Cassava Annual Report 2019 The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) delivers research-based solutions that address the global crises of malnutrition, climate change, biodiversity loss, and environmental degradation. The Alliance focuses on the nexus of agriculture, environment, and nutrition. We work with local, national, and multinational partners across Africa, Asia, and Latin America and the Caribbean, and with the public and private sectors and civil society. With novel partnerships, the Alliance generates evidence and mainstreams innovations to transform food systems and landscapes so that they sustain the planet, drive prosperity, and nourish people in a climate crisis. The Alliance is part of CGIAR, the world’s largest agricultural research and innovation partnership for a food-secure future dedicated to reducing poverty, enhancing food and nutrition security, and improving natural resources. www.alliancebioversityciat.org www.bioversityinternational.org www.ciat.cgiar.org www.cgiar.org
CIAT. 2020. Cassava Annual Report 2019. International Center for Tropical Agriculture (CIAT). Cassava Program. Cali, Colombia. 43 p.
Corresponding authors:
Luis Augusto Becerra, Cassava Program Leader Crops for Nutrition and Health [email protected] Jonathan Newby, Cassava Program, Asia Coordinator Crops for Nutrition and Health [email protected]
Some Rights Reserved. This work is licensed under a Creative Commons Attribution NonCommercial 4.0 International License (CC-BY-NC) https://creativecommons.org/licenses/by-nc/4.0/
© Copyright CIAT 2020. Some rights reserved.
Design and layout: Daniel Gutiérrez, Alliance of Bioversity International and CIAT, Communications Unit
Photo credits: Dominique Dufour/CIRAD (pages 32 and 35). Unless otherwise indicated, the photos used for this report are credited to the International Center for Tropical Agriculture (CIAT).
November 2020 Cassava Annual Report 2019 Partners acronyms
AUSTRALIA ACIAR Australian Center for International Agricultural Research UQ University of Queensland UWA The University of Western Australia BRAZIL EMBRAPA Empresa Brasileira de Pesquisa Agropecuária CAMBODIA CARDI Cambodian Agricultural Research and Development Institute CAVAC Cambodia-Australia Agricultural Value Chain Program GDA General Directorate of Agriculture CHINA CATAS Chinese Academy of Tropical Agriculture Sciences COLOMBIA AGROSAVIA Corporación Colombiana de Investigación Agropecuaria ASOMUSACEAS Asociación Musáceas del Valle COLCIENCIAS Departamento Administrativo de Ciencia, Tecnología e Innovación UNAL Universidad Nacional de Colombia-Sede Palmira URG-CIAT Unit of Genetic Resources at the Alliance of Bioversity International and CIAT ENGLAND NRI Natural Resources Institute RHUL Royal Holloway University of London FRANCE CIRAD Agricultural Research for Development RTBFoods Breeding Roots, Tubers and Banana products for end user preferences GERMANY DSMZ Leibniz Institute INDONESIA ILETRI Indonesian Legumes and Tuber Crops Research Institute UB Brawijaya University LAOS DOA-LAO Ministry of Agriculture and Forestry NAFRI National Agriculture and Forestry Research Institute PPC The Plant Protection Center MYANMAR DAR Department of Agricultural Research DOA-Myanmar Ministry of Agriculture, Livestock and Irrigation NIGERIA IITA International Institute of Tropical Agriculture PERU CIP International Potato Center CRP-RTB CGIAR Research Program on Roots, Tubers and Bananas FECONAYA Federación de Comunidades Nativas Yaneshas IBC Instituto del Bien Común INIA Instituto Nacional de Innovación Agraria UNDAC Universidad Nacional Daniel Alcides Carrión YANESHA Peru Yanesha TANZANIA TARI Tanzania Agricultural Research Institute THAILAND KU Kasetsart University UGANDA NaCRRI National Crops Resources Research Institute NARO National Agricultural Research Organization UNITED STATES B&MGF Bill & Melinda Gates Foundation CORNELL Cornell University INGREDION Ingredion Incorporated MSU Michigan State University UCR University of California, Riverside VIETNAM AGI Agricultural Genetics Institute HLARC Hung Loc Research Agricultural Research Center IAS Institute of Agricultural Sciences for Southern Vietnam NOMAFSI Northern Mountainous Agriculture and Forestry Science Institute PPRI Plant Protection Research Institute RDRDC Root Crop Research and Development Center, Vietnam TNU Tay Nguyen University Contents
2 RSA-1. Research and Service Area-1: ZERO HUNGER through the Enhancement of Genetic Resources Scientists contributing to RSA-1: Adriana Bohórquez, Erik Delaquis, Hernán Ceballos, Katherine Castillo, Luis Augusto Becerra, Paul Chavarriaga, Tatiana Ovalle, and Xiaofei Zhang Research results Xiaofei Zhang and Hernán Ceballos: Prebreeding, Breeding, and Next-generation breeding Adriana Bohórquez and Luis Augusto Becerra: Next-generation breeding Luis Augusto Becerra, Tatiana Ovalle, and Katherine Castillo: Prebreeding, Breeding, Next- generation breeding, Metabolomics, Cassava agrobiodiversity and genetic resources, Cytogenetics, Varietal identification, Carotene expression profile, Waxy cassava variation, Small-granule expression profile, and Cassava endophytes Paul Chavarriaga: Next-generation breeding: gene editing Erik Delaquis: Cassava agrobiodiversity and genetic resources
16 RSA-2. Research and Service Area-2: LIFE ON LAND through Agronomy and Soil Management Scientist contributing to RSA-2: Imran Malik Research results Imran Malik: Ensure high-quality root products and reliable seed stakes, and Demonstrate economically robust fertilizer management with farmers and value-chain actors
20 RSA-3. Research and Service Area-3: CLIMATE ACTION through diagnostics and surveillance for early warning and management of emergent threats Scientists contributing to RSA-3: Ana María Leiva, Imran Malik, Juan Manuel Pardo, María Isabel Gómez, Roosevelt Escobar, and Wilmer Cuéllar Research results Wilmer Cuéllar and Juan Manuel Pardo: Diagnostic and surveillance for pest and disease management and early warning M. I. Gómez and W. Cuéllar: Building a knowledge bank of pests and diseases to protect crops Roosevelt Escobar and J. M. Pardo: Management of pests and diseases to secure productivity
26 RSA-4. Research and Service Area-4: RSA-4: NO POVERTY through Seed System and Harvesting Scientists contributing to RSA-4: Imran Malik, Erik Delaquis, and Roosevelt Escobar Research results Imran Malik: Identify priority varieties for multiplication and distribution Roosevelt Escobar: Rapid multiplication Imran Malik: Optimize agronomic management practices Erik Delaquis: Seed system characterization and modeling
32 RSA-5. Research and Service Area-5: GOOD HEALTH and WELL-BEING through Postharvest and Enhanced Nutrition Scientist contributing to RSA-5: Thierry Tran Research results Thierry Tran: Cassava food processing
36 RSA-6. Research and Service Area-6: GENDER Equality through Value Chains, Markets, and Policies Scientists contributing to RSA-6: Jonathan Newby, Ricardo Labarta, and Vanya Slavchevska Research results Jonathan Newby: Market update and outlook, and Adoption and impact Vanya Slavchevska: Gender and social inclusion Ricardo Labarta: Achieving impact at scale through partnerships and knowledge platforms 6 Introduction
Cassava cultivation is an entry point for program created an effective multidisciplinary employment and income creation for small- work plan across six strategic Research and Service farm owners and landless farmers as well as for Areas (RSAs), which are strategically aligned to best countless processors and traders worldwide. respond to the demands of our main stakeholders: Cassava thrives in poor soils with unpredictable the CGIAR Research Program for Roots, Tubers and rainfall; thus, it is an ideal crop to grow on marginal Bananas (CRP-RTB), USAID, BMGF, HarvestPlus, lands where cereals and other crops have limited ACIAR, as well as public (i.e., EMBRAPA, INIA, or no options to succeed. What’s more, cassava and AGROSAVIA) and private organizations (i.e., will be a key crop to make crop production systems INGREDION and TTDI) primarily interested in more resilient to climate change in tropical better cassava varieties, access to clean planting environments. This potential will also increase the materials, monitoring and surveillance of pests crop’s susceptibility to pests and diseases, which and diseases, improved farming and postharvest will have a greater range of mobility. In most parts practices, and the development of sustainable of the tropics, cassava production is now labor- cassava value chains to unlock new cassava market intensive and subsistence-oriented, with low levels growth. of technology uptake, high production costs and postharvest losses, and weak linkages to markets, The following are some of the remarkable results despite being a feedstock for numerous industrial the Cassava Program achieved during 2019, applications, including food, feed, and starch. working under the six Research and Service Areas.
