New opportunities and challenges to engineer disease resistance in cassava, a staple food of African small-holder farmers

Genome editing in Sub-Saharan Africa: a game-changing strategy for climate change mitigation and sustainable agriculture

Sub-Saharan Africa's agricultural sector faces a multifaceted challenge due to climate change consisting of high temperatures, changing precipitation trends, alongside intensified pest and disease outbreaks. Conventional plant breeding methods have historically contributed to yield gains in Africa, and the intensifying demand for food security outpaces these improvements due to a confluence of factors, including rising urbanization, improved living standards, and population growth. To address escalating food demands amidst urbanization, rising living standards, and population growth, a paradigm shift toward more sustainable and innovative crop improvement strategies is imperative. Genome editing technologies offer a promising avenue for achieving sustained yield increases while bolstering resilience against escalating biotic and abiotic stresses associated with climate change. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein (CRISPR/Cas) is unique due to its ubiquity, efficacy, alongside precision, making it a pivotal tool for Sub-Saharan African crop improvement. This review highlights the challenges and explores the prospect of gene editing to secure the region's future foods.

Trends and practices of weaning in infants across India: A comprehensive review

Weaning is a critical phase in an infant's life, during which there is a transition from exclusive breastfeeding or formula feeding to consuming solid foods. Weaning is a critical step in determining a child's nutritional status, growth, and general health. India is a multiethnic and culturally diverse nation and has a variety of weaning practices that are affected by local customs, religious beliefs, and socioeconomic concerns. Malnutrition brought on by inadequate weaning methods used in infancy and early childhood may have an impact on cognitive, motor and social, development and productivity of the child, more importantly manifesting in later ages. Weaning customs in India have a long history of being ingrained in both family and cultural traditions. The variety of Indian cuisine is reflected in the meals that are offered to the infant during weaning. Homemade food commonly prepared like mashed fruits and vegetables, lentil soups, and rice porridge are the most popular. However, the inclination by parents toward professionally produced infant foods and formulas has increased because of urbanization and globalization; there have been observable changes in weaning practices over the past few decades because of changing lifestyles and easier access. These foods are frequently thought of as more convenient but may not be as nutrient-dense as homemade alternatives. Not following the medically recommended mandate of an exclusive diet of mother's breast milk to the infant, many parents often begin introducing complementary foods as early as four months. Still most concerningly also the timing of weaning commencement varies significantly across areas and communities. Overall, this review offers valuable insights into the current trends and practices of weaning in infants across India, underscoring the importance of culturally sensitive and informed strategies to ensure the well-being of the nation's youngest population.

CPK1-HSP90 phosphorylation and effector XopC2-HSP90 interaction underpin the antagonism during cassava defense-pathogen infection

Cassava is one of the most important tropical crops, but it is seriously affected by cassava bacteria blight (CBB) caused by the bacterial pathogen Xanthomonas phaseoli pv manihotis (Xam). So far, how pathogen Xam infects and how host cassava defends during pathogen-host interaction remains elusive, restricting the prevention and control of CBB. Here, the illustration of HEAT SHOCK PROTEIN 90 kDa (MeHSP90.9) interacting proteins in both cassava and bacterial pathogen revealed the dual roles of MeHSP90.9 in cassava-Xam interaction. On the one hand, calmodulin-domain protein kinase 1 (MeCPK1) directly interacted with MeHSP90.9 to promote its protein phosphorylation at serine 175 residue. The protein phosphorylation of MeHSP90.9 improved the transcriptional activation of MeHSP90.9 clients (SHI-RELATED SEQUENCE 1 (MeSRS1) and MeWRKY20) to the downstream target genes (avrPphB Susceptible 3 (MePBS3) and N-aceylserotonin O-methyltransferase 2 (MeASMT2)) and immune responses. On the other hand, Xanthomonas outer protein C2 (XopC2) physically associated with MeHSP90.9 to inhibit its interaction with MeCPK1 and the corresponding protein phosphorylation by MeCPK1, so as to repress host immune responses and promote bacterial pathogen infection. In summary, these results provide new insights into genetic improvement of cassava disease resistance and extend our understanding of cassava-bacterial pathogen interaction.

Coat protein of cassava common mosaic virus targets RAV1 and RAV2 transcription factors to subvert immunity in cassava

Cassava common mosaic virus (CsCMV, genus Potexvirus) is a prevalent virus associated with cassava mosaic disease, so it is essential to elucidate the underlying molecular mechanisms of the coevolutionary arms race between viral pathogenesis and the cassava (Manihot esculenta Crantz) defense response. However, the molecular mechanism underlying CsCMV infection is largely unclear. Here, we revealed that coat protein (CP) acts as a major pathogenicity determinant of CsCMV via a mutant infectious clone. Moreover, we identified the target proteins of CP-related to abscisic acid insensitive3 (ABI3)/viviparous1 (VP1) (MeRAV1) and MeRAV2 transcription factors, which positively regulated disease resistance against CsCMV via transcriptional activation of melatonin biosynthetic genes (tryptophan decarboxylase 2 (MeTDC2), tryptamine 5-hydroxylase (MeT5H), N-aceylserotonin O-methyltransferase 1 (MeASMT1)) and MeCatalase6 (MeCAT6) and MeCAT7. Notably, the interaction between CP, MeRAV1, and MeRAV2 interfered with the protein phosphorylation of MeRAV1 and MeRAV2 individually at Ser45 and Ser44 by the protein kinase, thereby weakening the transcriptional activation activity of MeRAV1 and MeRAV2 on melatonin biosynthetic genes, MeCAT6 and MeCAT7 dependent on the protein phosphorylation of MeRAV1 and MeRAV2. Taken together, the identification of the CP-MeRAV1 and CP-MeRAV2 interaction module not only illustrates a molecular mechanism by which CsCMV orchestrates the host defense system to benefit its infection and development but also provides a gene network with potential value for the genetic improvement of cassava disease resistance.

