Characterization of Coconut cadang-cadang viroid variants from oil palm affected by orange spotting disease in Malaysia

New Method for Enhancing Coconut (Cocos nucifera L.) Embryo Dehydration: An Important Step Towards Proficient Cryopreservation

The coconut (Cocos nucifera L.), a valuable tropical crop, is rapidly declining in genetic diversity due to natural disasters, pest and disease attack, and land clearing for other crops. Seed banking is impractical for coconut conservation due to its large, recalcitrant seed, and maintaining field gene bank collections is costly and vulnerable to environmental pressures. Cryopreservation offers a promising alternative method for conserving coconut genetic diversity, but the success in recovering cryopreserved materials remains limited, with few studies consistently reporting high rates of recovery. This highlights the need for improved cryopreservation protocols, particularly in tissue dehydration, which is one of the critical steps in the process of cryopreservation and plant recovery. A desiccator was developed that enabled rapid embryo dehydration with ultra-dry airflow. The desiccator reduced embryo moisture content to 20% (the predetermined viability threshold) within 6 h representing a 2-h improvement when compared to a previous dehydration approach, while maintaining a high germination rate (71%). Smaller embryos (500 to 550 mg fresh weight) desiccated faster than larger embryos (800 to 900 mg fresh weight) but germination was reduced (30%), making small embryos unsuitable for cryopreservation. A 5-day sucrose (0.4 M) pre-treatment further reduced the dehydration time to 4 h, while maintaining a high germination rate (70%). These advances in the use of a sucrose pre-treatment, the rapid embryo dehydration, and selection of large embryos size will help to enhance the success of coconut embryo cryopreservation and recovery.

Analysis of Coconut cadang-cadang viroid variants on field samples exhibiting variation in orange spotting symptom expression and severity

BACKGROUND

Sequence variation has been attributed to symptom variations but has not been investigated in Orange Spotting-Coconut cadang-cadang viroid (OS-CCCVd) infected palms. Likewise, the relationship between Coconut cadang-cadang viroid (CCCVd) variants, Orange Spotting (OS) severity and the accumulation of the viroid in the palms have not been elucidated. This paper describes the characterization of CCCVd variants by cloning and sequencing, followed by correlation with symptom expression.

METHODS AND RESULTS

Total nucleic acids were extracted from leaf samples harvested from frond 20 of seven Dura × Pisifera (D × P) African oil palm (Elaeis guineensis Jacq.) aged between 13 and 21 years old collected from local plantations. The nucleic acids were fractionated using 5% non-denaturing polyacrylamide gel electrophoresis (PAGE) before being subjected to detection by reverse transcribed polymerase chain reaction (RT-PCR). The PCR products were cloned into a plasmid vector and the sequence of the clones was analyzed. CCCVd variants were quantified using real-time qPCR assay with CCCVd specific primers. Sixteen randomly selected clones of (OP246) had an arbitrary 100% identity with CCCVdOP246 (GeneBank Accession No: HQ608513). Meanwhile, four clones had >93% similarity with several minor sequence variations forming variants of OP234, OP235, OP251 and OP279.

CONCLUSION

The OS symptoms observed in the field were characterized into three categories based on the size and morphology of the orange spots on the affected fronds. In addition, there was no direct correlation between disease severity and the accumulation of CCCVd variants in oil palm. This finding is the first report describing the sequence variation of the CCCVd RNA and symptom variation in OS oil palm field samples.

EFSA Panel on Plant Health (PLH), Bragard C, Baptista P, Chatzivassiliou E, Gonthier P, Miret JAJ, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Stefani E, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Carluccio AV, Chiumenti M, Di Serio F, Rubino L, Maiorano A, Pautasso M, Reignault PL. Pest categorisation of coconut cadang-cadang viroid