The fact that Latin America is the center of origin for cassava was a compelling factor for CIAT to create its Global Cassava Program in the early 1970s, prioritizing cassava research that could not only serve the region but also provide diverse germplasm for the planned Cassava Program at the International Institute of Tropical Agriculture (IITA). After nearly 50 years, the program continues to deliver on its initial objective and has embraced the challenges outlined in the United Nations’ Sustainable Development Goals. The Global Cassava Program is now part of the Alliance of Bioversity International and CIAT’s Lever 6 – Crops for Nutrition and Health. The newly formed Alliance recognizes the role cassava has in generating farmers’ income where poverty is widespread. Therefore, during 2017 and 2018, the
Cassava Annual Report 2019 1 RSA-1 RESEARCH AND SERVICE AREA-1: Zero hunger through the enhancement of genetic resources
2 This work contributes to decreasing hunger through the enhancement of genetic resources by targeting agronomic or economic problems that can have either genetic or agronomic solutions, thus increasing productivity, sustainability, and use of cassava in LAC and ASEAN regions.
Plant genetic resources underpin crop improvement. Thousands of cassava landraces have been collected by CIAT in their center of origin, which constitute the global cassava reference collection, but added-value traits have been discovered and integrated into variety development, for example, high pro- Vitamin A, waxy starch and disease resistance. The challenge is to efficiently and effectively use the untapped genetic resources to continuously improve cassava production and sustainability. The Alliance of Bioversity and CIAT Cassava Program has strategically invested both in genomics-based germplasm characterization and population improvement and in high-throughput and accurate phenotyping to understand the genetic diversity of the global cassava reference population, discover and integrate the favorable haplotype into elite populations, and deliver improved populations or final products to the global cassava community.
Scientists contributing to RSA-1: Adriana Bohórquez Erik Delaquis Hernán Ceballos Katherine Castillo Luis Augusto Becerra Paul Chavarriaga Tatiana Ovalle Xiaofei Zhang
Other contributing scientists and staff: Carlos A. Ordóñez Eugenio Bolaños Francisco J. Sánchez Janneth Gutiérrez John Belalcázar Jorge I. Lenis Juan P. Arciniégas Marcela Pineda Nelson Morante Sandra Salazar Thuy Cu Thi Le
Cassava Annual Report 2019 3 RSA-1 | RESEARCH RESULTS
Xiaofei Zhang and Hernán Ceballos
Prebreeding, breeding, and next-generation breeding
We successfully induced earlier flowering (from 12 months to 5 months) and higher seed set (from 0 to 125 seeds) by extending photoperiod and pruning in combination with plant growth regulators.
A B
Figure 1. Effect of pruning in flower inducing. (A) Without pruning; (B) After pruning in the first branching event.
Seven clones immune to cassava brown streak disease (CBSD) were identified by collaborating with Leibniz Institut-DSMZ, Germany. The clones provided the best resistance and were delivered to African programs for developing new CBSD-resistant varieties.
A B C
Figure 2. Seven CBSD-resistant accessions were identified from the genebank at the Alliance of Bioversity International and CIAT. Highly resistant varieties (A) do not become infected; resistant varieties (B) remain symptomless in aboveground plant parts and restrict the virus to the roots, where necrotic symptoms can be observed. Sensitive varieties (C) responded with symptoms on leaves and stems as well as marked root necrosis (from Sheat et al., 2019 - doi: 10.3389/fpls.2019.00567). Credits: Samar Sheat, DSMZ Plant Virus Department, Braunschweig, Germany.
4 We developed biofortified cassava clone SM3536-44 (beta-carotene, 5.0 ug/g fresh weight) with comparable yield and other agronomic traits with check clone Costeña.
Figure 3. Yield performance of biofortified cassava clones in regional yield trials at Caribbean dry (a) and wet (b) locations in Colombia. The best biofortified clone, SM3536-44 (beta-carotene, 5.0 ug/g fresh weight), has comparable yield and other agronomic traits with check clone Costeña.
We introduced six source populations of cassava mosaic disease (CMD) resistance to Southeast Asia by collaborating with IITA and other NextGen partners. One source of CMD resistance was identified from the core collections from the genebank at the Alliance of Bioversity International and CIAT.
We identified ten accessions with short cooking time (<25 min) from the genebank and included these accessions as progenitors for good cooking quality.
Figure 4. Ten accessions from the genebank at the Alliance of Bioversity International and CIAT showed short cooking time (<25 min) in four harvests. These ten clones were used as progenitors for good cooking quality.
Cassava Annual Report 2019 5 We proposed a new genomics-assisted breeding scheme for cassava breeding. We will be able to diminish the duration of the selection cycle from 5 to 3 years, increase the capacity of breeding programs, and enhance collaboration among breeding programs.
Genomics-assisted cassava breeding
SEEDS FROM CROSSING NURSERY SIT Seed Increase Trial TPY Training Population Yield trial BREEDING POPULATION TRAINING POPULATION PYT Preliminary Yield Trial AYT Advanced Yield Trial
F1 (25,000) SIT (400) 1 plant | 1 rep | 1 site 5 plants | 1 rep | 1 loc
F1 C1 (2,000) TPY (400) Establish SIT & TPY GS 4 plants | 1 rep | 1 site 4 plants | 2 reps | 2 loc VIETNAM Planning GS NIGERIA
PYT (250) 10 plants | 3 reps | 2 sites
Evaluate Breeding Populations & Training Populations AYT (80) COLOMBIA 25 plants | 3 reps | 3 sites
Figure 5. Genomics-assisted breeding scheme for cassava breeding at the Alliance. In brief, a small part of the breeding population will be used as the training population to develop prediction models. The performance of the remaining breeding population will be estimated using the prediction models. Selections will be made based on the prediction values. These selections will be used as progenitors for the next cycle of selection and/ or be advanced to the next selection stage. The seeds of the training population can be easily shared among collaborators and evaluated in a TPE.
Publications
Pineda M; Morante N; Salazar S; Cuasquer J; Hyde PT; Setter TL; Ceballos H. 2020. Induction of earlier flowering in cassava through extended photoperiod. Agronomy 10:1273. Doi: 10.3390/agronomy10091273
Pineda M; Yu B; Tian Y; Morante N; Salazar S; Hyde PT; Setter TL; Ceballos H. 2020. Effect of pruning young branches on fruit and seed set in cassava. Frontiers in Plant Science 11:1107. Doi: 10.3389/fpls.2020.01107
Partners
6 RSA-1 | RESEARCH RESULTS
Adriana Bohórquez and Luis Augusto Becerra
Next-generation breeding
In the African Cassava Whitefly Project (ACWP) phase I, we conducted a study of whitefly resistance in cassava developing two segregating families (CM8996 and GM8586), whose source of resistance is genotype ECU72. We built two linkage maps and obtained 22 significant QTLs for the trait number of nymphs of the whitefly Aleurotrachelus socialis. These genomic regions associated with resistance to A. socialis are located mainly on chromosomes 2, 7, 10, and 14.
Based on the previous results, for ACWP phase II, we carried out crossings between the most resistant progenies of the segregating families to obtain F2 in order to narrow the genomic regions that explain whitefly resistance. We have obtained 13 F2s that are in the process of phenotyping for whitefly resistance.
We have successfully developed a high-throughput phenotyping methodology and ImageJ plugin for the count of nymphs of the third and fourth instars for the quantification of whitefly resistance in cassava.
We have successfully sent in vitro seedlings of 102 genotypes with resistance to CMD (AR and CR families) to AGI in Vietnam. These genotypes were evaluated in Vietnam and 34 immune to CMD clones were identified. These genotypes provided the best resistance to CMD for ASEAN programs.
We successfully established 41 genotypes with high beta-carotene content in Haiti. We carried the seedlings in vitro and trained the Haitian staff to strengthen capacity in the management of in vitro cassava plants, hardening of seedlings in soil, and finally plant establishment in fields.
We have collaborated with AGROSAVIA (Colombia), so far sending in vitro seedlings of eight commercial varieties of cassava (for different purposes) for phytosanitary cleaning and indexing.
