Sequence diversity in the coat protein coding region of twelve sugarcane mosaic potyvirus isolates from Australia, USA and South Africa

Eight Species of Poaceae Are Hosting Different Genetic and Pathogenic Strains of Sugarcane Mosaic Virus in the Everglades Agricultural Area

Sugarcane mosaic virus (SCMV) was detected by reverse transcription polymerase chain reaction in eight different species of the Poaceae family in the Everglades Agricultural Area (EAA) of south Florida: broadleaf signalgrass (Urochloa platyphylla), Columbus grass (Sorghum almum), goosegrass (Eleusine indica), maize (Zea mays), sorghum (Sorghum bicolor), St. Augustine grass (Stenotaphrum secundatum), southern crabgrass (Digitaria ciliaris), and sugarcane (Saccharum interspecific hybrids). Based on their coat protein (CP) gene sequence, 62 isolates of SCMV from Florida and 29 worldwide isolates representing the known genetic diversity of this virus were distributed into eight major phylogenetic groups. SCMV isolates infecting Columbus grass, maize, and sorghum in Florida formed a unique group, whereas virus isolates infecting sugarcane in the United States (Florida and Louisiana) clustered with isolates from other countries. Based on the entire genome coding region, SCMV isolates infecting sugarcane in Florida were closest to virus isolates infecting sorghum species or St. Augustine grass. Virus isolates from Columbus grass, St. Augustine grass, and sugarcane showed different virulence patterns after mechanical inoculation of Columbus grass, St. Augustine grass, and sugarcane plants, thus proving that these isolates were different pathogenic strains. Sugarcane was symptomless and tested negative for SCMV by tissue blot immunoassay after inoculation with crude sap from SCMV-infected Columbus grass, indicating that Columbus grass was not a reservoir for SCMV infecting sugarcane in the EAA. Close CP sequence identity between isolates of SCMV from Columbus grass, maize, and sorghum suggested that the same virus strain was naturally spreading between these three plants in south Florida.

Genetic analysis of tropical maize inbred lines for resistance to maize lethal necrosis disease

Maize lethal necrosis (MLN) disease is a recent outbreak in eastern Africa and has emerged as a significant threat to maize production in the region. The disease is caused by the co-infection of Maize chlorotic mottle virus and any member of potyviridae family. A total of 28 maize inbred lines with varying levels of tolerance to MLN were crossed in a half-diallel mating design, and the resulting 340 F1 crosses and four commercial checks were evaluated under MLN artificial inoculation at Naivasha, Kenya in 2015 and 2016 using an alpha lattice design with two replications. The objectives of the study were to (i) investigate the magnitude of general combining ability variance (σGCA 2) and specific combining ability variance (σSCA 2) and their interaction with years; (ii) evaluate the efficiencies of GCA based prediction and hybrid performance by means of a cross-validation procedure; (iii) estimate trait correlations in the hybrids; and (iv) identify the MLN tolerant single cross hybrids to be used as female parents for three-way cross hybrids. Results of the combined analysis of variance revealed that both GCA and SCA effects were significant (P < 0.05) for all traits except for ear rot. For MLN scores at early and late stages, GCA effects were 2.5-3.5 times higher than SCA effects indicating that additive gene action is more important than non-additive gene action. The GCA based prediction efficiency for MLN resistance and grain yield accounted for 67-90% of the variations in the hybrid performance suggesting that GCA-based prediction can be proposed to predict MLN resistance and grain yield prior to field evaluation. Three parents, CKDHL120918, CML550, and CKLTI0227 with significant GCA effects for GY (0.61-1.21; P < 0.05) were the most resistant to MLN. Hybrids "CKLTI0227 × CML550", "CKDHL120918 × CKLTI0138", and "CKDHL120918 × CKLTI0136" ranked among the best performing hybrids with grain yield of 6.0-6.6 t/ha compared with mean yield of commercial check hybrids (0.6 t/ha). The MLN tolerant inbred lines and single cross hybrids identified in this study could be used to improve MLN tolerance in both public and private sector maize breeding programs in eastern Africa.

