RSA3 - Crop Protection

Enhanced plant health and insect control

Leader: Wilmer Cuéllar

The RSA-3 team develops, integrates, and implements economically viable and environmentally sound surveillance and preemptive pest and disease management approaches to help protect crop and human health in Latin America and the Caribbean (LAC) and Southeast Asia (SEA).

One of the main impacts of climate change is its effect on the distribution and spread of pests and diseases, reducing the yield and quality of crops and thus affecting the livelihood of millions of smallholder farmers and disadvantaged populations. Generally, information on and methods for tracking diseases in these regions are unreliable. Traditional methods rely on a sketchy description of disease symptoms and limited information on the specific pathogen involved and are thus prone to misidentification of the causal agent due to masking of symptoms and mixed-pathogen infections. Meanwhile, lack of awareness of known diseases emerging in neighboring countries contributes to a delayed measures and thus missing the opportunity to control disease spread.

In 2020, RSA-3 continued developing, integrating and implementing an economically viable and environmentally sound approach for pest and disease surveillance and preemptive management that also helps protect human health in the LAC and SEA regions. We standardized molecular diagnostic protocols, monitored cassava brown streak disease (CBSD) in Asia, optimized a method to identify cassava mites and developed a high-quality DNA isolation protocol for fall armyworm (Spodoptera frugiperda). This was done to improve disease symptom interpretation and pathogen identification while raising awareness of emerging diseases.

We also updated distribution maps for priority cassava diseases, initiated a multiplication scheme for germplasm resistant to cassava mosaic disease (CMD) and cassava witches’ broom disease (CWBD) in the in-vitro genebank collection.

Management of pest and diseases to secure productivity gains
Collaborators: María Isabel Gómez, Juan Manuel Pardo, Jenyfer Jiménez, Ana María Leiva, Roosevelt Escobar, Adriana Bohorquez, Imran Malik, Sophearith Sok, Diana Katherine Castillo, Tatiana Melissa Ovalle, Luis Augusto Becerra
Standardization of molecular diagnostic protocols

The RSA-3 team validates and implements robust protocols for pest and pathogen detection and identification used to monitor pathogen distribution and evolution, screen for disease-tolerant genotypes and guarantee the pathogen-free status of cassava planting material. Detailed protocols, are available and are being implemented through our network of collaborators (Ovalle et al., 2020; Jiménez et al., 2021; Marín et al., 2021).

Pathogen characterization

Standardization of protocols for pathogen characterization. (A) distribution of nucleic acid concentrations (ng/μL) obtained before (i) and after (ii) DNase treatment; (B) pathogen genome sequencing carried out in our laboratory using nanopore technology; and (C) sequence assembly and coverage of pathogen genomes.

CMD monitoring in Southeast Asia

The RSA-3 team, in collaboration with colleagues from the PPC in Laos, achieved early detection of CMD symptoms and confirmed the identity of the pathogen in the southern provinces of Attapeu and Champassack (Chittarath et al., 2021).

Reports and other details:

CMD monitoring

Monitoring CMD in Southeast Asia. (A) and (B) the team from PPC in Laos collecting the first images of CMD in the country; (C) and (D) colleagues from the GDA in Cambodia and PPRI in Vietnam monitoring the spread of CMD; and E) the team from Kasetsart University in Thailand performing nucleic acid extractions.

Improved identification of cassava pests

The RSA-3 team has optimized a method for identifying cassava mites at the species level by using morphological and molecular data. The method, which is intended to facilitate surveillance and monitoring of mite pests in cassava by crop protection programs in Africa, Asia and Latin America (Ovalle et al., 2020) enables simple and accurate identification of Mononychellus caribbeanae, M. tanajoa, M. mcgregori, and Tetranychus urticae.

Disease characterization

Characteristic symptoms of cassava frogskin disease in genotypes Valencia (A), BRA383 (B) and CM6740-7 (C). This disease affects cassava in the Americas, reducing yield and root quality.

Spodoptera frugiperda biotype characterization

An optimized high-quality DNA isolation protocol for fall armyworm (FAW) was developed. The use of body segment tissue facilitates study of the genetic variability of biotypes to monitor the pest’s distribution and population dynamics. The quality of the DNA produced using this protocol is suitable for subsequent molecular applications, such as (i) next-generation whole genome sequencing, (ii) conventional polymerase chain reaction for genotyping, (iii) barcodes, and (iv) gene cloning.