Figure 6. Main putative QTLs in the biparental mapping population of ECU72 × COL2246 (CM8996). (LOD significance threshold calculated by permutation tests for a significance ofP <0.05.) Different colors of QTLs correspond to five experiments carried out in four years (2013, 2016, 2017, and 2018) of phenotyping evaluations for whitefly resistance.
Cassava Annual Report 2019 7 Publications
Behnam B; Bohorquez-Chaux A; Castañeda-Mendez OF; Tsuji H; Ishitani M; Becerra López-Lavalle LA. 2019. An optimized isolation protocol yields high-quality RNA from cassava tissues (Manihot esculenta Crantz). FEBS Open Biology 9:814-825.
Irigoyen ML; Garceau DC; Bohorquez-Chaux A; Becerra López-Lavalle LA; Perez-Fons L; Fraser PD; Walling LL. 2020. Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid. BMC Genomics 21:93.
Perez-Fons L; Bohorquez-Chaux A; Irigoyen ML; Garceau DC; Morreel K; Boerjan W; Walling LL; Becerra López- Lavalle LA; Fraser PD. 2019. A metabolomics characterization of natural variation in the resistance of cassava to whitefly. BMC Plant Biology 19:518.
Partners
8 RSA-1 | RESEARCH RESULTS
Luis Augusto Becerra, Tatiana Ovalle and Katherine Castillo
• Prebreeding • Breeding • Next-generation breeding • Metabolomics • Cassava agrobiodiversity and genetic resources • Cytogenetics • Varietal identification • Carotene expression profile • Waxy cassava variation • Small-granule expression profile • Cassava endophytes
Genetic diversity information and population differentiation are relevant in breeding programs to work on developing outstanding products for commercialization. We completed fingerprinting analysis of 12,000 cassava samples included in the Alliance cassava collection. We identified 3,470 genotypes as unique to conform the largest reference collection of cassava samples and relationships were inferred through kinship coefficient (Figure 7). We assessed the cassava global genetic diversity present in farmers’ fields, genebanks, and some breeding program elite accessions. Cluster analysis resolved that six groups accumulate enough genetic differences to explain the ecogeographic signature of cassava cultivation.
Genome size variation has been linked to diversity and adaptation to altitude, temperature, and precipitation. Traits are essential to overcome the challenges of improving crop plants. In this study, we evaluated the genome size variation in 264 cassava genotypes and 26 samples of wild species. The chromosome number of 48 genotypes of cultivated and wild cassava from Latin American subpopulations was determined. We found genome size variation from 585 Mb to 1,134 Mb. Cassava genotypes with genome size higher than 1,100 Mb were characterized as triploids (Figure 8).
Varietal identification was developed considering morphological and molecular data in 400 cassava samples. Subsequently, the information from the top 30 was consolidated in the cassava varietal catalogue that also includes agronomic information, harvested area, and yield reported by farmers (Figure 9).
Samples with contrasting content of beta-carotene were selected to perform RNAseq analysis. Leaf and root tissue were collected 7 months after planting. The results showed three regulator genes in root transcriptome and nine regulator genes in leaf transcriptome overexpressed during β-carotene accumulation (Figure 10).
The carotene expression profiling aims to characterize the expression of nine candidate genes associated with high carotene content in cassava and be able to use at least one of them as a marker to identify cassava genotypes with high carotene content. Monthly, we evaluated the expression pattern of six cassava carotene-associated genotypes. Up to December 2019, we recorded data from 1 month in vitro, 1 month in the greenhouse, and 4 months in the field for the cassava plants. One of the candidate genes, Beta6, had up to a 100-fold expression change in the six genotypes evaluated relative to a calibrator (PAR39) and could be a good candidate to discriminate from cassava populations genotypes with high carotene content (Figure 11).
Cassava Annual Report 2019 9 In cassava waxy variation, we found evidence of multiple allelism (MA) and alternative splicing (AS), which generated evidence in silico of protein diversity over the GBSSI gene. A set of antibodies was designed at amino and carboxyl regions over highly conserved sequences according to the alignment of GBSSI-predicted proteins. The antibody at the amino region was able to discriminate from a set of proteins the presence of waxy protein, indicating that waxy protein starts its translation upstream, at exon 4 (Figure 12). These findings suggest that deletion of cytosine at exon 8, instead of generating a premature stop codon at exon 8, generates a switch in the start codon selection using the presence of an alternative start codon, in which the ribosomal machinery seeks the best translation context to keep the integrity and functionality of the protein. These results give an overview of the mutation behavior and the possibility of generating allelic markers to trace the selection of the waxy mutation in cassava germplasm.
Small-granule expression profiling aims to determine the expression pattern of starch synthase (SS) genes and starch debranching enzyme (DBE) genes in four cassava genotypes with special starch characteristics (waxy, small granule, double mutant, and sugary). So far, we have clues that two genes, BAM (beta amylase) and SSIIa (Starch Synthase II), are responsible for triggering the signal as bulking begins in 5G160-13 (small granule mutant – up to 30% amylose content) (Figure 13). This preliminary evidence will allow understanding the mechanism of small granule phenotype in evaluating separately the contribution of genes belonging to the cassava starch pathway to this phenotype for posterior breeding programs focused on starch diversity.
Cassava endophyte research aims to discover the fungal diversity living within cassava tissues and assay its potential as a biocontroller. A total of 61 fungal isolates were recovered and sequenced, yielding 24 unique rDNA-ITS genotypes. The most abundant fungal endophytic taxa were Cladosporium, Diaporthe, and Peyronellaea, and fungal isolates from the genus Diaporthe were found in all cassava varieties (Figure 14). This study demonstrates that cassava plants serve as a reservoir for a wide variety of fungal endophytes that can be isolated from vascular tissues and illustrates the different fungal communities encountered by M. esculenta in two different cassava-growing regions.
Figure 7. Relationship matrix in our cassava reference sample set. Based on fingerprinting of 3,470 samples with 96 SNP markers, using kinship coefficient for relationship inference.
10 Genome size clustering in cassava Mega bases
Samples
Figure 8. Cassava genome size variation. Optimal univariate clustering with k estimated. Number of clusters is estimated to be five and each cluster is delimited with a dotted line. In the black square, DAPI-stained chromosomes of triploid genotypes with 3n=3x=54.
COL 1522 Algodona Forma de la planta Compacta. Planta muy o poco ramificada pero siempre tiende hacia arriba. Las ramas no tocan el suelo y el lote aunque se cierra en el dosel no lo hace en el suelo. Altura total 143-283 cm Niveles de ramificación 3-5 Altura de Habito de ramificación Tricotómica o tres tallos la primera ramificación emergiendo de la primera 22-130 cm ramificación reproductiva
CARACTERÍSTICAS AGRONÓMICAS ÁREA Y RENDIMIENTO REGISTRADA EN CAMPOS DE AGRICULTORES Rendimiento 25.80 T/ha
DESCRIPCIÓN MORFOLÓGICA MS 36.1 % Área reportada Rendimiento HCN- 42ppm 21.2 ha 12.8 T/ha Haz Color de hojas apicales Verde-Morado (proporción 50-50) Panificación 7.17 Pubescencia de hojas apicales Abundantes tricomas fáciles de ver Altura Pandebono 5.4cm Forma del lóbulo central Oblonga-lanceolada Color del peciolo Rojo-verde Color de hoja Verde oscuro Color de la vena foliar Verde Orientación peciolo Irregular No. lóbulos de la hoja 3-7 Largo peciolo 9.4cm – 32.5cm Inflorescencia Yema axilar Color del córtex del tallo Verde Claro Color de la epidermis del tallo Café oscuro
Envés Hábito de crecimiento de tallos jóvenes Derecho Color de ramas apicales de plantas adultas Verde-Morado Código genético Margen estípula Dividida o bifurcada T A C G NA Semilla 1-3 Fruto Esqueje Hoja joven Tallo con peciolos
6 | Catálogo de variedades de yuca Algodona | 7
Figure 9. Cassava varietal catalogue from the Cauca region. This catalogue includes the relevant morphological, molecular, and agronomic data for each variety.
Figure 10. Gene regulation network found in genotypes that accumulate high content of beta-carotene.
Cassava Annual Report 2019 11 Expression profile of BETA6 relative to PAR
Figure 11. Expression profile ofBETA6 candidate gene on six cassava carotene families. The expression pattern was evaluated using two housekeeping genes (ubiquitin and histidine) as expression normalizers and relative to PAR39. Light orange indicates cassava genotypes with low carotenoid content. Medium orange indicates cassava genotypes with medium carotenoid content. Dark orange indicates cassava genotypes with high carotenoid content.
