Agricultural Research Knowledge

Permanent URI for this collectionhttps://hdl.handle.net/20.500.11766/187

Browse

Now showing 1 - 20 of 13536

Novel Technological and Management Options for Accelerating Transformational Changes in Rice and Livestock Systems
Author(s): Chirinda, Ngonidzashe; Arenas, Laura; Loaiza, Sandra; Trujillo, Catalina; Katto, Maria; Chaparro, Paula; Nuñez, Jonathan; Arango, Jacobo; Martínez Barón, Deissy; Loboguerrero, Ana María; Becerra, Augusto; Avila, Ivan; Guzmán, Myriam; Peters, Michael; Twyman, Jennifer; Rosa, María García; Serna, Laura; Escobar, Daniel; Arora, Diksha; Tapasco, Jeimar; Mazabel, Lady; Correa, Fernando; Ishitani, Manabu; Da Silva, Mayesse; Graterol, Eduardo; Jaramillo, Santiago; Pinto, Adriana; Zuluaga, Andres; Lozano, Nelson; Byrnes, Ryan; LaHue, Gabriel; Alvarez, Carolina; Rao, Idupulapati; Barahona, Rolando (MDPI, 2017-10-27)
Date: 2017-10-27
Type: Journal Article
Status: Open access
Agricultural producers grapple with low farm yields and declining ecosystem services within their landscapes. In several instances, agricultural production systems may be considered largely unsustainable in socioeconomic and ecological (resource conservation and use and impact on nature) terms. Novel technological and management options that can serve as vehicles to promote the provision of multiple benefits, including the improvement of smallholder livelihoods, are needed. We call for a paradigm shift to allow designing and implementing agricultural systems that are not only efficient (serving as a means to promote development based on the concept of creating more goods and services while using fewer resources and creating less waste) but can also be considered synergistic (symbiotic relationship between socio-ecological systems) by simultaneously contributing to major objectives of economic, ecological, and social (equity) improvement of agro-ecosystems. These transformations require strategic approaches that are supported by participatory system-level research, experimentation, and innovation. Using data from several studies, we here provide evidence for technological and management options that could be optimized, promoted, and adopted to enable agricultural systems to be efficient, effective, and, indeed, sustainable. Specifically, we present results from a study conducted in Colombia, which demonstrated that, in rice systems, improved water management practices such as Alternate Wetting and Drying (AWD) reduce methane emissions (~70%). We also show how women can play a key role in AWD adoption. For livestock systems, we present in vitro evidence showing that the use of alternative feed options such as cassava leaves contributes to livestock feed supplementation and could represent a cost-effective approach for reducing enteric methane emissions (22% to 55%). We argue that to design and benefit from sustainable agricultural systems, there is a need for better targeting of interventions that are co-designed, co-evaluated, and co-promoted, with farmers as allies of transformational change (as done in the climate-smart villages), not as recipients of external knowledge. Moreover, for inclusive sustainability that harnesses existing knowledge and influences decision-making processes across scales, there is a need for constant, efficient, effective, and real trans-disciplinary communication and collaboration.
First report of a ‘Candidatus Phytoplasma asteris’ isolate associated with banana elephantiasis disease in Colombia
Author(s): Aliaga, Flavio; Hopp, E.; Alvarez, Elizabeth; Becerra, Augusto (British Society for Plant Pathology (BSPP), 2018-06-01)
Date: 2018-03-01
Type: Journal Article
Status: Open access
First report of a ‘Candidatus Phytoplasma asteris’ isolate associated with banana elephantiasis disease in Colombia
An optimized isolation protocol yields high-quality RNA from cassava tissues (Manihot esculenta Crantz)
Author(s): Behnam, Babak; Bohorquez-Chaux, Adriana; Castañeda, Oscar; Tsuji, Hiroyuki; Ishitani, Manabu; Becerra, Augusto (Wiley Open Access, 2018-11-24)
Date: 2018-11-24
Type: Journal Article
Status: Open access
We developed and modified a precise, rapid, and reproducible protocol isolating high-quality RNA from tissues of multiple varieties of cassava plants (Manihot esculenta Crantz). The resulting method is suitable for use in mini, midi, and maxi preparations and rapidly achieves high total RNA yields (170–600 μg·g−1) using low-cost chemicals and consumables and with minimal contamination from polysaccharides, polyphenols, proteins, and other secondary metabolites. In particular, A260 : A280 ratios were > 2.0 for RNA from various tissues, and all of the present RNA samples yielded ribosomal integrity number values of greater than six. The resulting high purity and quality of isolated RNA will facilitate downstream applications (quantitative reverse transcriptase-polymerase chain reaction or RNA sequencing) in cassava molecular breeding.
