated with these genotypes in Réunion Island, respectively. Genotypes BRA-PER and CUB could be transmitted to all eight sugarcane cultivars, but genotype REU could never be transmitted to resistant sugarcane cvs. H78-4153 and H78-3567. SCYLV genotype REU was transmitted successfully to sugarcane cv. R570 in Guadeloupe, but not in Réunion Island. Genotypes BRA-PER and CUB induced yellow leaf symptoms in susceptible or highly susceptible sugarcane cultivars, whereas genotype REU induced very few symptoms. SCYLV was not found in several symptomatic plants, suggesting an association of disease with undetectable populations of the virus or a nonviral cause. This is the first report of variation in infection capacity and in virulence of SCYLV.

Geographical Distribution of Four Sugarcane yellow leaf virus Genotypes.

Specific primer pairs were designed to distinguish four genotypes (BRA for Brazil, CUB for Cuba, PER for Peru, and REU for Réunion Island) of Sugarcane yellow leaf virus (SCYLV) by reverse transcription-polymerase chain reaction (RT-PCR). A unique genome fragment was amplified from each genotype, with the exception of genotypes BRA and PER that are phylogenetically relatively close and were designated genotype BRA-PER. These RT-PCR primers were then used to identify the SCYLV genotype(s) present in 18 different sugarcane growing locations in the world, and 245 leaf samples infected by the virus were analyzed. Most samples were infected by only one of the three genotypes, but mixed infections occurred. Genotype BRA-PER was found in all sugarcane growing locations, whereas genotypes CUB and REU were each found in four geographical locations only. Genotypes BRA-PER, CUB, and REU were all three detected in locally bred sugarcane cultivars in Guadeloupe, indicating local transmission of these genotypes. In contrast, only genotypes BRA-PER and CUB were found in locally bred cultivars in Brazil, whereas genotype REU was detected in this country in cultivar R570 imported from Réunion. Similarly, genotypes BRA-PER and REU are both present in Réunion, but genotype BRA-PER has not, as of yet, spread on this island. Presence of several SCYLV genotypes in Brazil, Colombia, Guadeloupe, Mauritius, and Réunion suggests different virus introductions and/or different evolution histories of the virus after its introduction into a new environment.