Occurrence and Evolutionary Analysis of Coat Protein Gene Sequences of Iranian Isolates of Sugarcane mosaic virus

Sugarcane mosaic virus (SCMV) is one of the most damaging viruses infecting sugarcane, maize and some other graminaceous species around the world. To investigate the genetic diversity of SCMV in Iran, the coat protein (CP) gene sequences of 23 SCMV isolates from different hosts were determined. The nucleotide sequence identity among Iranian isolates was more than 96%. They shared nucleotide identities of 75.5-99.9% with those of other SCMV isolates available in GenBank, the highest with the Egyptian isolate EGY7-1 (97.5-99.9%). The results of phylogenetic analysis suggested five divergent evolutionary lineages that did not completely reflect the geographical origin or host plant of the isolates. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. Our results indicated that natural selection might have contributed to the evolution of isolates belonging to the five identified SCMV groups, with infrequent genetic exchanges occurring between them. Phylogenetic analyses and the estimation of genetic distance indicated that Iranian isolates have low genetic diversity. No recombination was found in the CP cistron of Iranian isolates and the CP gene was under negative selection. These findings provide a comprehensive analysis of the population structure and driving forces for the evolution of SCMV with implications for global exchange of sugarcane germplasm. Gene flow, selection and somehow homologous recombination were found to be the important evolutionary factors shaping the genetic structure of SCMV populations.

Genetic analysis of tropical maize inbred lines for resistance to maize lethal necrosis disease

Maize lethal necrosis (MLN) disease is a recent outbreak in eastern Africa and has emerged as a significant threat to maize production in the region. The disease is caused by the co-infection of Maize chlorotic mottle virus and any member of potyviridae family. A total of 28 maize inbred lines with varying levels of tolerance to MLN were crossed in a half-diallel mating design, and the resulting 340 F₁ crosses and four commercial checks were evaluated under MLN artificial inoculation at Naivasha, Kenya in 2015 and 2016 using an alpha lattice design with two replications. The objectives of the study were to (i) investigate the magnitude of general combining ability variance (σ_GCA ²) and specific combining ability variance (σ_SCA ²) and their interaction with years; (ii) evaluate the efficiencies of GCA based prediction and hybrid performance by means of a cross-validation procedure; (iii) estimate trait correlations in the hybrids; and (iv) identify the MLN tolerant single cross hybrids to be used as female parents for three-way cross hybrids. Results of the combined analysis of variance revealed that both GCA and SCA effects were significant (P < 0.05) for all traits except for ear rot. For MLN scores at early and late stages, GCA effects were 2.5-3.5 times higher than SCA effects indicating that additive gene action is more important than non-additive gene action. The GCA based prediction efficiency for MLN resistance and grain yield accounted for 67-90% of the variations in the hybrid performance suggesting that GCA-based prediction can be proposed to predict MLN resistance and grain yield prior to field evaluation. Three parents, CKDHL120918, CML550, and CKLTI0227 with significant GCA effects for GY (0.61-1.21; P < 0.05) were the most resistant to MLN. Hybrids "CKLTI0227 × CML550", "CKDHL120918 × CKLTI0138", and "CKDHL120918 × CKLTI0136" ranked among the best performing hybrids with grain yield of 6.0-6.6 t/ha compared with mean yield of commercial check hybrids (0.6 t/ha). The MLN tolerant inbred lines and single cross hybrids identified in this study could be used to improve MLN tolerance in both public and private sector maize breeding programs in eastern Africa.

Maize Lethal Necrosis (MLN), an Emerging Threat to Maize-Based Food Security in Sub-Saharan Africa

In sub-Saharan Africa, maize is a staple food and key determinant of food security for smallholder farming communities. Pest and disease outbreaks are key constraints to maize productivity. In September 2011, a serious disease outbreak, later diagnosed as maize lethal necrosis (MLN), was reported on maize in Kenya. The disease has since been confirmed in Rwanda and the Democratic Republic of Congo, and similar symptoms have been reported in Tanzania, Uganda, South Sudan, and Ethiopia. In 2012, yield losses of up to 90% resulted in an estimated grain loss of 126,000 metric tons valued at $52 million in Kenya alone. In eastern Africa, MLN was found to result from coinfection of maize with Maize chlorotic mottle virus (MCMV) and Sugarcane mosaic virus (SCMV), although MCMV alone appears to cause significant crop losses. We summarize here the results of collaborative research undertaken to understand the biology and epidemiology of MLN in East Africa and to develop disease management strategies, including identification of MLN-tolerant maize germplasm. We discuss recent progress, identify major issues requiring further research, and discuss the possible next steps for effective management of MLN.