A metabolomics characterisation of natural variation in the resistance of cassava to whitefly
Author(s): Perez-Fons, Laura; Bohorquez-Chaux, Adriana; Irigoyen, Maria; Garceau, Danielle; Morreel, Kris; Boerjan, Wout; Walling, Linda; Becerra, Augusto; Paul, Fraser (BioMed Central, 2019-11-27)
Date: 2019-11-27
Type: Journal Article
Status: Open access
Background Cassava whitefly outbreaks were initially reported in East and Central Africa cassava (Manihot esculenta Crantz) growing regions in the 1990’s and have now spread to other geographical locations, becoming a global pest severely affecting farmers and smallholder income. Whiteflies impact plant yield via feeding and vectoring cassava mosaic and brown streak viruses, making roots unsuitable for food or trading. Deployment of virus resistant varieties has had little impact on whitefly populations and therefore development of whitefly resistant varieties is also necessary as part of integrated pest management strategies. Suitable sources of whitefly resistance exist in germplasm collections that require further characterization to facilitate and assist breeding programs. Results In the present work, a hierarchical metabolomics approach has been employed to investigate the underlying biochemical mechanisms associated with whitefly resistance by comparing two naturally occurring accessions of cassava, one susceptible and one resistant to whitefly. Quantitative differences between genotypes detected at pre-infestation stages were consistently observed at each time point throughout the course of the whitefly infestation. This prevalent differential feature suggests that inherent genotypic differences override the response induced by the presence of whitefly and that they are directly linked with the phenotype observed. The most significant quantitative changes relating to whitefly susceptibility were linked to the phenylpropanoid super-pathway and its linked sub-pathways: monolignol, flavonoid and lignan biosynthesis. These findings suggest that the lignification process in the susceptible variety is less active, as the susceptible accession deposits less lignin and accumulates monolignol intermediates and derivatives thereof, differences that are maintained during the time-course of the infestation. Conclusions Resistance mechanism associated to the cassava whitefly-resistant accession ECU72 is an antixenosis strategy based on reinforcement of cell walls. Both resistant and susceptible accessions respond differently to whitefly attack at biochemical level, but the inherent metabolic differences are directly linked to the resistance phenotype rather than an induced response in the plant.
Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops
Author(s): Price, Elliot; Drapal, Margit; Perez-Fons, Laura; Amah, Delphine; Bhattacharjee, Ranjana; Heider, Bettina; Rouard, Mathieu; Swennen, Rony; Becerra, Augusto; Paul, Fraser (Wiley, 2021-03-01)
Date: 2019-12-19
Type: Journal Article
Status: Open access
Roots, tubers, and bananas (RTB) are vital staples for food security in the world’s poorest nations. A majorconstraint to current RTB breeding programmes is limited knowledge on the available diversity due to lackof efficient germplasm characterization and structure. In recent years large-scale efforts have begun to eluci-date the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemicalmeasurements have often been overlooked despite metabolite composition being directly associated withagronomic and consumer traits. Here we present a compound database and concentration range formetabolites detected in the major RTB crops: banana (Musaspp.), cassava (Manihot esculenta), potato(Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscoreaspp.), following metabolomics-based diversity screening of global collections held within the CGIAR institutes. The dataset including 711chemical features provides a valuable resource regarding the comparative biochemical composition of eachRTB crop and highlights the potential diversity available for incorporation into crop improvement pro-grammes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex com-positional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) thanthat of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20%of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics withthe on-going genomic and phenotypic studies will enhance ’omics-wide associations of molecular signa-tures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discoveryand functional characterization.