A
B
Figure 12. (A) More frequent protein types in cassava GBSSI. (B) Western blot. Cassava starch SDS/PAGE gel and membrane hybridization. Two types of antibodies were tested at amino and carboxyl regions. In red is identified the size of the waxy-type protein.
12 5G160-13 expression profile across time for SSIIa 5G160-13 expression profile across time for BAM2
Figure 13. Expression profile for SSIIa and BAM2 in genotype 5G160-13.
Species Genus Classes Nigrospora sphaerica (MH854879.1) Nigrospora sacchari (MH858154.1) 0.05 8A; 27A; 44An & 90 Nigrospora Nigrospora zimmermanii (KY385310.1) Nigrospora sp. (HQ631070.1) 0.05 Xylaria aff. adscendens (KP133301.1) Xylaria sp. (JQ341079.1) 0.05 0.01 Xylaria curta (KP133352.1) Xylaria 0.01 70A; 73An; 74B; 75C2 & 79A2 0.01 0.03 Xylariaceae sp. Vega421 (EU009999.1) 4A; 6A; 26 & 27_1 0.08 Sarocladium kiliense (KT878333.1) Sarocladium Acremonium sp (GQ867783.1) Corallomycetella repens (LT576166.1) Sordariomycetes 0.03 A Diaporthe melonis (KT972129.1) Diaporthe phaseolorum (EU272524.1) 0.08 0.01 104 &105 Phomopsis sp. (MF185334.2) Diaporthe phaseolorum (KT964565.1) 17A; 20B; 27An & 44 Figure 14. Phylogenetic tree inferred using the neighbor-joining method Diaporthe aspalathi (KX769841.1) Diaporthe 0.03 53A; 108 & 112A Diaporthe phaseolorum (AY577815.1) Diaporthe miriciae (KJ197283.1) (Saitou and Nei, 1987 - doi: 10.1093/oxfordjournals.molbev.a040454). Diaporthe phaseolorum (KT964567.1) 19A &101A 90A1n Aspergillus ustus (HQ607918.1) The optimal tree with the sum of branch length = 1.57112936 is shown. 0.14 101A2 Aspergillus Aspergillus puniceus (AY373863.1)
0.01 Cladophialophora chaetospira (EU035403.1) Eurotiomycetes 0.12 Cladophialophora sp. (AB986343.2) The tree is drawn to scale, with branch lengths (next to the branches) 0.01 Cladophialophora 0.01 0.01 43 0.05 79A1 Lasiodiplodia theobromae (FJ904912.1) 0.05 Macrophoma theicola (KP179222.1) Lasiodiplodia in the same units as those of the evolutionary distances used to infer Lasiodiplodia brasiliensis (MF952733.2) 0.01 22A 44A 6A2; 20A; 43_1; 75C1; 76; 79A1n the phylogenetic tree. The branch distances were computed using the 0.15 Cladosporium angustisporum (MF422159.1) 0.11 Cladosporium vicinum (MF473312.1) Cladosporium cladosporioides (MF422160.1) Cladosporium sp (FJ612648.1) maximum composite likelihood method (Tamura et al., 2004 - doi: 10.1073/ 72A Cladosporium sp. (FJ176478.1) Cladosporium 2C; 4C; 35_1; 35_2n & 75Cn B Cladosporium sp. (MF422154.1) pnas.0404206101) and are in the units of the number of base substitutions Cladosporium cladosporioides (AB763554.1) Cladosporium cladosporioides (JQ936096.1) Dothideomycetes 27_2 & 43_2 (HM596871.1) per site. The analysis involved 72 nucleotide sequences. Codon positions Cladosporium sp. 35_2n 19B & 30 3A 0.02 included were 1st + 2nd + 3rd + noncoding. All positions containing Phoma sojicola (MH857118.1) Uncultured Phoma (KF385301.1) Phoma Uncultured Ascomycota (HM161963.1) Phoma sp. (AJ972865.1) 0.11 gaps and missing data were eliminated. There were 462 positions in the 9A;18A; 50A; 51An & 53Bn
0.01 Didymella glomerata (MG840666.1) Peyronellaea glomerata (KR012905.1) - CIAT’s Beans 0.02 Cumuliphoma omnivirens (MH861962.1) Peyronellaea final dataset. Phylogenetic analyses were conducted in MEGA7 (Kumar 3A2; 4C_1; 4D; 6C; 10D & 17B 0.01 Peyronellaea glomerata (JQ936273.1) Phoma herbarum (JQ936274.1) 54A2 et al., 2016 - doi: 10.1093/molbev/msw054) and three well-defined 0.09 Panaeolus foenisecii (KC176293.1) Panaeolus 0.01 Uncultured Panaeolus (HG936444.1) Agaricomycetes 0.15 46 C (KP686447.1) Phanerochaete 0.09 Phanerochaete sp. clusters corresponded to taxonomic super classes (a) Dothideomyceta, Phanerochaete chrysosporium (KC881189.1) (b) Sordariomyceta, and (c) Dacrymycetales.
Publications
Friedmann M; Becerra L; Fraser P. 2019. Metabolomics in CGIAR Research Program on Roots, Tubers and Bananas (RTB). 11 p. Lima, Peru, CGIAR. Johnston-Monje D; Castillo-Avila DK; Raizada MN; Becerra López-Lavalle LA. 2019. Paying the rent: How endophytic microorganisms help plant hosts obtain nutrients. In: Comprehensive Biotechnology (Third Edition), Moo-Young M (ed.). Oxford: Pergamon. p 770-788. Le DP; Labarta RA; de Haan S; Maredia M; Becerra López-Lavalle LA; Nhu L; Ovalle T; Nguyen V; Pham N; Nguyen H; Nguyen H; Le K; Le HH. 2019. Characterization of cassava production systems in Vietnam. Working Paper. CIAT Publication No. 480. International Center for Tropical Agriculture (CIAT), Hanoi, Vietnam. 54 p. Available at https://hdl.handle.net/10568/103417. Price EJ; Drapal M; Perez-Fons L; Amah D; Bhattacharjee R; Heider B; Rouard M; Swennen R; Becerra López- Lavalle LA; Fraser PD. 2019. Metabolite database for root, tuber and banana crops to facilitate modern breeding in understudied crops. The Plant Journal, in press. Partners
Cassava Annual Report 2019 13 RSA-1 | RESEARCH RESULTS
Paul Chavarriaga
Next-generation breeding: gene editing
Characterizing genes involved in embryogenesis of cassava.*
Changing starch composition in cassava roots with CRISPR-Cas9.**
Figure 15. Applications of genetic transformation (GT) and gene editing (GE) in cassava are often limited by the diversity of cultivars grown by farmers. Developing genotype-independent GT/GE systems is therefore crucial. We characterized two genes that promote embryogenesis in cassava, the transcription factors MeLEC1 and MeLEC2. The single overexpression of MeLEC2 was enough to reprogram vegetative cells to induce direct somatic embryogenesis on leaves of in vitro plants (H through G). These results suggested that MeLEC genes are tools to improve the recovery of transformed/edited plants and to boost GE through the development of genotype-independent and DNA-free protocols.
Figure 16. Gene-edited waxy (left) and conventional roots of cassava harvested from the Alliance-Palmira Station fields on June 30, 2020.
Publications
*Brand A; Quimbaya M; Tohme J; Chavarriaga-Aguirre P. 2019. Arabidopsis LEC1 and LEC2 orthologous genes are key regulators of somatic embryogenesis in cassava. Frontiers in Plant Science 10:673. doi: 10.3389/fpls.2019.00673 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6541005/
Partners
* **
14 RSA-1 | RESEARCH RESULTS
Erik Delaquis
Cassava agrobiodiversity and genetic resources
Research in Peru’s Yanesha indigenous communities continued on documenting cassava in situ diversity. This project aims to document cassava diversity in Yanesha communities to evaluate patterns of maintenance or loss of crop genetic resources over time. Over 2019, UNDAC students built on past results and consolidated data in anticipation of plant genetic sampling of collected varieties to be completed in late 2020.
Figure 17. Documenting cassava diversity in Peru: 23 cassava varieties documented Figure 18. UNDAC students taking cassava measurements in from a single Yanesha community. the diversity collection maintained in the Yanesha community of Nuevo Progreso.