LESION SIMULATING DISEASE 3 regulates disease resistance via fine-tuning histone acetylation in cassava

Bacterial blight seriously affects the growth and production of cassava (Manihot esculenta Crantz), but disease resistance genes and the underlying molecular mechanism remain unknown. In this study, we found that LESION SIMULATING DISEASE 3 (MeLSD3) is essential for disease resistance in cassava. MeLSD3 physically interacts with SIRTUIN 1 (MeSRT1), inhibiting MeSRT1-mediated deacetylation modification at the acetylation of histone 3 at K9 (H3K9Ac). This leads to increased H3K9Ac levels and transcriptional activation of SUPPRESSOR OF BIR1 (SOBIR1) and FLAGELLIN-SENSITIVE2 (FLS2) in pattern-triggered immunity, resulting in immune responses in cassava. When MeLSD3 was silenced, the release of MeSRT1 directly decreased H3K9Ac levels and inhibited the transcription of SOBIR1 and FLS2, leading to decreased disease resistance. Notably, DELLA protein GIBBERELLIC ACID INSENSITIVE 1 (MeGAI1) also interacted with MeLSD3, which enhanced the interaction between MeLSD3 and MeSRT1 and further strengthened the inhibition of MeSRT1-mediated deacetylation modification at H3K9Ac of defense genes. In summary, this study illustrates the mechanism by which MeLSD3 interacts with MeSRT1 and MeGAI1, thereby mediating the level of H3K9Ac and the transcription of defense genes and immune responses in cassava.

Developing broad-spectrum resistance in cassava against viruses causing the cassava mosaic and the cassava brown streak diseases

Growing cassava in Africa requires resistance against the viruses causing cassava mosaic disease (CMD) and the viruses causing cassava brown streak disease (CBSD). A dominant CMD2 resistance gene from a West African cassava landrace provides strong resistance against the cassava mosaic viruses. However, resistance against cassava brown streak viruses is limited to cassava varieties that show tolerance to the disease. A recently identified cassava germplasm that cannot be infected with cassava brown streak viruses provides a new source of the resistance required to protect cassava from CBSD. We present a synopsis of the status of virus resistance in cassava and report on the research to combine resistance against CBSD and CMD. We improve the lengthy and erratic screening for CBSD resistance by proposing a virus infection and screening protocol for the viruses causing CBSD and CMD, which allows a rapid and precise assessment of cassava resistance under controlled conditions. Using this approach, we classified the virus responses of cassava lines from Africa and South America and identified truly virus-resistant clones that cannot be infected with any of the known viruses causing CBSD even under the most stringent virus infections. A modification of this protocol was used to test seedlings from cassava crosses for resistance against both diseases. A broad-spectrum resistance was identified in a workflow that lasted 9 months from seed germination to the identification of virus resistance. The workflow we propose dramatically reduces the evaluation and selection time required in a classical breeding workflow to reach the advanced field trial stage in only 9 months by conducting selections for virus resistance and plant multiplication in parallel. However, it does not bypass field evaluations; cassava resistance assessment prior to the field limits the evaluation to candidates with virus resistance defined as the absence of symptoms and the absence of the virus. The transfer of our virus screening workflow to cassava breeding programs enhances the efficiency by which resistance against viruses can be selected. It provides a precise definition of the plant's resistance response and can be used as a model system to tackle resistance in cassava against other diseases.

CRISPR for accelerating genetic gains in under-utilized crops of the drylands: Progress and prospects

Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances.

The coordination of melatonin and anti-bacterial activity by EIL5 underlies ethylene-induced disease resistance in cassava

Ethylene and melatonin are widely involved in plant development and environmental stress responses. However, the role of their direct relationship in the immune response and the underlying molecular mechanisms in plants remain elusive. Here, we found that Xanthomonas axonopodis pv. manihotis (Xam) infection increased endogenous ethylene levels, which positively modulated plant disease resistance through activating melatonin accumulation in cassava. In addition, the ethylene-responsive transcription factor ETHYLENE INSENSITIVE LIKE5 (MeEIL5), a positive regulator of disease resistance, was essential for ethylene-induced melatonin accumulation and disease resistance in cassava. Notably, the identification of heat stress transcription factor 20 (MeHsf20) as an interacting protein of MeEIL5 indicated the association between ethylene and melatonin in plant disease resistance. MeEIL5 physically interacted with MeHsf20 to promote the transcriptional activation of the gene encoding N-acetylserotonin O-methyltransferase 2 (MeASMT2), thereby improving melatonin accumulation. Moreover, MeEIL5 promoted the physical interaction of MeHsf20 and pathogen-related gene 3 (MePR3), resulting in improved anti-bacterial activity of MePR3. This study illustrates the dual roles of MeEIL5 in fine-tuning MeHsf20-mediated coordination of melatonin biosynthesis and anti-bacterial activity, highlighting the ethylene-responsive MeEIL5 as the integrator of ethylene and melatonin signals in the immune response in cassava.