Genetic diversity of the rain tree (Albizia saman) in Colombian seasonally dry tropical forest for informing conservation and restoration interventions
Author(s): Aguirre-Morales, Carolina Adriana; Thomas, Evert; Cardozo, Carlos Ivan; Gutierrez, Janeth; Alcázar-Caicedo, Carolina; Moscoso-Higuita, Luis Gonzalo; Becerra, Augusto; González, Mailyn Adriana (Wiley Open Access, 2020-02-05)
Date: 2020-02-05
Type: Journal Article
Status: Open access
Albizia saman is a multipurpose tree species of seasonally dry tropical forests (SDTFs) of Mesoamerica and northern South America typically cultivated in silvopastoral and other agroforestry systems around the world, a trend that is bound to increase in light of multimillion hectare commitments for forest and landscape restoration. The effective conservation and sustainable use of A. saman requires detailed knowledge of its genetic diversity across its native distribution range of which surprisingly little is known to date. We assessed the genetic diversity and structure of A.saman across twelve representative locations of SDTF in Colombia, and how they may have been shaped by past climatic changes and human influence. We found four different genetic groups which may be the result of differentiation due to isolation of populations in preglacial times. The current distribution and mixture of genetic groups across STDF fragments we observed might be the result of range expansion of SDTFs during the last glacial period followed by range contraction during the Holocene and human-influenced movement of germplasm associated with cattle ranching. Despite the fragmented state of the presumed natural A. saman stands we sampled, we did not find any signs of inbreeding, suggesting that gene flow is not jeopardized in humanized landscapes. However, further research is needed to assess potential deleterious effects of fragmentation on progeny. Climate change is not expected to seriously threaten the in situ persistence of A. saman populations and might present opportunities for future range expansion. However, the sourcing of germplasm for tree planting activities needs to be aligned with the genetic affinity of reference populations across the distribution of Colombian SDTFs. We identify priority source populations for in situ conservation based on their high genetic diversity, lack or limited signs of admixture, and/or genetic uniqueness.
The metabotyping of an East African cassava diversity panel: A core collection for developing biotic stress tolerance in cassava
Author(s): Perez-Fons, Laura; Ovalle, Tatiana; Maruthi, Gowda; Colvin, John; Becerra, Augusto; Paul, Fraser (Public Library of Science, 2020-11-08)
Date: 2020-11-08
Type: Journal Article
Status: Open access
Cassava will have a vital role to play, if food security is to be achieved in Sub-Saharan Africa, especially Central and East Africa. The whitefly Bemisia tabaci poses a major threat to cassava production by small holder farmers in part due to their role as a vector of cassava mosaic begomoviruses (CMBs) and cassava brown streak ipomoviruses (CBSIs). In the present study untargeted metabolomics has been used as a tool to assess natural variation, similarities and attempts to identify trait differentiators among an East African cassava diversity panel that displayed tolerance/resistance to the effects of Bemisia tabaci infestation. The metabolome captured, was represented by 1529 unique chemical features per accession. Principal component analysis (PCA) identified a 23% variation across the panel, with geographical origin/adaption the most influential classification factors. Separation based on resistance and susceptible traits to Bemisia tabaci could also be observed within the data and was corroborated by genotyping data. Thus the metabolomics pipeline represented an effective metabotyping approach. Agglomerative Hierarchical Clustering Analysis (HCA) of both the metabolomics and genotyping data was performed and revealed a high level of similarity between accessions. Specific differentiating features/metabolites were identified, including those potentially conferring vigour to whitefly tolerance on a constitutive manner. The implications of using these cassava varieties as parental breeding material and the future potential of incorporating more exotic donor material is discussed.
