Detection of Sugarcane yellow leaf virus and Sugarcane mosaic virus in arthropods collected from corn, sorghum and sugarcane in Florida

In Florida, sugarcane (Saccharum spp.), Columbus grass (Sorghum almum), and grain sorghum (S. bicolor) are three hosts of sugarcane yellow leaf virus (SCYLV) and sugarcane mosaic virus (SCMV). SCYLV is the causal agent of yellow leaf disease and is mainly vectored by the sugarcane aphid (Melanaphis sacchari). SCMV, the causal agent of mosaic disease, is spread by several aphid vectors. The objective of this study was to investigate the occurrence of SCYLV and SCMV in arthropods collected in the Everglades Agricultural Area in order to better understand the epidemiology of these viruses. Reverse transcription-polymerase chain reaction (RT-PCR) or nested RT-PCR was used to detect both viruses in plants and arthropods. SCYLV and SCMV were detected in sugarcane, Columbus grass, and grain sorghum. SCYLV was also found in M. sacchari, Oligonychus grypus (spider mite), and Sipha flava (yellow sugarcane aphid) but SCMV was not detected in any of the tested arthropods. Populations of M. sacchari collected from sugarcane belonged to haplotype H3 whereas populations colonizing Columbus grass and grain sorghum belonged to haplotype H1. This suggested that cross-infections of SCYLV between sugarcane and the two sorghum species do not frequently occur under field conditions. Capacity of the spider mite and the yellow sugarcane aphid to transmit SCYLV needs to be investigated. Vectors of SCMV in Florida are different from those of SCYLV, and remain to be identified

Metagenomic screening of the sugarcane virome in Florida. [P.36]

Viral metagenomics has revolutionized the way pathologists decipher viral diseases. While the impact of this new approach is still debatable in plant virus diagnostics, viral metagenomics has already produced key advances in viral ecology and has the potential to become a central approach for viral surveillance at the ecosystem scale. A viral metagenomics study of the sugarcane virome in Florida was carried out in 2013/2014. One hundred and eighty sugarcane leaf samples were collected from different commercial sugarcane (Saccharum interspecific hybrids) fields in Florida and from other Saccharum and related species taken from two local germplasm collections. Sequence-independent next generation sequencing (NGS) of virion-associated nucleic acids (VANA) was used for detection and identification of viruses present within the collected leaf samples. All four previously reported sugarcane viruses occuring in Florida were detected: Sugarcane yellow leaf virus (149 infected samples out of 180), Sugarcane mosaic virus (2/180), Sugarcane mild mosaic virus (10/180) and Sugarcane bacilliform virus (51/180). Interestingly, this viral metagenomics approach also resulted in the detection of potential new viruses of sugarcane, including Chrysovirus, Mastrevirus, and Umbravirus. This study provided a snapshot vision of the SCYLV genetic diversity in 2013/2014 in Florida where several genotypes of this virus are present. It also allowed us to assemble the whole genome of at least one new mastrevirus species. (Résumé d'auteur

Detection of Sugarcane yellow leaf virus by a novel reverse transcription loop-mediated isothermal amplification method from three sugarcane production regions in Kenya

Sugarcane yellow leaf is a disease caused by Sugarcane yellow leaf virus (SCYLV). It is a major emerging disease of sugarcane that has been reported worldwide the last two decades. Efficient tools have been developed for detecting SCYLV but their use requires sophisticated facilities and still remains expensive. Our partners from developing countries cannot easily use them, which hamper an efficient and early diagnostic of the disease in sugarcane production regions. The main goal of this study was to develop an "easy-to-use" method for detecting SCYLV at the level of partner laboratories and potentially at the field level. We develop a novel reverse transcription loop-mediated isothermal amplification method (RTLAMP) for detecting SCYLV. This method was compared to the classical methods routinely used at CIRAD Montpellier sugarcane quarantine facilities (RT-PCR and Tissue Blot Immunoassay). The three methods were then used for detecting SCYLV in three sugarcane production regions from Kenya, for which no data of prevalence of the disease existed so far. The first results showed that the RT-LAMP is more efficient than the reference methods. SCYLV is present in the three sugarcane production regions with prevalence rate ranging from 5% to 20%. This is the first report of sugarcane yellow leaf disease in Kenya. Furthermore, this is the first report on the application of the LAMP assay for early diagnostic of sugarcane yellow leaf disease from sugarcane production regions. Due to its simplicity, sensitivity and cost-effectiveness for common use, we believe that this assay should be used as an early diagnostic tool by our partners at the field level. (Texte intégral

