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

Yellow Leaf Disease Resistance and Melanaphis sacchari Preference in Commercial Sugarcane Cultivars

Sugarcane yellow leaf disease (YLD) caused by sugarcane yellow leaf virus (ScYLV) is a major threat for the sugarcane industry worldwide, and the aphid Melanaphis sacchari is its main vector. Breeding programs in Brazil have provided cultivars with intermediate resistance to ScYLV, whereas the incidence of ScYLV has been underestimated partly due to the complexity of YLD symptom expression and identification. Here, we evaluated YLD symptoms in a field assay using eight sugarcane genotypes comprising six well-established commercial high-sucrose cultivars, one biomass yield cultivar, and a susceptible reference under greenhouse conditions, along with estimation of virus titer through RT-qPCR from leaf samples. Additionally, a free-choice bioassay was used to determine the number of aphids feeding on the SCYLV-infected cultivars. Most of the cultivars showed some degree of resistance to YLD, while also revealing positive RT-qPCR results for ScYLV and virus titers with non-significant correlation with YLD severity. The cultivars IACSP01-5503 and IACBIO-266 were similar in terms of aphid preference and ScYLV resistance traits, whereas the least preferred cultivar by M. sacchari, IACSP96-7569, showed intermediate symptoms but similar virus titer to the susceptible reference, SP71-6163. We conclude that current genetic resistance incorporated into sugarcane commercial cultivars does not effectively prevent the spread of ScYLV by its main aphid vector.

Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations

Yellow leaf disease caused by sugarcane yellow leaf virus (SCYLV) is one of the most prevalent diseases worldwide. In this study, six near-complete genome sequences of SCYLV were determined to be 5775-5881 bp in length. Phylogenetic analysis revealed that the two SCYLV isolates from Réunion Island, France, and four from China were clustered into REU and CUB genotypes, respectively, based on 50 genomic sequences (this study = 6, GenBank = 44). Meanwhile, all 50 isolates were clustered into three phylogroups (G1-G3). Twelve significant recombinant events occurred in intra- and inter-phylogroups between geographical origins and host crops. Most recombinant hotspots were distributed in coat protein read-through protein (RTD), followed by ORF0 (P0) and ORF1 (P1). High genetic divergences of 12.4% for genomic sequences and 6.0-24.9% for individual genes were determined at nucleotide levels. The highest nucleotide diversity (π) was found in P0, followed by P1 and RdRP. In addition, purifying selection was a main factor restricting variability in SCYLV populations. Infrequent gene flow between Africa and the two subpopulations (Asia and America) were found, whereas frequent gene flow between Asia and America subpopulations was observed. Taken together, our findings facilitate understanding of genetic diversity and evolutionary dynamics of SCYLV.

Genetic Transformation of Sugarcane, Current Status and Future Prospects

Sugarcane (Saccharum spp.) is a tropical and sub-tropical, vegetative-propagated crop that contributes to approximately 80% of the sugar and 40% of the world's biofuel production. Modern sugarcane cultivars are highly polyploid and aneuploid hybrids with extremely large genomes (>10 Gigabases), that have originated from artificial crosses between the two species, Saccharum officinarum and S. spontaneum. The genetic complexity and low fertility of sugarcane under natural growing conditions make traditional breeding improvement extremely laborious, costly and time-consuming. This, together with its vegetative propagation, which allows for stable transfer and multiplication of transgenes, make sugarcane a good candidate for crop improvement through genetic engineering. Genetic transformation has the potential to improve economically important properties in sugarcane as well as diversify sugarcane beyond traditional applications, such as sucrose production. Traits such as herbicide, disease and insect resistance, improved tolerance to cold, salt and drought and accumulation of sugar and biomass have been some of the areas of interest as far as the application of transgenic sugarcane is concerned. Although there have been much interest in developing transgenic sugarcane there are only three officially approved varieties for commercialization, all of them expressing insect-resistance and recently released in Brazil. Since the early 1990's, different genetic transformation systems have been successfully developed in sugarcane, including electroporation, Agrobacterium tumefaciens and biobalistics. However, genetic transformation of sugarcane is a very laborious process, which relies heavily on intensive and sophisticated tissue culture and plant generation procedures that must be optimized for each new genotype to be transformed. Therefore, it remains a great technical challenge to develop an efficient transformation protocol for any sugarcane variety that has not been previously transformed. Additionally, once a transgenic event is obtained, molecular studies required for a commercial release by regulatory authorities, which include transgene insertion site, number of transgenes and gene expression levels, are all hindered by the genomic complexity and the lack of a complete sequenced reference genome for this crop. The objective of this review is to summarize current techniques and state of the art in sugarcane transformation and provide information on existing and future sugarcane improvement by genetic engineering.