“Rambo root” to the rescue: How a simple, low-cost solution can lead to multiple sustainable development gains
Author(s): Villarino, Maria; Da Silva, Mayesse; Becerra, Augusto; Castro-Nuñez, Augusto (John Wiley & Sons Ltd., 2020-11-20)
Date: 2020-11-20
Type: Journal Article
Status: Open access
Rugged and resilient, cassava is a bulky root crop that can thrive on poor soils. Cultivating it offers the potential to restore degraded land, which in turn may reduce hunger, generate livelihoods, fight climate change and even promote peace. As such, farming cassava offers a nature-based solution that can contribute to achieving numerous sustainable development targets. The authors acknowledge that scaling up production of any commodity may bring risks of deforestation and biodiversity loss through clearing forest areas. In the case of increasing cassava production, though, this may not be the case because cassava can be cultivated on land affected by degradation, and this resource is abundant; policies and initiatives exist to mitigate those risks; and the principal goal is to scale up a sustainable land use system.
An optimized high-quality DNA isolation protocol for spodoptera frugiperda J. E. smith (Lepidoptera: Noctuidae)
Author(s): Marín, Diana Victoria; Castillo, Diana Katherine; Becerra, Augusto; Chalarca, Jairo Rodríguez; Pérez, Cristo Rafael (Elsevier, 2021-02-03)
Date: 2021-02-03
Type: Journal Article
Status: Open access
An optimized high-quality DNA isolation protocol was developed using body segment tissue from the Fall Armyworm (Spodoptera frugiperda), that will allow documenting genetic variability based on biotypes, facilitating studies on the appearance, distribution and population dynamics of the fall armyworm at the molecular level. The resulting protocol is an easy-to-use, timesaving method that can rapidly achieve high quality, high-yielding total genomic DNA, using chemicals and everyday consumables available in a molecular laboratory. This new method of DNA extraction avoids the contamination of polysaccharides, salts, phenols, proteins and other cellular by-products that can interfere with subsequent reactions. DNA purity estimates reveal A260: A280 ratios greater than 1.9, which were evidenced by quality test on agarose gel, observing complete integrity and high purity of the resulting samples, and yielded 30–99 µg/g of total DNA. Therefore, the quality of the DNA produced from this extraction is suitable for subsequent molecular applications: (i) next generation whole genome sequencing, (ii) conventional polymerase chain reaction for genotyping, (iii) barcodes and (iv) gene cloning. In addition, to become an anticipating diagnostic tool for invasive lepidopteran larval stages: •The resulting protocol is an easy-to-use time-saving method. •This new extraction method prevents contamination from polysaccharides, salts, phenols, proteins, and other cellular sub-products. •DNA purity estimations reveal A260:A280 ratios above 1.9.
Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes
Author(s): Johnston-Monje, David; P. Gutiérrez, Janneth; Becerra, Augusto (Frontiers Media, 2021-10-22)
Date: 2021-10-22
Type: Journal Article
Status: Open access
Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.
Dynamic seed zones to guide climate-smart seed sourcing for tropical dry forest restoration in Colombia
Author(s): Fremout, Tobias; Thomas, Evert; Bocanegra-González, Kelly Tatiana; Aguirre-Morales, Carolina Adriana; Morillo-Paz, Anjuly Tatiana; Atkinson, Rachel; Kettle, Christopher; González-M., Roy; Alcázar-Caicedo, Carolina; González, Mailyn Adriana; Gil-Tobón, Carlos; P. Gutiérrez, Janneth; Moscoso-Higuita, Luis Gonzalo; Becerra, Augusto; de Carvalho, Dulcinéia; Muys, Bart (Elsevier (12 months), 2021-06-01)
Date: 2021-03-16
Type: Journal Article
Status: Timeless limited access
Tree-based forest landscape restoration interventions require knowledge on the suitability and origin of seed sources and planting material. A common recommendation is to select locally sourced material based on the assumption that it is well adapted to local environmental conditions and to avoid introduction of maladapted genes. However, faced with accelerating climate change, it may be prudent to supplement local provenances with ‘climate-matched’ provenances, i.e. where current climate conditions are similar to those anticipated in the future at the planting site. Restoration practitioners usually do not have access to the necessary information to implement such climate-smart seed sourcing. Here, we combine genetic data of 11 socio-economically important tree species of the tropical dry forests of Colombia with spatial environmental data to inform the delineation of dynamic seed zones for the restoration of this highly threatened ecosystem. Analysis of Molecular Variance (AMOVA) indicates significant population genetic differentiation within all 11 species. We fitted linear mixed effects models to evaluate if the genetic distance between trees was mainly related to geographic distance (i.e. isolation by distance; IBD), environmental distance (i.e. isolation by environment; IBE), or both. Observed scales of genetic differentiation were best explained by the model including both geographic and environmental distance (IBD + IBE) for 6 out of 11 species, and by the IBE model for the remaining species, suggesting that the observed differentiation is at least partly driven by adaptive processes. Aiming at capturing as much as possible of the observed genetic differentiation, we propose a set of 36 provisional seed zones that are applicable across species and dynamic under climate change, based on the clustering of environmental data and geographical coordinates. We project these seed zones to future climate conditions using five general circulation models and two emission scenarios, and discuss how they can be used to implement different climate-smart seed sourcing strategies in a pragmatic way. The seed zone maps are made available in a user-friendly online tool.