The EFSA Panel on Plant Health updated its 2017 pest categorisation of coconut cadang cadang viroid (CCCVd) for the EU territory due to new data on its host range. The identity of CCCVd, a member of the genus Cocadviroid (family Pospiviroidae), is established and detection and identification methods are available. It is included as a quarantine pest for the EU in the Commission Implementing Regulation (EU) 2019/2072. CCCVd has been reported from the Philippines and Malaysia. It is not known to be present in the EU. The host range of CCCVd is restricted to Arecaceae species (palms), in particular, coconut palm (Cocos nucifera) to which it causes a lethal disease. Oil palm (Elaeis guineensis) and buri palm (Corypha utan) are other natural hosts of CCCVd. Palm species of several genera, including Phoenix spp. and other species grown and/or cultivated in the EU, have been identified as potential hosts. The viroid is naturally transmitted at low rate by seeds and pollen and possibly by additional not yet identified natural transmission means. It can be transmitted through vegetative propagation applied to some palm species. Plants for planting including seeds of its hosts have been identified as the main entry pathway of CCCVd. Potential hosts of CCCVd are present in the EU, therefore establishment is possible. Should the pest establish in the EU, an impact is expected, with uncertainty on its magnitude. The Panel identified the susceptibility of palm species grown in the EU as a key uncertainty potentially affecting the conclusion of this pest categorisation. Nevertheless, the pest satisfies the criteria that are within the remit of EFSA to assess for this viroid to be regarded as potential Union quarantine pest.

Current State of Hyperspectral Remote Sensing for Early Plant Disease Detection: A Review

The development of hyperspectral remote sensing equipment, in recent years, has provided plant protection professionals with a new mechanism for assessing the phytosanitary state of crops. Semantically rich data coming from hyperspectral sensors are a prerequisite for the timely and rational implementation of plant protection measures. This review presents modern advances in early plant disease detection based on hyperspectral remote sensing. The review identifies current gaps in the methodologies of experiments. A further direction for experimental methodological development is indicated. A comparative study of the existing results is performed and a systematic table of different plants' disease detection by hyperspectral remote sensing is presented, including important wave bands and sensor model information.

Jeger M, Bragard C, Caffier D, Candresse T, Dehnen-Schmutz K, Gilioli G, Gregoire JC, Jaques Miret JA, MacLeod A, Navajas Navarro M, Niere B, Parnell S, Potting R, Rafoss T, Rossi V, Urek G, Van Bruggen A, der Werf WV, West J, Chatzivassiliou E, Winter S, Hollo G, Candresse T. Pest categorisation of Cadang-Cadang viroid

The EFSA Panel on Plant Health performed a pest categorisation of Cadang-Cadang viroid for the European Union (EU) territory. Coconut cadang-cadang viroid (CCCVd) is a well-known viroid for which efficient molecular detection assays are available. It is transmitted by vegetative multiplication of infected hosts, by seed and pollen and, possibly, by the action of unknown vector(s). CCCVd is reported from a few countries in Asia and is not known to occur in the EU. It therefore does not meet one of the criteria for being a Union regulated non-quarantine pest. The host range of CCCVd is restricted to Arecaceae species (palms), in particular coconut and it is listed on all known hosts in Annex IIAI of Directive 2000/29/EC. CCCVd is expected to be able to enter in the EU and to be able to establish in the open in the southernmost regions of the EU and elsewhere under protected cultivation. It has the potential to subsequently spread via plants for planting and possibly other mechanisms. CCCVd is able to cause severe symptoms in some Arecaceae species while others seem less affected. The potential impact of CCCVd if introduced in the EU is very difficult to assess. Given that the spread potential is, as for other viroids, likely to be limited, the potential impact is estimated to be limited in extent but this judgement is affected by large uncertainties. Overall, CCCVd meets all the criteria evaluated by EFSA to qualify as Union quarantine pest. The main knowledge gaps concern (1) the relationships between CCCVd-related RNAs and CCCVd, (2) the origin and volume of the trade in palm seeds and plants for planting imported in the EU (3) the efficiency of natural spread under EU conditions and (4) host status and susceptibility of many palm species grown in the EU.

Detection of Coconut cadang-cadang viroid (CCCVd) in oil palm by reverse transcription loop-mediated isothermal amplification (RT-LAMP)

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) detected Coconut cadang-cadang viroid (CCCVd) within 60 min at 60 °C in total nucleic acid extracted from oil palm leaves infected with CCCVd. Positive reactions showed colour change from orange to green in the reaction mix after the addition of fluorescent reagent, and a laddering pattern band on 2% agarose gel electrophoresis. Conventional RT-PCR with LAMP primers produced amplicons with a sequence identical to the 297-nt CCCVd oil palm variant with the primers being specific for CCCVd and not for other viroids such as PSTVd and CEVd. RT-LAMP was found to be rapid and specific for detecting oil palm CCCVd.