Present Status and Future Management Strategies for Sugarcane Yellow Leaf Virus: A Major Constraint to the Global Sugarcane Production

Sugarcane yellow leaf virus (SCYLV) is a distinct member of the Polerovirus genus of the Luteoviridae family. SCYLV is the major limitation to sugarcane production worldwide and presently occurring in most of the sugarcane growing countries. SCYLV having high genetic diversity within the species and presently ten genotypes are known to occur based on the complete genome sequence information. SCYLV is present in almost all the states of India where sugarcane is grown. Virion comprises of 180 coat protein units and are 24-29 nm in diameter. The genome of SCYLV is a monopartite and comprised of single-stranded (ss) positive-sense (+) linear RNA of about 6 kb in size. Virus genome consists of six open reading frames (ORFs) that are expressed by sub-genomic RNAs. The SCYLV is phloem-limited and transmitted by sugarcane aphid Melanaphis sacchari in a circulative and non-propagative manner. The other aphid species namely, Ceratovacuna lanigera, Rhopalosiphum rufiabdominalis, and R. maidis also been reported to transmit the virus. The virus is not transmitted mechanically, therefore, its transmission by M. sacchari has been studied in different countries. SCYLV has a limited natural host range and mainly infect sugarcane (Sachharum hybrid), grain sorghum (Sorghum bicolor), and Columbus grass (Sorghum almum). Recent insights in the protein-protein interactions of Polerovirus through protein interaction reporter (PIR) technology enable us to understand viral encoded proteins during virus replication, assembly, plant defence mechanism, short and long-distance travel of the virus. This review presents the recent understandings on virus biology, diagnosis, genetic diversity, virus-vector and host-virus interactions and conventional and next generation management approaches.

Lack of transmission of Sugarcane yellow leaf virus in Florida from Columbus grass and sugarcane to sugarcane with aphids or mites

Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf disease, naturally infects at least three plant species in Florida: sugarcane (Saccharum spp.), the weed Columbus grass (Sorghum almum) and cultivated sorghum (S. bicolor). All three hosts are also colonized by the sugarcane aphid (Melanaphis sacchari), the main vector of SCYLV worldwide. To understand the high incidence of SCYLV observed in sugarcane commercial fields and in germplasm collections, we investigated the transmission efficiency of SCYLV from sugarcane and Columbus grass to sugarcane using the sugarcane aphid and a spider mite (Oligonychus grypus) that also tested positive for SCYLV in Florida. Healthy and SCYLV-infected leaf pieces of sugarcane and Columbus grass carrying viruliferous aphids or spider mites were transferred to virus-free plants of the yellow leaf susceptible sugarcane cultivar CP96-1252. Three- and 6-months post inoculation, the 108 aphid-inoculated plants of Columbus grass and the 90 mite-inoculated plants of sugarcane tested negative for SCYLV by tissue blot immunoassay (TBIA) or reverse transcription polymerase chain reaction (RT-PCR). Similar results were obtained for 162 aphid-inoculated plants of sugarcane, except for two plants that tested positive for SCYLV by TBIA and RT-PCR. In two field experiments planted with SCYLV-free and virus-infected sugarcane (cultivar CP96-1252), only 18–28% of healthy plants became infected during a 24- to 28-month period. SCYLV prevalence in these field experiments did not differ between aphicide treated and untreated plots. Incidence of M. sacchari haplotypes in the Everglades agricultural area also indicated that the predominant haplotype that is currently colonizing sugarcane was not a vector of SCYLV in Florida. Lack of virus transmission by the spider mite suggested that this arthropod only acquired the virus when feeding on infected plants but was unable to transmit SCYLV. The current vector of SCYLV in Florida remains to be identified.