Visacane, an innovative quarantine tool for the exchange of pest and disease-free sugarcane germplasm

Sugarcane varietal improvement can not exclusively rely upon exchange and introduction of genetic resources via true seeds (fuzz). It also requires the introduction of vegetative propagation material (cuttings, tissue-cultured plantlets). The continued increase in international and intercontinental trade in plants has led to the enforcement of quarantine measures before introduction into a country because many plant pathogens can be carried and transmitted by vegetatively propagated material. Visacane is the new name of Cirad's sugarcane quarantine (http://visacane.cirad.fr/en/). It covers three main quarantine procedures: detection of pests and pathogens, elimination of pests and pathogens, and transfer of plant material free of pests and pathogens. It has been devoted to sugarcane quarantining for several decades. Besides phytosanitary constraints, Visacane takes also into account legal constraints and ensures, through appropriate contracts, that plant breeders' intellectual property rights over the transferred material are respected. Unlike most sugarcane quarantines that are essentially used to import sugarcane germplasm into a country, Visacane can import and export varieties from and to most sugarcane growing countries in the world, ensuring that the material is free from any important pest and disease causing pathogen. Until recently, the sugarcane quarantine process was aimed at detecting known pathogens harbored by the plant material and eliminating these pathogens whenever possible. It is an a priori process, because it only takes into account the pathogens that have been previously described and for which efficient detection tools exist. During the last three decades, several new viruses infecting sugarcane have been discovered, including Sugarcane bacilliform virus, Sugarcane yellow leaf virus, Sugarcane streak mosaic virus and the virus associated with Ramu stunt. In addition, the etiology of chlorotic streak, a disease known since 1929, has not been elucidated so far, although there is evidence for its infectious nature. Therefore, it can be assumed that unknown pathogens are still to be discovered in sugarcane, especially if these pathogens do not cause symptoms that can be easily observed. For these reasons, the research team associated with Visacane is setting up a new strategy of diagnostics, the so-called sequence-independent approach which aims at deciphering the virome (= the genomes of all the viruses that inhabit a particular organism). We believe that our forthcoming combined process, that will include our traditional approaches in addition to the metagenomics approach, will drastically improve our routine quarantine diagnostics. (Texte intégral