Sharka: the past, the present and the future

Members the Potyviridae family belong to a group of plant viruses that are causing devastating plant diseases with a significant impact on agronomy and economics. Plum pox virus (PPV), as a causative agent of sharka disease, is widely discussed. The understanding of the molecular biology of potyviruses including PPV and the function of individual proteins as products of genome expression are quite necessary for the proposal the new antiviral strategies. This review brings to view the members of Potyviridae family with respect to plum pox virus. The genome of potyviruses is discussed with respect to protein products of its expression and their function. Plum pox virus distribution, genome organization, transmission and biochemical changes in infected plants are introduced. In addition, techniques used in PPV detection are accentuated and discussed, especially with respect to new modern techniques of nucleic acids isolation, based on the nanotechnological approach. Finally, perspectives on the future of possibilities for nanotechnology application in PPV determination/identification are outlined.

Identification of new variants of SCMV causing sugarcane mosaic in India and assessing their genetic diversity in relation to SCMV type strains

Sugarcane mosaic virus (SCMV) is one of the two causative viruses of mosaic in sugarcane, a sugar crop widely grown under tropical and subtropical conditions worldwide. Although molecular characterization of SCMV strains was reported from many countries, strains occurring in India, a major sugarcane producer have not been reported so far. Twenty-six sugarcane samples represented by seven major sugarcane growing states in India and USA were subjected to reverse-transcription polymerase chain reaction (RT-PCR) using a pair of newly designed coat protein specific primers. Among them 17 were found positive to the SCMV infection. The lengths of the sequences derived in this study using the new set of primers varied between 812 and 866 nt. The amino acid sequence comparison of 30 Indian SCMV isolates showed wide range of sequence similarities in core region (88.80-100%) and hyper variable region (51.3-100%). In the N-terminal region of the five Indian isolates, a deletion of 12 aa residues between aa 11 and 30 was observed, whereas the deletion was between aa 45 and 50 in SCMV-B and -D and between aa 61 and 70 in SCMV-A. The phylogenetic analyses performed with 46 SCMV CP sequences for both hyper variable region and core region separated the isolates mostly according to their geographical origin. The 30 Indian SCMV isolates were included exclusively in four groups besides SCMV-IND, which was grouped with SCMV-SC, a type of strain from Australia. Nearly 97.0% of the Indian isolates have no signs for close relationships with previously characterized SCMV type strains (SCMV-A, -B, -D, -E, and -SC) reported from other countries. Our studies revealed that the sugarcane mosaic in India are caused by at least nine new SCMV variants (IND-CC1, -CC2, -CC3, -CC4, -CO1, -CO2, -CP, -CS, and -J) and a type strain SCMV-SC represented by SCMV-IND. This is the first report on the variability and occurrence of new SCMV population in India.

Simultaneous detection and identification of four sugarcane viruses by one-step RT-PCR

Sugarcane mosaic disease (SMD) caused by the Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV) and Sugarcane streak mosaic virus (SCSMV) and sugarcane yellow leaf disease (SYLD) caused by the Sugarcane yellow leaf virus (SCYLV) are the two most prevalent and economically important viral diseases of sugarcane. In this study, a one-step quadruplex reverse transcription (RT)-PCR method that employed virus-specific primers was developed for the simultaneous detection and differentiation of SCMV, SrMV, SCSMV and SCYLV. Several sets of primers for each target virus were evaluated for their sensitivity and specificity by simplex and quadruplex RT-PCR. The optimum primer combinations and concentrations, RT temperature and time, and PCR annealing temperature and extension time were determined for the quadruplex RT-PCR. The assay was then validated using sugarcane samples affected with SMD and/or SYLD collected from sugarcane breeding fields and farmers' fields in southern China.