Partners
Peru Yanesha:
Cassava Annual Report 2019 15 RSA-2 RESEARCH AND SERVICE AREA-2: Life on land through agronomy and soil management
16 RSA-2 targets chemical, physical, biological or technological problems limiting cassava yield, while implementing land- use practices that are highly productive, sustainable, economically viable, and environmentally safe in LAC and ASEAN regions.
The Alliance Cassava Program has developed an agronomic package for sustainable production systems that includes (1) timely planting, (2) appropriate fertilizer application practice (i.e., organic and inorganic), and (3) weed control. These practices have been adopted by farmers to some extent. However, there is a large gap in terms of the farmers implementing the technology in an efficient and sustainable manner. Furthermore, research on fertilizer management needs to focus on site-specific nutrient management. For best-practice farming, soil testing is an important tool as test results provide the basic facts on fertilizer use and it is better at predicting the probability of a profitable response to nutrient application.
Scientist contributing to RSA-2: Imran Malik
Other contributing scientists and staff: Lao Thao Yao Bee Sophearith Sok
Cassava Annual Report 2019 17 RSA-2 | RESEARCH RESULTS
Imran Malik
• Ensure high-quality root products and reliable seed stakes • Demonstrate economically robust fertilizer management with farmers and value-chain actors
A field experiment was carried out to determine the field’s K balance over the cropping season at different K fertilizer rates. The results indicate that there was a net removal of K from the field, even at a high K fertilization rate.
Participatory demonstrations with farmers and value-chain actors in Lao PDR, Vietnam, Cambodia, Indonesia, and Myanmar highlight the economic potential of enhancing the adoption of improved management practices to increase farmer, trader, and processor income.
Figure 19. MSc student Ms. Ming Fung Chua from the University of Figure 20. Drone images of fertilizer management trials in Lao PDR used Western Australia and Mr. Laotho Youbee harvesting the experiment to show farmers the impact of balanced fertilizer application together with at the National Agricultural and Forestry Research Institute in Naphok, economic analysis during farmer field days. Vientiane, Laos (18°0’45.1”N; 102°44’20.7”E).
Publications
ACIAR proceedings published. https://aciar.gov.au/publication/cassava-value-chains
Chua MF; Youbee L; Oudthachit S; Khanthavong P; Veneklaas EJ; Malik AI. 2020. Potassium fertilisation is required to sustain cassava yield and soil fertility. Agronomy 2020, 10, 1103.
Newby J; Smith D; Cramb R; Delaquis E; Yadav L. 2020, Cassava value chains and livelihoods in South-East Asia, a regional research symposium held at Pematang Siantar, North Sumatra, Indonesia, 1–5 July 2019, ACIAR Proceedings Series, No. 148, Australian Centre for International Agricultural Research, Canberra, 114 pp. Partners
18 Cassava Annual Report 2019 19 RSA-3 RESEARCH AND SERVICE AREA-3: Climate action through diagnostics and surveillance for early warning and management of emergent threats
20 RSA-3 is developing, integrating, and implementing an economically viable and environmentally sound surveillance and preemptive pest and disease management approach that will help to protect crop and human health in LAC and ASEAN regions.
One of the main impacts of climate change, is its effect on the distribution and spread of pests and pathogens that reduce the yield and quality of crops. Generally, information on and methods for tracking them in these regions are unreliable. These methods depend on a loose recognition of disease symptoms and limited information on the specific pathogen, and are prone to misidentification due to masking of symptoms and mixed-pathogen infections. Meanwhile, a lack of awareness of known diseases emerging in neighboring countries contributes to a “little- too-late reaction,” to the point that some diseases have spread out of control.
Scientists contributing to RSA-3: Ana María Leiva Imran Malik Juan Manuel Pardo María Isabel Gómez Roosevelt Escobar Wilmer Cuéllar
Other contributing scientists and staff: Diana López-Álvarez Jenyfer J. Polo Lao Thao Yao Bee Sophearith Sok
Cassava Annual Report 2019 21 RSA-3 | RESEARCH RESULTS
Wilmer Cuéllar and Juan Manuel Pardo
Diagnostic and surveillance for pest and disease management and early warning
Starting with clean seed material and keeping it clean is the simplest way to maximize production while minimizing the introduction of pathogens (applicable also to resistant and tolerant genotypes, if any). This is connected to the use of cost-effective diagnostic tools (from symptoms to molecular indexing). During 2019, we made progress in validating protocols (tunnels and thermal chambers) for indexing and rapid propagation of disease-free planting material (cassava and banana), including capacity building for farmers on the use and application of these technologies.
Figure 21. Through the project Ideas para el Cambio, we implemented a system for the rapid propagation of cassava stakes using a thermal chamber. This is the same technology used for rapid propagation of plantain via the COLCIENCIAS plantain seed project. (A) Photo of a cassava stem after 1.5 months in a thermal chamber. Notice that from a single stem we can obtain approximately four plantlets. (B) Propagated cassava stems inside a thermal chamber.
We are developing protocols to evaluate the resistance of different plant genotypes to specific strains of pathogens. Indexing results (diagnostics), early detection, and genetic analysis of pathogen occurrence are communicated through the PestDisPlace platform, and results and maps are available to all registered project collaborators.
A Wounded B No Wound 4 R1 R2 R1 R2 r=0 r=0.439 r=0.439 r_se=0 r_se=0.915 r_se=0.915 r_p=0 r_p=0.633 r_p=0.633 auc_l=0 auc_l=51.7 3 auc_l=51.7 1 auc_e=0 auc_e=132 auc_e=70 Figure 22. Evaluating resistance screening protocols. 2 0 Severity
1 Disease severity for two genotypes of plantain, FHIA- -1
0 21 and Dominico Hartón, inoculated with Ralstonia 4 R3 R4 R3 R4 r=0.197 r=0.107 r_se=0.162 r_se=0.119
FHIA-21 solanacearum strain CIAT-078. Results of four repetitions r_p=0.229 r_p=0.372 3 auc_l=113 auc_l=26.1 1 auc_e=176 auc_e=75.5 (R1-R4) assessed on 21 time points (intervals of 1–3 2 0 Severity days) are shown. Each assessment corresponds to 1 -1 severity of symptoms in three independent plants. 0 20 30 40 50 20 30 40 50 20 30 40 50 20 30 40 50 (a and b) FHIA-21 plants inoculated using the C 4 R1 R2 D 4 R1 R2
3 3 “Wounded” and “No Wound” methods, respectively.
2 2 (c and d) Dominico Hartón plants inoculated using the Severity
1 r=0.301 r=0.385 1 r=0.234 r=0.392 “Wounded” and “No Wound” methods, respectively. r_se=0.0453 r_se=0.0503 r_se=0.0629 r_se=0.0803 r_p=1.06E-08 r_p=1.89E-10 r_p=0.00045 r_p=8.15E-06 auc_l=139 auc_l=148 auc_l=56.9 auc_l=104 0 auc_e=247 auc_e=252 0 auc_e=3.5 auc_e=144 Each dot corresponds to an observation per plant and R3 R4 4 R3 R4 4 the solid lines indicate the adjusted logistic curves. r: 3 3
Dominico Hartón growth rate; r_se: standard error of growth rate; r_p: 2 2 Severity P value of growth rate; auc l: area under the curve of 1 r=0.311 r=0.415 1 r=0.322 r=0.282 r_se=0.0486 r_se=0.0511 r_se=0.0613 r_se=0.0585 r_p=2.62E-08 r_p=2.98E-11 r_p=2.02E-06 r_p=1.02E-05 auc_l=140 auc_l=147 auc_l=88.9 auc_l=80.4 the fitted logistic equation from time 0 to time t; auc_e: 0 auc_e=231 auc_e=250 0 auc_e=101 auc_e=77 20 30 40 50 20 30 40 50 20 30 40 50 20 30 40 50 Days Days Days Days area under the curve of the measurements. (Pardo et al., 2019 - doi: 10.1007/s40858-019-00282-3).
22 Genome surveillance protocols have been developed using the case of SLCMV in Southeast Asia, as part of an early warning system for crop pests and pathogens.