Field-transcriptome analyses reveal developmental transitions during flowering in cassava (Manihot esculenta Crantz)
Author(s): Behnam, Babak; Higo, Asuka; Yamaguchi, Kaho; Tokunaga, Hiroki; Utsumi, Yoshinori; Selvaraj Gomez, Michael; Seki, Motoaki; Ishitani, Manabu; Ceballos, Hernan; Becerra, Augusto; Tsuji, Hiroyuki (Springer Verlag (Germany), 2021-04-15)
Date: 2021-04-15
Type: Journal Article
Status: Timeless limited access
Cassava is an important crop for both edible and industrial purposes. Cassava develops storage roots that accumulate starch, providing an important source of staple food in tropical regions. To facilitate cassava breeding, it is important to elucidate how flowering is controlled. Several important genes that control flowering time have been identified in model plants; however, comprehensive characterization of these genes in cassava is still lacking. In this study, we identified genes encoding central flowering time regulators and examined these sequences for the presence or absence of conserved motifs. We found that cassava shares conserved genes for the photoperiodic flowering pathway, including florigen, anti-florigen and its associated transcription factor (GIGANTEA, CONSTANS, FLOWERING LOCUS T, CENTRORADIALIS/TERMINAL FLOWER1 and FD) and florigen downstream genes (SUPRESSOR OF OVEREXPRESSION OF CONSTANS1 and APETALA1/FRUITFUL). We conducted RNA-seq analysis of field-grown cassava plants and characterized the expression of flowering control genes. Finally, from the transcriptome analysis we identified two distinct developmental transitions that occur in field-grown cassava.
Calibration and validation of the FAO AquaCrop water productivity model for cassava (Manihot esculenta Crantz)
Author(s): Wellens, Joost; Raes, Dirk; Fereres, Elias; Diels, Jan; Coppye, Cecilia; Adiele Joy, Geraldine; Ezui, Kodjovi; Becerra, Augusto; Selvaraj Gomez, Michael; Dercon, Gerd; Kheng Heng, Lee (Elsevier, 2022-04-01)
Date: 2022-01-20
Type: Journal Article
Status: Open access
FAO’s water-driven crop growth simulation model, AquaCrop, was calibrated and validated for cassava (Manihot esculenta Crantz). Existing datasets, used in similar published works, were shared covering several years and regions (Colombia, Nigeria and Togo). Different varieties were tested for the case of Colombia and a single variety (TME-419) for Nigeria and Togo. Overall calibrated biomass simulations resulted in an R2 of 0.96 and a RMSE of 1.99 tonne DM/ha. As for dry tuber yield estimates, it was not possible to find a single harvest index for the ensembled varieties given their varying characteristics and limited data per variety. However, for the TME-419 variety (Nigeria and Togo) calibrated root tuber simulations yielded and R2 of 0.94 and a RMSE of 2.37 tonne DM/ha. A single crop-file was developed for different cassava varieties and agro-ecological regions, which can be applied with confidence to further study cassava related food security, water productivity, improved agronomic practices, etc.