Modern tools for safe detection of diseases in sugarcane quarantine

Aims: Use of modern molecular tools in disease detection, different detection methods, visual observation, serological tests, PCR or RT-PCR tests have been described for elimination of pests and diseases from infected sugarcane germplasm. Application of strict quarantine measures to control movement of sugarcane germplasm is advocated. Methods and Results: Improvement of sugar crops relies, to a large extent, upon the cultivation of new sugarcane varieties that are either bred locally or imported from other geographical locations. In either case, there is a need for importing sugarcane germplasm from abroad. Because sugarcane is vegetatively propagated (stem cuttings, tissue-cultured plantlets), there is a high risk of introducing infectious diseases or pests from countries of origin. Therefore, strict quarantine measures must be applied to control movement of sugarcane germplasm. In the past, quarantine procedures relied almost exclusively upon the cultivation of imported varieties in isolated and closed premises (greenhouses), and the access to these areas was limited to a few duly authorized persons. Additionally, visual search for disease symptoms was performed during the entire growth cycle of the plants. These procedures are still in use at present time, but a wide range of tools for detecting and controlling diseases have been developed during the last decades, resulting in quarantine practices that are much safer and reliable. Nowadays, most of the efforts must be focused on the detection and elimination of symptomless or latent diseases such as leaf scald (Xanthomonas albilineans), ratoon stunting (Leifsonia xyli subsp. xyli) or yellow leaf (Sugarcane yellow leaf virus or SCYLV). Additionally, special attention must be paid to emerging diseases, the symptoms of which are sometimes rather unusual or difficult to detect, and for which efficient detection tools are not always available. Finally, detection tools must be very efficient in detecting low populations of the pathogen as well as all variants of this pathogen. Within the last decade, CIRAD's sugarcane quarantine had to face two emerging diseases, streak mosaic (Sugarcane streak mosaic virus or SCSMV) and yellow leaf. SCSMV appeared to be a heterogeneous virus, and none of the antisera used allowed us to detect all the isolates of our collection. Fortunately, an RT-PCR test developed in our laboratory has been quite sensitive and efficient. Since the end of the 1990s, sugarcane yellow leaf has been routinely detected in our quarantine using a tissue blot immuno-assay (TBIA) and RT-PCR tests. However, recent studies of the genetic diversity of SCYLV showed that some isolates of this virus were not systematically detected, and new and more universal primers were designed. A similar situation was experienced for the detection of sugarcane mosaic, a disease caused by two variable viruses: Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV). Following genetic diversity studies of SCMV, including virus isolates from various geographical origins, new primer pairs were designed and used in RT-PCR. Significance of study: Even though modem molecular tools have greatly improved disease detection in sugarcane quarantine, their exclusive use is not advisable. Very often, a combination of different detection methods must be performed: visual observation of the plants at several growth stages, isolation of bacterial pathogens on selective media, serological tests, PCR or RT-PCR tests. Additionally, the use of physical (hot water or hot air), chemical (fungicide and pesticide) treatments and apical meristem culture allow the elimination of many pests and diseases from infected sugarcane germplasm. (Texte intégral

The effect of heat compression on mechanical behaviour and moisture content of pineapple leaf fibre and sugarcane bagasse waste for plate disposal

The waste from farming and industry could be reduced and used as raw materials in construction to achieve sustainable technologies. This study focuses on the use of waste products from the pineapple leaf and sugarcane bagasse as compounds in replacing polystyrenes and others plastics glass in the manufacture of plate disposal. This platter is made from pineapple leaf and sugarcane bagasse by six (6) series of mixtures with different percentages namely series 1 (20% of pineapple leaf), series 2 (30% of pineapple leaf) series 3 (40% of pineapple leaf), series 4 (60 % of pineapple leaf), series 5 (70% of pineapple leaf) and series of 6 (80% of pineapple leaf). Two (2) series is N8T2 (80% of pineapple leaf and 20 % sugarcane bagasse waste) and N2T8 (20% of pineapple leaf and 80% sugarcane bagasse waste) focusing on this study for furthermore understanding the effect of replacing plate disposal from pineapple laef fiber and sugarcane bagasse waste material. A platter hot press machine is built with variable adjustment temperature on the surface of the mold according parameters required are 50°C, 100°C and 150°C. The effect of heat compression on physical and mechanical behavior of the pineapple leave and sugarcane bagasse waste plate disposal was evaluated. From observation and results showed the best roughness surface appearance on N2T8.The Optimum percentage pineapple leaf and sugarcane bagasse waste is good present at heat parameter 50°C for specimen N2T8. The best water absorption on specimen series N8T2 because pineapple leaf potential to hydroscopic and water resistance. It can be concluded that pineapple leaf and sugarcane bagasse waste have potential raw material for strength and lightweight of paper disposal composition applications

Diversity of plant growth-promoting bacteria associated with sugarcane

The sugarcane (Saccharum spp) presents economic importance, mainly for tropical regions, being an important Brazilian commodity. However, this crop is strongly dependent on fertilizers, mainly nitrogen (N). This study assessed the plant growth-promoting bacteria (PGPB) associated with sugarcane that could be used as a potential inoculant to the crop. We evaluated the genetic diversity of PGPB in the plant tissue of sugarcane varieties (RB 867515, RB 1011, and RB 92579). The primer BOX-A1R was used to differentiate the similar isolated and further sequencing 16S rRNA ribosomal gene. The 16S rRNA gene showed the presence of seven different genera distributed into four groups, the genus Bacillus, followed by Paenibacillus (20%), Burkholderia (14%), Herbaspirillum (6%), Pseudomonas (6%), Methylobacterium (6%), and Brevibacillus (3%). The molecular characterization of endophytic isolates from sugarcane revealed a diversity of bacteria colonizing this plant, with a possible biotechnological potential to be used as inoculant and biofertilizers