Figure 23. We have implemented the use of the Nextstrain open tool to track the genomic evolution of pathogens. In this figure, we show the map elaborated for Sri Lankan cassava mosaic virus (SLCMV), which is an emergent threat to cassava cultivation in Southeast Asia. The map is updated in real time as we continue characterizing the genome of the virus in collaboration with our partners in the region. (Hadfield et al., 2018 - doi: 10.1093/bioinformatics/bty407). The interactive tool can be accessed via the following link: https://nextstrain.org/community/pestdisplace/CMDASIA?c=virus&r=location
Publications
Leiva AM. et al., 2020. Nanopore-based complete genome sequence of a Sri Lankan cassava mosaic virus (Geminivirus) strain from Thailand. Microbiology Resource Announcements. https://doi.org/10.1128/MRA.01274-19 López-Álvarez D. et al., 2020. Complete genome sequence of the plant pathogen Ralstonia solanacearum CIAT-078 from Colombia using Oxford Nanopore Technology. Microbiology Resource Announcements. https://doi.org/10.1128/MRA.00448-20 Pardo JM. et al. 2019. Detection of Ralstonia solanacearum phylotype II, race 2 causing Moko disease and validation of genetic resistance observed in the hybrid plantain FHIA-21. Tropical Plant Pathology. https://link.springer.com/article/10.1007/s40858-019-00282-3 PestDisPlace 2019 for SLCMV is available at https://nextstrain.org/community/pestdisplace/CMDASIA?c=virus&r=location https://pestdisplace.org//embed/news/map/pathogen/3 Siriwan W. et al., 2020. Surveillance and diagnostics of the emergent Sri Lankan cassava mosaic virus in Southeast Asia. Virus Research. https://doi.org/10.1016/j.virusres.2020.197959 More about the COLCIENCIAS plantain seed project is available at https://blog.ciat.cgiar.org/es/platano-con-sello-vallecaucano-llega-al-mercado-de-estados-unidos/ More about the IDEAS PARA EL CAMBIO cassava seed project is available at https://ideasparaelcambio.minciencias.gov.co/reto/tronco-e-yuca-pelao
Partners
Cassava Annual Report 2019 23 RSA-3 | RESEARCH RESULTS
María Isabel Gómez and Wilmer Cuéllar
Building a knowledge bank of pests and diseases to protect crops
We developed a database of crowd-sourced information from the scientific literature and preserved specimens of CIAT’s Arthropod Reference Collection Database (CIATARC) as inputs for PestDisPlace. These maps include distribution data for Cassava Mosaic disease in Southeast Asia and Cassava frogskin Disease in the Americas (https://pestdisplace.org). Additionally, we included in this platform several tools for acquiring surveillance data from field georeferenced images of pests and diseases and to analyze them (Imaget, Tumaini, Nymphstar).
Figure 24. Distribution map of Mononychellus tanajoa in northern South America, including records from CIAT’s Arthropod Reference Collection Database (CIATARC).
Partners
CIAT: Data Management Team Cassava Whitefly Project Phenomics Team
24 RSA-3 | RESEARCH RESULTS
Roosevelt Escobar and Juan Manuel Pardo
Management of pests and diseases to secure productivity
A set of 2,600 planting materials of Dominico Hartón in greenhouse facilities was produced, moved to ASOMUSACEAS, and established at field stations as mother plants.
A method for plant production has been implemented, which includes sand beds instead of wood sawdust, and using growth regulators and fertilization of corms to allow rapid propagation and better quality of plantlets.
A low rate of losses in field transplanting occurred (0.23%).
A B
C D
Figure 25. (A) Corms treated at the Alliance, sprouting and producing planting material. (B) Training section by farmers’ association and visit to the Alliance’s greenhouse facilities when plantain plantlets are growing. (C) Material transplanted and established in ASOMUSACEAS fields. (D) Technician of ASOMUSACEAS using adjusted method provided by the Alliance. Replacement of substrate and treated corms allows decreasing time and obtaining good-quality planting material.
Partners
Cassava Annual Report 2019 25 RSA-4 RESEARCH AND SERVICE AREA-4: No poverty through seed system and harvesting
26 RSA-4 provides healthy seed of the more productive cassava varieties, leading to the adoption of new varieties to improve productivity in farmers’ fields.
Cassava seed systems (CSS) include the many ways in which cassava farmers or industries can access, maintain, exchange, produce, and store planting material. Seed systems are often broadly categorized as formal or informal, whereas in reality producers often draw on a mixture of sources, thus blurring these categories to fulfill their needs. Nevertheless, CSS are overwhelmingly informal for most farmers across the world, with few government, NGO, or privately sponsored initiatives to produce good-quality planting material. Interventions aiming at introducing improved germplasm, giving support to a new variety adoption program, maintaining varietal purity, increasing the quality and quantity of planting material, and assuring phytosanitary health are critical for maintaining prosperous cassava-based cropping systems.
Scientists contributing to RSA-4: Erik Delaquis Imran Malik Roosevelt Escobar
Other contributing scientists and staff: Lao Thao Yao Bee Sophearith Sok
Cassava Annual Report 2019 27 RSA-4 | RESEARCH RESULTS
• Identify priority varieties that are least susceptible to major biotic and abiotic stresses for multiplication and distribution • Increase the functionality, sustainability, health, and resilience of cassava seed systems globally to secure the highest productivity • Optimize agronomic management practices by examining the biological and economic tradeoffs between clean stem production and starch yield
Imran Malik
Identify priority varieties for multiplication and distribution
Field experiments in fields heavily infected with cassava mosaic disease (CMD) were carried out to quantify yield loss of six popular varieties during the 2018-19 season. A clear trend was observed: plants demonstrating symptoms at the early stage of development (i.e., 60 days after planting, DAP) produced less than plants that showed symptoms at a later stage of development (i.e., 270 DAP) or no symptoms until harvest (i.e., asymptomatic). Disease diagnostics through PCR were also carried out at the end of the season and detected the presence of virus in asymptomatic plants.
Figure 26. Recommended multiplication of KU50 for areas under high CMD pressure and Rayong 11 in areas with cassava witches’ broom disease (CWBD). However, KU50 is highly susceptible to CWBD and Rayong 11 is susceptible to CMD. Maintaining clean sources of both varieties should be a priority for NARES while new sources of resistance are identified.
28 RSA-4 | RESEARCH RESULTS
Roosevelt Escobar
Rapid multiplication
We built tunnel facilities and greenhouse infrastructure in Laos, and held technical discussions with partners on how they work (high temperature and humidity plus QC/QA of cutting and management) and how to implement the system.
500 in vitro planting materials were sent from The Alliance’s Colombia genebank to each national program (NAFRI in Laos and CARDI in Cambodia). That material will be used as a source of certified KU50 planting material for the CCS program.
Training was given on-site along with online group discussions on how to implement in vitro propagation, which has been developed for the expected propagation rate by cycle.
Figure 27. Cage made of PVC and mesh used to test sprouting behavior of field material with and without CWB symptoms under control conditions. This could allow us to obtain ideas on how to integrate grafting tests in the evaluation phase.
Figure 28. Tunnel infrastructure adapted with local materials in Laos. Future facilities must be filled with clean material that allows subsequent scaling-up and establishing a mother planting source. A team with breeders, virologists/pathologists, and in vitro nursery must be developed to ensure the implementation of CSS in place. Four tunnels and a screenhouse to be established in Laos will be known as “Future Stems”.
Figure 29. Box with in vitro material prepared at the Alliance’s genebank in Colombia prior to dispatch to Cambodia. One week later, the material arrived in Cambodia and the propagation phase started.
Partners RSA-4 | RESEARCH RESULTS
Imran Malik
Optimize agronomic management practices
The variety × irrigation × harvesting/planting date trial established in Lao PDR is ongoing.
Figure 30. Irrigation × variety × harvest/planting date trial established in Laos.
Partners
30 RSA-4 | RESEARCH RESULTS
Erik Delaquis
Seed system characterization and modeling
The results of the first-ever national-scale surveillance of cassava mosaic disease in Cambodia and Vietnam were published in a PLOS One article, providing knowledge of seed-transmitted disease and existing distribution. Further modeling work based on the seed network and disease occurrence reports will be published in early 2020 to help stakeholders evaluate different strategies for the dissemination of clean seed with the highest impact.
A B C
C E F
Symptoms observed on SLCMV positive plants identified in Cambodia. (A)-(C) Typical CMD symptoms on leaves. (A) mosaic, (B) deformation, and (C) curl. (D) Asymptomatic plant testing positive by PCR for SLCMV infection. (E) Plant with mosaic symptoms only on upper leaves and (F) plant with systemic mosaic symptoms.
Figure 31. The 2019 SLCMV publication demonstrating tablet-captured photos of disease symptoms.