Processors' Experience in the Use of Flash Dryer for Cassava-derived Products in Nigeria
Author(s): Ojide, Makuachukwu; Suraju Adeyemi, Adegbite; Tran, Thierry; Taborda, Luis; Chapuis, Arnaud; Lukombo, Simon; Totin, Edmond; Sartas, Murat; Schut, Marc; Becerra, Augusto; Dufour, Dominique; Abass, Adebayo (Frontiers Media S.A., 2022-02-17)
Date: 2022-02-17
Type: Journal Article
Status: Open access
This study was designed and carried out to ascertain the situation and perceptions of end users of cassava flash drying equipment in Nigeria with the aim of giving suggestions to policies and approaches for improved technology. Forty-one processing firms were selected and interviewed. Descriptive analyses were used and a logistic regression model was estimated. The results revealed that 49% of the firms stopped using their flash dryers due to the low demand for high-quality cassava flour (HQCF) resulting from the high cost of processing occasioned by an inefficient heat-generating component. The estimated model provides evidence that cost effectiveness (p < 0.05) and energy cost (p < 0.10) are the two major determinants of the continuous usage of flash dryers in the study area. Forty-one percent of the firms indicated willingness to pay for any technical adjustment of their flash dryers, supposing such adjustment would improve on drying and the energy efficiency of the equipment up to 40%. The study recommends that machine fabricators in Nigeria and other African countries should be trained on the production of energy- and cost-efficient small-scale flash dryers. Again, the design and commercialization of flash dryers that can be mounted on mobile trucks for farm-gate processing should be encouraged to facilitate farm-gate processing, thereby reducing postharvest losses resulting from transporting perishable and bulky roots over a long distance.
Characterization of cassava ORANGE proteins and their capability to increase provitamin A carotenoids accumulation
Author(s): Jaramillo, Angelica; Sierra, Santiago; Chavarriaga, Paul; Castillo, Diana Katherine; Gkanogiannis, Anestis; Becerra, Augusto; Arciniegas, Juan Pablo; Sun, Tianhu; Li, Li; Welsch, Ralf; Boy, Erick; Álvarez, Daniel (Public Library of Science, 2022-01-07)
Date: 2022-01-07
Type: Journal Article
Status: Open access
Cassava (Manihot esculenta Crantz) biofortification with provitamin A carotenoids is an ongoing process that aims to alleviate vitamin A deficiency. The moderate content of provitamin A carotenoids achieved so far limits the contribution to providing adequate dietary vitamin A levels. Strategies to increase carotenoid content focused on genes from the carotenoids biosynthesis pathway. In recent years, special emphasis was given to ORANGE protein (OR), which promotes the accumulation of carotenoids and their stability in several plants. The aim of this work was to identify, characterize and investigate the role of OR in the biosynthesis and stabilization of carotenoids in cassava and its relationship with phytoene synthase (PSY), the rate-limiting enzyme of the carotenoids biosynthesis pathway. Gene and protein characterization of OR, expression levels, protein amounts and carotenoids levels were evaluated in roots of one white (60444) and two yellow cassava cultivars (GM5309-57 and GM3736-37). Four OR variants were found in yellow cassava roots. Although comparable expression was found for three variants, significantly higher OR protein amounts were observed in the yellow varieties. In contrast, cassava PSY1 expression was significantly higher in the yellow cultivars, but PSY protein amount did not vary. Furthermore, we evaluated whether expression of one of the variants, MeOR_X1, affected carotenoid accumulation in cassava Friable Embryogenic Callus (FEC). Overexpression of maize PSY1 alone resulted in carotenoids accumulation and induced crystal formation. Co-expression with MeOR_X1 led to greatly increase of carotenoids although PSY1 expression was high in the co-expressed FEC. Our data suggest that posttranslational mechanisms controlling OR and PSY protein stability contribute to higher carotenoid levels in yellow cassava. Moreover, we showed that cassava FEC can be used to study the efficiency of single and combinatorial gene expression in increasing the carotenoid content prior to its application for the generation of biofortified cassava with enhanced carotenoids levels.
Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants
Author(s): Johnston-Monje, David; P. Gutiérrez, Janneth; Becerra, Augusto (MDPI, 2022-09-02)
Date: 2022-09-02
Type: Journal Article
Status: Open access
A plant’s health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant–microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.