Field Infection of Virus-Free Sugarcane by Sugarcane Yellow Leaf Virus and Effect of Yellow Leaf on Sugarcane Grown on Organic and on Mineral Soils in Florida

Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf, is widespread in Florida. Two field trials were set up, one on organic soil and one on mineral soil, to investigate the rate and timing of sugarcane infection by SCYLV under field conditions and the effect of the virus on yield. Each trial consisted of plots planted with healthy or SCYLV-infected seed cane of two commercial cultivars. Virus prevalence varied from 83 to 100% in plots planted with infected seed cane regardless of cultivar, location, and crop season. On organic soil, plants of virus-free plots became progressively infected in plant cane and first ratoon crops. On mineral soil, healthy sugarcane became initially infected in the first ratoon crop. After three crop seasons, the highest SCYLV prevalence rates were 33 and 7% on organic and mineral soils, respectively. No significant negative effect of SCYLV on yield was found in plant cane crop regardless of cultivar and soil type. However, yield reductions in ratoon crops varied from nonsignificant to 27% depending on cultivar and soil type. Low virus prevalence observed after three crop seasons suggested that planting virus-free seed cane should limit the impact of SCYLV on sugarcane production in Florida.

Genome characterization of Sugarcane Yellow Leaf Virus with special reference to RNAi based molecular breeding

Sugarcane is an essential crop for sugar and biofuel. Globally, its production is severely affected by sugarcane yellow leaf disease (SCYLD) caused by Sugarcane Yellow Leaf Virus (SCYLV). Many aphid vectors are involved in the spread of the disease which reduced the effectiveness of cultural and chemical management. Empirical methods of plant breeding such as introgression from wild and cultivated germplasm were not possible or at least challenging due to the absence of resistance in cultivated and wild germplasm of sugarcane. RNA interference (RNAi) transformation is an effective method to create virus-resistant varieties. Nevertheless, limited progress has been made due to lack of comprehensive research program on SCYLV based on RNAi technique. In order to show improvement and to propose future strategies for the feasibility of the RNAi technique to cope SCYLV, genome-wide consensus sequences of SCYLV were analyzed through GenBank. The coverage rates of every consensus sequence in SCYLV isolates were calculated to evaluate their practicability. Our analysis showed that single consensus sequence from SCYLV could not work well for RNAi based sugarcane breeding programs. This may be due to high mutation rate and continuous recombination within and between various viral strains. Alternative multi-target RNAi strategy is suggested to combat several strains of the viruses and to reduce the silencing escape. The multi-target small interfering RNA (siRNA) can be used together to construct RNAi plant expression plasmid, and to transform sugarcane tissues to develop new sugarcane varieties resistant to SCYLV.

Host Plant Specialization in the Sugarcane Aphid Melanaphis sacchari

Most aphids are highly specialized on one or two related plant species and generalist species often include sympatric populations adapted to different host plants. Our aim was to test the hypothesis of the existence of host specialized lineages of the aphid Melanaphis sacchari in Reunion Island. To this end, we investigated the genetic diversity of the aphid and its association with host plants by analyzing the effect of wild sorghum Sorghum bicolor subsp. verticilliflorum or sugarcane as host plants on the genetic structuring of populations and by performing laboratory host transfer experiments to detect trade-offs in host use. Genotyping of 31 samples with 10 microsatellite loci enabled identification of 13 multilocus genotypes (MLG). Three of these, Ms11, Ms16 and Ms15, were the most frequent ones. The genetic structure of the populations was linked to the host plants. Ms11 and Ms16 were significantly more frequently observed on sugarcane, while Ms15 was almost exclusively collected in colonies on wild sorghum. Laboratory transfer experiments demonstrated the existence of fitness trade-offs. An Ms11 isofemale lineage performed better on sugarcane than on sorghum, whereas an Ms15 lineage developed very poorly on sugarcane, and two Ms16 lineages showed no significant difference in performances between both hosts. Both field and laboratory results support the existence of host plant specialization in M. sacchari in Reunion Island, despite low genetic differentiation. This study illustrates the ability of asexual aphid lineages to rapidly undergo adaptive changes including shifting from one host plant to another.