Updated distribution maps for priority cassava diseases

Information about emerging pests and diseases is rapidly growing and being made available through public databases. The RSA-3 team routinely examines early detection and genetic analysis of pathogen occurrence in the context of historical and newly published scientific information, which is collected, curated and communicated through the PestDisPlace platform. Results and maps have now been updated for cassava frogskin disease in the Americas, CBSD in Africa and CMD in Southeast Asia, and are available to all registered project collaborators.


CMD management
Collaborator: Imran Malik
Partners: PPC, PPRI, GDA, INIA, SENASA, Univalle, INS

In an experiment on CMD management in Cambodia, KU50 consistently performed better than other tested varieties for the second year, with less infection and higher yields. The best options based on these results were shared with farmers through on-farm demonstrations using clean planting material of variety KU50.

Identifying sources of resistance in regional collaboration and information sharing
Collaborators: Roosevelt Escobar, Adriana Núñez, Auradela Ríos, Mónica Vélez, Lao Thao, Imran Malik, Erik Delakis, Peter Wenzl, Xiaofei Zhang, Wilmer Cuellar, Jonathan Newby, Luis-Augusto Becerra, Joe Tohme

The genebank in-vitro collection was used to start a multiplication scheme with a cassava core collection (CCC). Materials were transferred to Laos and Vietnam to be tested for CMD and CWBD resistance. Of the 625 clones that make up the CCC, 80% are available, meaning that they are clean or pathogen free and thus can be sent to end-users. The first batch of the CCC, with 160 in-vitro clones (10 plants/clone/recipient), was sent to the National Agriculture and Forestry Research Institute (NAFRI) in Laos and Agricultural Genetics Institute (AGI) in Vietnam. Cassava clone KU50 was also prepared for shipment to Laos to start a clean seed production program (500 plants).

Protocols for propagation, root induction, hardening and management have been adapted to local conditions, permitting the production of enough planting material for testing.


(A) in vitro materials subcultured in NAFPRI´s lab. (B), (C, and D, hardening and transfer to ex-vitro conditions. (B and (C) use of clear cups to control humidity and avoid dessication of plants during the hardening phase. E) local formulation of fertilizers for greenhouse management. In each country, a protocol for propagation, root induction, hardening and management has been adapted to local conditions, permitting the production of enough planting material for testing. Putting aside a set of tubes as a backup is important for ensuring that a stock of this germplasm is available for future research.

  1. Jiménez J; Leiva AM; Olaya C; Acosta-Trujillo D; Cuéllar WJ (2021) An optimized nucleic acid isolation protocol for virus detection in cassava (Manihot esculenta Crantz.). MethodsX.
  2. Chittarath K; Jiménez J; Vongphachanh P; Leiva AM; Sengsay S; López-Álvarez D; Bounvilayvong T; Lourido D; Vorlachith V; Cuéllar WJ (2021) First report of cassava mosaic disease and Sri Lankan cassava mosaic virus in Laos. Plant Disease.
  3. Ovalle TM; Vásquez-Ordóñez AA; Jiménez J; Parsa S; Cuellar WJ; Becerra López-Lavalle LA (2020) A simple PCR-based method for the rapid and accurate identification of cassava mites. Scientific Reports.
  4. Marín DV; Castillo DK; Becerra López-Lavalle LA; Chalarca JR; Pérez CR (2021) An optimized high-quality DNA isolation protocol for Spodoptera frugiperda JE smith (Lepidoptera: Noctuidae). MethodsX 8:101255.
  5. Cuéllar WJ; Mwanzia L; Lourido D; Martínez AF; Rodríguez R; García C (2020) Monitoring the distribution of pests and diseases. PestDisPlace: Version 3.0. International Center for Tropical Agriculture (CIAT).
  6. López-Álvarez D; Parra B; Cuéllar WJ (2020) Genome sequence of SARS-CoV-2 isolate Cali-01 from Colombia, obtained using Oxford Nanopore Technology. Microbiology Resource Announcements.