Integrated genetic and metabolic characterization of Latin American cassava (Manihot esculenta) germplasm
Author(s): Perez-Fons, Laura; Ovalle, Tatiana Maria; Drapal, Margit; Ospina, Maria Alejandra; Gkanogiannis, Anestis; Bohorquez-Chaux, Adriana; Becerra, Augusto; Paul, Fraser (American Society of Plant Biologists, 2023-08-01)
Date: 2023-05-06
Type: Journal Article
Status: Open access
Cassava (Manihot esculenta Crantz) is an important staple crop for food security in Africa and South America. The present study describes an integrated genomic and metabolomic approach to the characterization of Latin American cassava germplasm. Classification based on genotyping correlated with the leaf metabolome and indicated a key finding of adaption to specific eco-geographical environments. In contrast, the root metabolome did not relate to genotypic clustering, suggesting the different spatial regulation of this tissue's metabolome. The data were used to generate pan-metabolomes for specific tissues, and the inclusion of phenotypic data enabled the identification of metabolic sectors underlying traits of interest. For example, tolerance to whiteflies (Aleurotrachelus socialis) was not linked directly to cyanide content but to cell wall–related phenylpropanoid or apocarotenoid content. Collectively, these data advance the community resources and provide valuable insight into new candidate parental breeding materials with traits of interest directly related to combating food security.
Integrative transcriptomics reveals association of abscisic acid and lignin pathways with cassava whitefly resistance
Author(s): G. Nye, Danielle; Irigoyen, Maria; Perez-Fons, Laura; Bohorquez-Chaux, Adriana; Hur, Manhoi; Medina-Yerena, Diana; Becerra, Augusto; Paul, Fraser; Walling, Linda (BMC, 2023-12-20)
Date: 2023-12-20
Type: Journal Article
Status: Open access
Background Whiteflies are a global threat to crop yields, including the African subsistence crop cassava (Manihot esculenta). Outbreaks of superabundant whitefly populations throughout Eastern and Central Africa in recent years have dramatically increased the pressures of whitefly feeding and virus transmission on cassava. Whitefly-transmitted viral diseases threaten the food security of hundreds of millions of African farmers, highlighting the need for developing and deploying whitefly-resistant cassava. However, plant resistance to whiteflies remains largely poorly characterized at the genetic and molecular levels. Knowledge of cassava-defense programs also remains incomplete, limiting characterization of whitefly-resistance mechanisms. To better understand the genetic basis of whitefly resistance in cassava, we define the defense hormone- and Aleurotrachelus socialis (whitefly)-responsive transcriptome of whitefly-susceptible (COL2246) and whitefly-resistant (ECU72) cassava using RNA-seq. For broader comparison, hormone-responsive transcriptomes of Arabidopsis thaliana were also generated. Results Whitefly infestation, salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) transcriptome responses of ECU72 and COL2246 were defined and analyzed. Strikingly, SA responses were largely reciprocal between the two cassava genotypes and we suggest candidate regulators. While susceptibility was associated with SA in COL2246, resistance to whitefly in ECU72 was associated with ABA, with SA-ABA antagonism observed. This was evidenced by expression of genes within the SA and ABA pathways and hormone levels during A. socialis infestation. Gene-enrichment analyses of whitefly- and hormone-responsive genes suggest the importance of fast-acting cell wall defenses (e.g., elicitor recognition, lignin biosynthesis) during early infestation stages in whitefly-resistant ECU72. A surge of ineffective immune and SA responses characterized the whitefly-susceptible COL2246’s response to late-stage nymphs. Lastly, in comparison with the model plant Arabidopsis, cassava’s hormone-responsive genes showed striking divergence in expression. Conclusions This study provides the first characterization of cassava’s global transcriptome responses to whitefly infestation and defense hormone treatment. Our analyses of ECU72 and COL2246 uncovered possible whitefly resistance/susceptibility mechanisms in cassava. Comparative analysis of cassava and Arabidopsis demonstrated that defense programs in Arabidopsis may not always mirror those in crop species. More broadly, our hormone-responsive transcriptomes will also provide a baseline for the cassava community to better understand global responses to other yield-limiting pests/pathogens.