Genetic diversity among viruses associated with sugarcane mosaic disease in Tucumán, Argentina

Sugarcane leaves with mosaic symptoms were collected in 2006--07 in Tucumán (Argentina) and analyzed by reverse-transcriptase polymerase chain reaction (RT-PCR) restriction fragment length polymorphism (RFLP) and sequencing of a fragment of the Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) coat protein (CP) genes. SCMV was detected in 96.6% of samples, with 41% showing the RFLP profile consistent with strain E. The remaining samples produced eight different profiles that did not match other known strains. SCMV distribution seemed to be more related to sugarcane genotype than to geographical origin, and sequence analyses of CP genes showed a greater genetic diversity compared with other studies. SrMV was detected in 63.2% of samples and most of these were also infected by SCMV, indicating that, unlike other countries and other Argentinean provinces, where high levels of co-infection are infrequent, co-existence is common in Tucumán. RFLP analysis showed the presence of SrMV strains M (68%) and I (14%), while co-infection between M and H strains was present in 18% of samples. Other SCMV subgroup members and the Sugarcane streak mosaic virus (SCSMV) were not detected. Our results also showed that sequencing is currently the only reliable method to assess SCMV and SrMV genetic diversity, because RT-PCR-RFLP may not be sufficiently discriminating.

Viruses causing mosaic disease in sugarcane and their genetic diversity in southern China

A survey of cultivated hybrid sugarcane (Saccharum inter-specific hybrid) and noble sugarcane (Saccharum officinarum) in southern China for the presence of Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV) and Sugarcane streak mosaic virus (SCSMV) was conducted by RT-PCR from the years 2003 to 2006. SCMV and SrMV, but not SCSMV, were found. A high incidence of SCMV and SrMV coinfection was revealed in both hybrid and noble sugarcanes. All coinfected plants showed mosaic symptom, whereas plants infected with a single virus were symptomatic or asymptomatic. It appears that virus mixtures are more virulent than single infections. The nucleotide sequences of the coat protein (CP) gene of 33 SCMV and 10 SrMV isolates from this study were compared to those of CP genes of SCMV and SrMV reported in GenBank. One hundred and seventy-three SCMV isolates, with the exception of MDB and Abaca strains, can be grouped into five groups, which include three previously known groups, the sugarcane (SCE), maize (MZ), and Thailand groups, and two newly identified groups, the noble sugarcane (NSCE) and Brazil groups. Twenty-two SrMV isolates were divided into two groups, HS (hybrid sugarcane) and NS (noble sugarcane) groups. Five out of eight SrMV hybrid isolates belonged to the HS group, and two SrMV noble isolates and three hybrid isolates were within the NS group. Interestingly, the three hybrid isolates within the NS group were isolated from hybrid sugarcane co-infected with SCMV. This indicates that SCMV helps the NS group SrMV to infect hybrid sugarcane.

Identification of a naturally occurring recombinant isolate of Sugarcane mosaic virus causing maize dwarf mosaic disease

The complete nucleotide sequence of a potyvirus causing severe maize dwarf mosaic disease in Shaanxi province, northwestern China was determined (GenBank accession No. AY569692). The full genome is 9596 nucleotides in length excluding the 3 '-terminal poly (A) sequence. It contains a large open reading frame (ORF) flanked by a 149 nt 5'-untranslated region (UTR) and a 255 nt 3'-UTR. The putative polyprotein encoded by this large ORF comprises of 3063 amino acid residues. Sequence comparisons and phylogenetic analyses showed that this potyvirus is an isolate of Sugarcane mosaic virus (SCMV). The entire sequences shared identities of 89.6-97.6 % and 79.3-93.3% with 9 sequenced SCMV isolates at the nucleotide and deduced amino acid levels, respectively. But it showed much lower identities with Maize dwarf mosaic virus (MDMV), Sorghum mosaic virus (SrMV) and Johnsongrass mosaic virus (JGMV) isolates. The putative coat protein sequence is identical to that of a Chinese maize isolate SCMV-HZ. However, partition comparisons and phylogenetic profile analyses of the viral nucleotide sequences indicated that it is a recombinant isolate of SCMV. The recombination sites are located within the 6K1 and CI coding regions.