Visacane, the Cirad quarantine tool for the exchange of pest and disease-free sugarcane germplasm

Sugarcane varietal improvement requires the introduction of vegetative propagation material. The continued increase of international and intercontinental trade of plants has led to the enforcement of quarantine measures in many countries before the introduction of vegetatively propagated material because many plant pathogens can be carried and transmitted by them. Visacane is the CIRAD's sugarcane quarantine (http://visacane.cirad.fr/en/). Visacane has been devoted to sugarcane quarantining for several decades. It covers detection of pests and pathogens, elimination of pests and pathogens, and transfer of plant material free of pests and pathogens. Besides phytosanitary constraints, this quarantine structure also takes into account legal constraints and ensures that plant breeders' intellectual property rights over the transferred material are respected. Visacane can import and export varieties from and to most sugarcane growing countries in the world, ensuring that the material is free from any well-known important pest and disease causing agent. Because it is integrated into a pathology research unit studying various aspects of plant-pathogen interactions, and thanks to its collaborations within a network of sugarcane technologists, Visacane can regularly update its expertise and propose plant material exhibiting the best possible phytosanitary quality. (Résumé d'auteur

Multi-temporal observations of sugarcane by Terrasar-X images

The objective of this study is to investigate the potential of TerraSAR-X (X-band) in monitoring sugarcane growth on Reunion Island. Multi-temporal TerraSAR data acquired at various incidence angles (17°, 31°, 37°, 47°, 58°) and polarizations (HH, HV, VV) were analyzed in order to study the behaviour of SAR (synthetic aperture radar) signal as a function of sugarcane height. The potential of TerraSAR for mapping the sugarcane harvest was also studied. Radar signal increased quickly with crop height until a threshold height, which depended on polarization and incidence angle. Beyond this threshold, the signal increased only slightly, remained constant, or even decreased. The threshold height is slightly higher with cross polarization and higher incidence angles (47° in comparison with 17° and 31°). TerraSAR data showed that after strong rains the soil contribution for the backscattering of sugarcane fields can be consequent for canes with heights of terminal visible dewlap (htvd) less than 50cm (total cane heights around 155cm). Finally, TerraSAR data at high spatial resolution were shown to be useful for monitoring sugarcane harvest when the fields are of small size or when the cut is spread out in time. The comparison between incidences of 17°, 37° and 58° shows that 37° is more suitable to monitor the sugarcane harvest. The cut is easily detectable on TerraSAR images for data acquired less than two or three months after the cut. The radar signal decreases of about 5dB for images acquired some days after the cut and of 3dB for data acquired two month after the cut (VV-37°). The difference in radar signal becomes negligible (<1dB) between harvested fields and mature canes for sugarcane harvested since three months or more. (Résumé d'auteur

Potentials of cellulosic wastes in media formulation

Potential use of cellulosic wastes as carbon and energy sources in selective media formulations was investigated. Two agar media, Czapek-Dox and Sabouraud’s agar, were modified by substituting their carbon sources with cellulose, sawdust and sugarcane pulps. Then, two fungi; Aspergillus niger ANL301 and Penicillium chrysogenum PCL501, newly isolated from wood-wastes, were transferred to the unmodified and modified media and their growth was monitored for 120 h. Growth of the organisms on modified media containing sawdust and sugarcane pulp compared favorably with that obtained for the unmodified equivalents. Modified Czapek-Dox agar containing 2% (w/v) sawdust (Wood agar) and sugarcane pulps (Cane agar) gave 78.9 – 93.3% of the maximum growth obtained on Sabouraud’s agar. The modified Sabouraud’s agar containing sawdust (Wood-Pep agar) and sugarcane pulps (Cane-Pep agar) yielded 84.4 – 100% of the maximum growth on Sabouraud’s agar. Cellulose-containing media gave a lower level of growth (60.0 – 66.7%) of that obtained for the unmodified media