Publications
Minato N; Sok S; Chen S; Delaquis E; Phirun I; Le VX; Burra DD; Newby JC; Wyckhuys KAG; de Haan S. 2019. Surveillance for Sri Lankan cassava mosaic virus (SLCMV) in Cambodia and Vietnam one year after its initial detection in a single plantation in 2015. PLOS ONE 14:e0212780. https://doi.org/10.1371/journal.pone.0212780
Partners
Cassava Annual Report 2019 31 RSA-5 RESEARCH AND SERVICE AREA-5: Good health and well-being through postharvest and enhanced nutrition
32 RSA-5 is developing technologies and strategies to diminish root losses and increase cassava value through starch specialized uses and micronutrient potential.
The expansion of the cassava industry has been a success in several countries over the past 30 years, such as Thailand, Nigeria, Vietnam, and Brazil, thus improving income for millions of small and medium farmers and processors. Cassava has potential to replicate this success in more countries, and indeed is expected to play a key role as a resilient source of carbohydrates to feed the growing populations. The Alliance’s Cassava Program addresses the following challenges toward cassava food processing: (1) identifying high-potential cassava genotypes produced by The Alliance’s breeding program through systematic high- throughput screening of users’ quality traits; (2) increasing cassava availability through decreased postharvest losses; (3) increasing cassava processing at small and medium scale through optimized processing equipment (energy efficiency, robustness, capacity matching the availability of raw material); and (4) increasing the profitability of cassava value chains through minimized production costs, value chain assessments, and market assessments.
Scientist contributing to RSA-5: Thierry Tran
Other contributing scientists and staff: Andrés Escobar Cristian Duarte Jhon L. Moreno John Belalcázar Jorge L. Luna María A. Ospina
Cassava Annual Report 2019 33 RSA-5 | RESEARCH RESULTS
Cassava food processing: • Identifying high-potential cassava genotypes • Increasing cassava availability through decreased postharvest losses • Increasing cassava processing at small and medium scale • Increasing the profitability of cassava value chains
Thierry Tran
To better identify and select improved genotypes that meet consumer expectations, RSA-5 developed four biophysical protocols for comprehensive characterization of the cooking quality of cassava (texture, water absorption, optimum cooking time, and closing angle). By correlating the biophysical data generated with NIRS spectra of fresh cassava roots, we then established a proof-of-concept predictive tool to quickly screen out unacceptable genotypes from the point of view of cooking quality (5 min/sample). When integrated in the screenings of cassava genotypes, this tool will help focus the selection efforts on good-cooking cassava genotypes.
Figure 32. Cooking parameters such as water absorption and closing angle may predict cooking time of boiled cassava (r2 = 0.63).
Publications
Rondet E; Dahdouh L; Escobar E; Ruiz E; Cuq B; Delalonde M. 2019. Development of a physicochemical method to quantify the extracellular liquid volume: Application to the transformation of cassava into gari. Food Science and Technology 108:1–5. https://www.sciencedirect.com/science/article/pii/S0023643819302634
Shen G; Lesnoff M; Baeten V; Dardenne P; Davrieux F; Ceballos F; Belalcázar J; Dufour D; Yang Z; Han L; Fernández Pierna JA. 2019. Local partial least squares based on global PLS scores. Journal of Chemometrics 33(5):1-12. https://onlinelibrary.wiley.com/doi/full/10.1002/cem.3117
Collaboration Partners with RSA-1
34 Cassava Annual Report 2019 35 RSA-6 RESEARCH AND SERVICE AREA-6: Gender equality through value chains, markets, and policies
36 RSA-6 understands the production process and cost related to each element of the production chain to add value to cassava products in LAC and ASEAN regions.
This RSA brings cross-cutting support to the Cassava Program, guiding it in fulfilling its mission by helping to set research priorities to better assess different stakeholders’ and end users’ demands and needs; to identify market opportunities and production and consumer trends; to develop business models inclusive toward poor farmers, women, and youth; and to generate evidence of the program’s outputs and impacts.
Scientists contributing to RSA-6: Jonathan Newby Ricardo Labarta Vanya Slavchevska
Other contributing scientists and staff: Lao Thao Yao Bee Sophearith Sok Thuy Cu Thi Le
Cassava Annual Report 2019 37 RSA-6 | RESEARCH RESULTS
• Guide Latin American and Asian cassava value-chain actors on investment opportunities and priorities for enhancing the productivity, sustainability, and inclusiveness of value chains • Understand market and policy developments and communicate the impacts on different cassava value-chain actors • Provide credible and relevant evidence of the Cassava Program contributions toward high-level outcomes for accountability and better targeting • Inform policymakers and global research agendas on the most cost-effective ways to achieve impact at scale by developing partnerships with public- and private-sector actors in cassava value chains • Understand how gender and socioeconomics shape cassava value chains and how cassava value chains can better work toward women’s economic empowerment and social inclusion • Provide evidence-based guidance on the opportunities for youth agri- entrepreneurship in cassava value chains • Implement a broader institutional learning process based on evidence from successes and failures that promotes critical reflections on continuously improving the Alliance’s capacity to deliver world-class solutions to a complex agricultural sector
Jonathan Newby
Market update and outlook
In 2019, significant shocks took place for both supply and derived demand for cassava-based products and substitutes. These affected the farm economics of management interventions, leading to investment uncertainty, and decreased the incentives for value actors to scale innovations to farmers in their supply zone. Therefore, the Cassava Program presented several market updates in research and policy forums and industry meetings in Asia. In 2019, cassava supply contracted as a result of drought and CMD. This resulted in high fresh root prices for farmers, and affected the competitiveness of the industry against substitutes.
Area (ha) Production (t) Yield (t/ha) Country 2016 2017 2018 2016 2017 2018 2016 2017 2018 Thailand 1,427,168 1,284,021 1,385,817 30,557,857 27,875,464 29,974,636 21.4 21.7 22.3 Indonesia 822,744 772,975 697,384 20,260,675 19,053,748 16,119,020 24.6 24.6 23.1 Vietnam 569,233 532,501 513,021 10,909,800 10,267,568 9,847,074 19.2 19.3 19.2 Cambodia 684,070 613,912 652,235 14,820,249 13,817,261 13,750,076 21.7 22.5 21.1 Laos 75,810 70,930 71,010 2,410,000 2,277,050 2,279,030 31.8 32.1 32.1 Myanmar 36,625 34,718 31,278 433,378 405,404 376,663 11.8 11.7 12.0 Philippines 229,769 234,540 227,644 2,755,146 2,806,668 2,723,033 12.0 12.0 12.0 Total 3,845,419 3,543,597 3,578,389 82,147,105 76,503,163 75,069,532 21.4 21.6 21.0
Figure 33. Thailand production revised down 8% because of the climate impact on yield.
38 Vietnam has increasing competition for fresh roots with a decreased supply due to CMD, extending into Cambodia to take advantage of an earlier harvest. Many factories report that they rely on Cambodia for 70-80% of their feedstock. However, this first cuts into the supply of chips and undermines the viability of new factories in Cambodia, which struggle to compete for roots at higher prices relative to established processors in Vietnam. Across the region, cassava remains very expensive as a feedstock for biofuel applications, posing a significant challenge to would-be bioethanol enterprises.
Overall, much uncertainty exists regarding both the supply and demand of cassava and cassava-based products for 2020.
Adoption and impact
There is an extremely high level of adoption of improved cassava varieties in Vietnam (85%). Varieties KM94 and KM419 were the two most important varieties with the highest adoption rates (households and area) by 2015. A large percentage of households (about 83%) believed that they did not have landraces in their fields but DNA fingerprinting found that 25% of the households were using landrace varieties. Approximately 86% of the cassava-growing households reported applying fertilizer in their fields, mostly during planting. Farmers in the Southeast reportedly applied the highest rate of chemical and bio-organic fertilizer, whereas farmers in the Central Coastal area applied the largest amount of manure compared with other regions. The average cassava yield in Vietnam was almost 21 t/ha. The Southeast was the most productive region, with an average yield of 26.35 t/ha. Most of the cassava harvested was used for selling and feed in the surveyed cassava season. Cassava in Vietnam was mostly commercialized, with 88.5% and 10.1% of cassava products sold as fresh roots and dried chips, respectively. Among the buyers, local traders were the most popular. They purchased 81% of the fresh roots and 54% of the dried chips from cassava producers at the farm gate. The Southeast region has the largest average cassava area per household (i.e., more than 3 ha vis-à- vis 0.7 ha nationally) and the highest cassava productivity. It also has the highest percentage of tractor use and fertilizer adoption. In addition, this region has the lowest percentage of households classified as “poor” or least likely to be poor based on both poverty score and consumption expenditure level. In contrast, the Central Highlands region has the largest percentage of poor and vulnerable households for all the measures of poverty considered. An ex ante economic evaluation suggests that the use of disease-free planting material coming from a thermotherapy chamber among banana producers in Colombia can generate positive economic benefits. The adoption of disease-free planting material would result in a productivity increase, cost decrease, and control of the spread of banana diseases. A farmer using this clean planting material could increase economic benefits up to 60%.