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 evolutionary history of Sugarcane yellow leaf virus based on sequence analysis of RNA-dependent RNA polymerase and putative aphid transmission factor-coding genes

RNA-dependent RNA polymerase (RdRp) encoded by ORF2 and putative aphid transmission factor (PATF) encoded by ORF5 of Sugarcane yellow leaf virus (SCYLV) were detected in six sugarcane cultivars affected by yellow leaf using RT-PCR and real-time RT-PCR assays. Expression of both genes varied among infected plants, but overall expression of RdRp was higher than expression of PATF. Cultivar H87-4094 from Hawaii yielded the highest transcript levels of RdRp, whereas cultivar C1051-73 from Cuba exhibited the lowest levels. Sequence comparisons among 25 SCYLV isolates from various geographical locations revealed an amino acid similarity of 72.1-99.4 and 84.7-99.8 % for the RdRp and PATF genes, respectively. The 25 SCYLV isolates were separated into three (RdRp) and two (PATF) phylogenetic groups using the MEGA6 program that does not account for genetic recombination. However, the SCYLV genome contained potential recombination signals in the RdRp and PATF coding genes based on the GARD genetic algorithm. Use of this later program resulted in the reconstruction of phylogenies on the left as well as on the right sides of the putative recombination breaking points, and the 25 SCYLV isolates were distributed into three distinct phylogenetic groups based on either RdRp or PATF sequences. As a result, recombination reshuffled the affiliation of the accessions to the different clusters. Analysis of selection pressures exerted on RdRp and PATF encoded proteins revealed that ORF 2 and ORF 5 underwent predominantly purifying selection. However, a few sites were also under positive selection as assessed by various models such as FEL, IFEL, REL, FUBAR, MEME, GA-Branch, and PRIME.

A near-complete genome sequence of a distinct isolate of Sugarcane yellow leaf virus from China, representing a sixth new genotype

The 5803 nt genomic sequence of a Sugarcane yellow leaf virus (SCYLV) isolate (SCYLV-chn1) from China was determined. It covered more than 98% of the complete viral genome and contained all the six ORFs and the entire intergenic untranslated region. This isolate was most closely related to SCYLV genotype CUB (isolates CUB-YL1 and CB86010) with identities of 95.2-97.4% (nt) (93.2-97.2% aa) in ORF0, ORF1, and ORF2. Sequence comparison and phylogenetic analyses supported the view that this isolate represents a new genotype; SCYLV CHN1 was suggested as the name for this new genotype.

Identification of three genotypes of sugarcane yellow leaf virus causing yellow leaf disease from India and their molecular characterization

Sugarcane yellow leaf virus (SCYLV) that causes yellow leaf disease (YLD) in sugarcane (recently reported in India) belongs to Polerovirus. Detailed studies were conducted to characterize the virus based on partial open reading frames (ORFs) 1 and 2 and complete ORFs 3 and 4 sequences in their genome. Reverse-transcriptase polymerase chain reaction (RT-PCR) was performed on 48 sugarcane leaf samples to detect the virus using a specific set of primers. Of the 48 samples, 36 samples (field samples with and without foliar symptoms) including 10 meristem culture derived plants were found to be positive to SCYLV infection. Additionally, an aphid colony collected from symptomatic sugarcane in the field was also found to be SCYLV positive. The amplicons from 22 samples were cloned, sequenced and acronymed as SCYLV-CB isolates. The nucleotide (nt) and amino acid (aa) sequence comparison showed a significant variation between SCYLV-CB and the database sequences at nt (3.7-5.1%) and aa (3.2-5.3%) sequence level in the CP coding region. However, the database sequences comprising isolates of three reported genotypes, viz., BRA, PER and REU, were observed with least nt and aa sequence dissimilarities (0.0-1.6%). The phylogenetic analyses of the overlapping ORFs (ORF 3 and ORF 4) of SCYLV encoding CP and MP determined in this study and additional sequences of 26 other isolates including an Indian isolate (SCYLV-IND) available from GenBank were distributed in four phylogenetic clusters. The SCYLV-CB isolates from this study lineated in two clusters (C1 and C2) and all the other isolates from the worldwide locations into another two clusters (C3 and C4). The sequence variation of the isolates in this study with the database isolates, even in the least variable region of the SCYLV genome, showed that the population existing in India is significantly different from rest of the world. Further, comparison of partial sequences encoding for ORFs 1 and 2 revealed that YLD in sugarcane in India is caused by at least three genotypes, viz., CUB, IND and BRA-PER, of which a majority of the samples were found infected with Cuban genotype (CUB) and lesser by IND and BRA-PER genotypes. The genotype IND was identified as a new genotype from this study, and this was found to have significant variation with the reported genotypes.