Content and distribution of cyanogenic compounds in cassava roots and leaves in association with physiological age
Author(s): Ospina, Maria Alejandra; Tran, Thierry; Pizarro Sanchez, Monica; Luna Meléndez, Jorge Luis; Salazar, Sandra; Londono Hernandez, Luis; Ceballos, Hernan; Becerra, Augusto; Dufour, Dominique (Wiley (12 months), 2024-02-23)
Date: 2023-11-14
Type: Journal Article
Status: Open access
Background: Cassava roots are widely consumed in tropical regions of Asia, Africa, and Latin America. Although the protein,vitamin, carotenoid, and mineral content in the leaves makes them a nutritionally attractive option, their consumption is limited due to their high levels of cyanogenic compounds (CCs). In this study, the CC content in different parts of the plant (leaves, storage root cortex, and parenchyma) was assessed at harvest for 50 landrace genotypes representative of cassava diversity in Latin America. The changes in CC in leaves at different physiological ages (3, 6, 9, and 11 months after planting) were also investigated. Results: The average CC was higher in the cortex (804 ppm) and leaves (655 ppm) than in root parenchyma (305 ppm). Geno-types from different regions of Latin America, as identiﬁed by seven genetic diversity groups, differed signiﬁcantly in CC levels. The Andean and Amazon groups had, respectively, the lowest (P = 0.0008) and highest (P < 0.0001) CC levels in all three partsof the plants. Cyanogenic compound concentrations were higher in leaves from young plants (P < 0.0001) and decreased with increasing physiological age. Conclusion: The results help to guide the selection of parental lines with low CC levels for breeding and to contribute to the expanded use of cassava and its by-products for food and feed. Cassava for fresh consumption, especially, requires varieties with low total CC content, especially in the root cortex and parenchyma. COL1108 (204, 213, and 174 ppm, respectively, in the parenchyma, cortex, and leaves) and PER297 (83, 238, and 299 ppm, respectively, in the parenchyma, cortex, and leaves)can fulﬁll this requirement
Identifying Cassava Genotypes Resistant to the African Cassava Whitefly, Bemisia tabaci (Gennadius)
Author(s): Atim, Jackie; Kalyebi, Andrew; Bohorquez-Chaux, Adriana; Becerra, Augusto; Abu Omongo, Christopher; Colvin, John; Maruthi, M. (MDPI, 2024-06-27)
Date: 2024-06-27
Type: Journal Article
Status: Open access
The whitefly, Bemisia tabaci, is a major pest of cassava in Africa. Developing whitefly-resistant cassava can control both whiteflies and viral diseases. The main aim of this study was to identify cassava genotypes resistant to four B. tabaci populations, sub-Saharan Africa 1—subgroups 1, 2, and 3 (SSA1-SG1, SSA1-SG2, and SSA1-SG3) and sub-Saharan Africa 2 (SSA2) that colonize cassava, as well as understand the mechanisms of resistance. Utilizing the antixenosis and antibiosis techniques in the choice and no-choice tests, respectively, to screen for whitefly resistance, we tested 46 cassava genotypes. Of these, 11 (Njule Red, Nase 3, Nase 1, Kibandameno, Sagonja, Aladu, Kiroba, Magana, 72-TME-14, Sauti, and PER 415) exhibited antixenosis, as they were least preferred for oviposition by all four whiteflies population in choice tests. Ten genotypes exhibited antibiosis (nymph mortality) against SSA1-SG1 and SSA1-SG3 in no-choice tests, and these were, Pwani, Nase 14, Kalawe, Eyope, NGA11, CoI2246, Mkumbozi, KBH2002/0066, Yizaso, and PER 608. Eight genotypes—Tongolo, Mbundumali, Colicanana, Orera, Ofumbachai, Nam 130, Tajirika, and MECU72—exhibited both antixenosis and antibiosis mechanisms against SSA1-SG1 and SSA1-SG3. And these can be considered the best sources of resistance for the potential development of whitefly-resistant cassava varieties in African countries.

Browse

Recent Submissions