Cassava Annual Report 2019 39 RSA-6 | RESEARCH RESULTS
Vanya Slavchevska
Gender and social inclusion
Using survey data collected in the context of the Cassava Value Chains and Livelihoods programs in Southeast Asia, we carried out analyses on how gender, ethnicity, and socioeconomic status influenced technology adoption and attitudes toward technologies in Lao PDR and Cambodia. In general, in the family farming systems of Southeast Asia, both men and women play important roles and tend to be rather equally engaged in cassava production. We find that there are few differences in practices adopted by men and practices adopted by women cassava farmers. This may be because cassava is not seen as an input-intensive crop, and many farmers invest little in their cassava fields. More differences exist, however, in the types of technologies women and more marginalized farmers would like to see trials on. The results vary by country, highlighting the importance of conducting country- and sub-country-specific analyses. Ensuring that technology development and transfers are inclusive of the needs of marginal farmers is key to building sustainable cassava farming systems.
Ricardo Labarta
Achieving impact at scale through partnerships and knowledge platforms
With the increasing need to show high impact from research funding, agencies have been compelled to consider alternative impact pathways for their research and development activities. This has often resulted in the private sector being identified as a potential next user of research outputs. However, limited analysis is actually conducted regarding the incentives and conditions for this to occur.
In particular contexts, private-sector value-chain actors have incentives to invest in the extension of research outputs to smallholder farmers. In other contexts, however, little incentive exists for private- sector involvement, and support from public-sector or non-government actors will be required, that is, the private sector will not be the panacea to generate impact at scale, and a more nuanced approach is required as farming systems and value chains evolve.
With activities and public-private partnerships across sites in Vietnam, Indonesia, Lao PDR, Cambodia, and Myanmar, we have shown how the value-chain structure impacts the scaling of research outputs and adoption by farmers. Second, we link this expanded typology of value chains to the inherent characteristics of various technologies to form a matrix of value-chain structures and technology characteristics, identifying combinations with differing potential for technology adoption.
The lessons learned from the successful models are being used to inform and develop public-private and regional partnerships to address cassava diseases in Southeast Asia.
40 Figure 34. ACIAR Cassava Value Chain and Livelihood Research Program, Research Symposium, Medan, Indonesia, 2019.
Figure 35. Sustainable Cassava Disease Solutions in Mainland Southeast Asia Inception Meeting, Vientiane, Lao PDR, 2019.
Publications
ACIAR proceedings published. https://aciar.gov.au/publication/cassava-value-chains
ACIAR Cassava Value Chain & Livelihood Program http://cassavavaluechains.net/ https://www.facebook.com/groups/1462662477369426/
Sustainable Cassava Disease Solutions https://cassavadiseasesolutionsasia.net/ https://www.facebook.com/groups/2394808117512232/
Le DP; Labarta RA; de Haan S; Maredia M; Becerra LA; Nhu L; Ovalle T; Nguyen V; Pham N; Nguyen H; Nguyen H; Le K; Le HH. 2019. Characterization of cassava production systems in Vietnam. Working Paper. CIAT Publication No. 480. International Center for Tropical Agriculture (CIAT), Hanoi, Vietnam. 54 p. Available at https://hdl.handle.net/10568/103417
Newby J; Smith D; Cramb R; Delaquis E; Yadav L. 2020. Cassava value chains and livelihoods in South-East Asia, a regional research symposium held at Pematang Siantar, North Sumatra, Indonesia, 1–5 July 2019, ACIAR Proceedings Series, No. 148, Australian Centre for International Agricultural Research, Canberra, 114 pp. Partners
AUSTRALIA VIETNAM
Field Crops Research Institute
THAILAND LAO PDR CAMBODIA INDONESIA MYANMAR The Plant Protection Center
COLOMBIA
Cassava Annual Report 2019 41 Global Cassava Partners
UNITED STATES CORNELL Cornell University
B&MGF Bill & Melinda Gates Foundation ENGLAND UCR University of California, Riverside NRI Natural Resources Institute MSU Michigan State University RHUL Royal Holloway University of London INGREDION Ingredion Incorporated
FRANCE RTBfoods Breeding Roots, Tubers and Banana products for end-user preferences
CIRAD Agricultural Research for Development
NIGERIA COLOMBIA IITA International Institute URG-ALLIANCE OF BIOVERSITY AND CIAT of Tropical Agriculture Unit of Genetic Resources at the Alliance of Bioversity International and CIAT PERU AGROSAVIA BRAZIL Corporación Colombiana de RTB EMBRAPA Investigación Agropecuaria Roots, Tubers and Bananas Empresa Brasileira de ASOMUSACEAS CIP Pesquisa Agropecuária Asociación Musáceas del Valle International Potato Center
UNAL YANESHA Universidad Nacional de Colombia Peru Yanesha Sede Palmira UNDAC MINCIENCIAS Universidad Nacional Ministerio de Ciencia, Daniel Alcides Carrión Tecnología e Investigación IBC Instituto del Bien Común
INIA Instituto Nacional de Innovación Agraria
FECONAYA Federación de Comunidades Nativas Yaneshas
42 MYANMAR LAOS VIETNAM DOA-MYANMAR NAFRI AGI Ministry of Agriculture, Livestock and Irrigation National Agriculture and Agricultural Genetics Institute Forestry Research Institute DAR RDRDC Department of Agricultural Research DOA-LAO Root Crop Research Ministry of Agriculture and Development Center and Forestry HLARC PPC Hung Loc Agricultural CHINA The Plant Protection Center CATAS Research Center Chinese Academy of NOMAFSI Tropical Agricultural Northern Mountainous Sciences Agriculture and Forestry Science Institute GERMANY TNU DSMZ Tay Nguyen University Leibniz Institute IAS Institute of Agricultural Sciences for Southern Vietnam
FCRI UGANDA Field Crops Research Institute NaCRRI National Crops Resources PPRI Research Institute Plant Protection Research Institute THAILAND NARO KU National Agricultural Kasetsart University INDONESIA Research Organization UB University of Brawijaya
ILETRI Indonesian Legumes and Tuber Crops Research Institute TANZANIA CAMBODIA TARI CAVAC Tanzania Agricultural Cambodia-Australia Research Institute Agricultural Value Chain Program
CARDI Cambodian Agricultural Research AUSTRALIA and Development ACIAR Institute Australian Center for International Agricultural Research
GDA UWA General Directorate The University of Western Australia of Agriculture USQ University of Queensland
Cassava Annual Report 2019 43 Contributing scientists
Luis Augusto Hernán Xiaofei Becerra Ceballos Zhang Former Cassava Program Cassava Cassava Leader Breeder Breeder
Jonathan Paul Thierry Newby Chavarriaga Tran Head Genetic Head Cassava Program Transformation Cassava Processing Coordinator Asia Lab Lab
Wilmer Roosevelt Adriana Cuéllar Escobar Bohórquez Head Research Research Virology Lab Associate Associate María Isabel Katherine Tatiana Gómez Castillo Ovalle Research Research Research Associate Associate Associate
Imran Vanya Malik Ricardo Slavchevska Labarta Cassava Gender Production Systems Former Specialist Specialist Impact Specialist
Ana María Juan Manuel Leiva Pardo Research Research Associate Associate Alliance
Bioversity International and the International Center for Americas Hub alliancebioversityciat.org Tropical Agriculture (CIAT) are part of CGIAR, a global research www.bioversityinternational.org Km 17 Recta Cali-Palmira CP 763537 partnership for a food-secure future. www.ciat.cgiar.org Apartado Aéreo 6713 www.cgiar.org Bioversity International is the operating name of the Cali, Colombia International Plant Genetic Resources Institute (IPGRI). Phone: (+57) 2 4450000