A comparison of ImageJ and machine learning based image analysis methods to measure cassava bacterial blight disease severity

BACKGROUND

Methods to accurately quantify disease severity are fundamental to plant pathogen interaction studies. Commonly used methods include visual scoring of disease symptoms, tracking pathogen growth in planta over time, and various assays that detect plant defense responses. Several image-based methods for phenotyping of plant disease symptoms have also been developed. Each of these methods has different advantages and limitations which should be carefully considered when choosing an approach and interpreting the results.

RESULTS

In this paper, we developed two image analysis methods and tested their ability to quantify different aspects of disease lesions in the cassava-Xanthomonas pathosystem. The first method uses ImageJ, an open-source platform widely used in the biological sciences. The second method is a few-shot support vector machine learning tool that uses a classifier file trained with five representative infected leaf images for lesion recognition. Cassava leaves were syringe infiltrated with wildtype Xanthomonas, a Xanthomonas mutant with decreased virulence, and mock treatments. Digital images of infected leaves were captured overtime using a Raspberry Pi camera. The image analysis methods were analyzed and compared for the ability to segment the lesion from the background and accurately capture and measure differences between the treatment types.

CONCLUSIONS

Both image analysis methods presented in this paper allow for accurate segmentation of disease lesions from the non-infected plant. Specifically, at 4-, 6-, and 9-days post inoculation (DPI), both methods provided quantitative differences in disease symptoms between different treatment types. Thus, either method could be applied to extract information about disease severity. Strengths and weaknesses of each approach are discussed.

Current status and impending progress for cassava structural genomics

KEY MESSAGE

We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.

Cassava shrunken-2 homolog MeAPL3 determines storage root starch and dry matter content and modulates storage root postharvest physiological deterioration

Among the five cassava isoforms (MeAPL1-MeAPL5), MeAPL3 is responsible for determining storage root starch content. Degree of storage root postharvest physiological deterioration (PPD) is directly correlated with starch content. AGPase is heterotetramer composed of two small and two large subunits each coded by small gene families in higher plants. Studies in cassava (Manihot esculenta) identified and characterized five isoforms of Manihot esculenta ADP-glucose pyrophosphorylase large subunit (MeAPL1-MeAPL5) and employed virus induced gene silencing (VIGS) to show that MeAPL3 is the key isoform responsible for starch and dry matter accumulation in cassava storage roots. Silencing of MeAPL3 in cassava through stable transgenic lines resulted in plants displaying significant reduction in storage root starch and dry matter content (DMC) and induced a distinct phenotype associated with increased petiole/stem angle, resulting in a droopy leaf phenotype. Plants with reduced starch and DMC also displayed significantly reduced or no postharvest physiological deterioration (PPD) compared to controls and lines with high DMC and starch content. This provides strong evidence for direct relationships between starch/dry matter content and its role in PPD and canopy architecture traits in cassava.

Knowledge, Attitude, and Practice of Weaning among Mothers in Najran Region, Saudi Arabia, 2021

Background

Weaning is a complex process of a gradual introduction of complementary foods to the infant's diet. It is recommended that solid food is introduced between 6 and 12 months of age. Weaning is difficult and potentially dangerous time for infants' growth and mother's education is an established determinant of its success. Little is known about weaning attitudes or practice among mothers in Najran Region of Saudi Arabia.

Method

The study is a cross-sectional questionnaire-based observational investigation using random sampling scheme. We utilized ordinal logistic regression modelling to evaluate the relationship between demographic variables and knowledge level among mothers.

Results

The total number included was n = 385 mothers who agreed to take part in the study. Good satisfactory knowledge rate was n = 135, 35.1%. Knowledge was mostly sought from other mothers (n = 102, 26.5%), followed by reliance on their own experience (n = 82, 21.3%). Seeking doctors' advice was associated with better knowledge levels. Worse adjusted knowledge scores were associated with bottle feeding (OR = 0.5383, p=0.0137), using cerelac preparations (OR = 0.0316, p=0.0092), development of weaning symptoms (OR = 0.5869, p=0.0260), seeking other mothers' advice (OR = 0.4750, p=0.0226), and feeding babies under 4 times daily (OR = 0.2742, p=0.0008). Mother education did not have significant impact on knowledge scores. Discussion. We confirmed, in this work, that knowledge levels were alarmingly unsatisfactory about weaning among our participants. Women were likely following local customs in terms of their choice of weaning methods even among the well-educated. The association between seeking doctors' advice and better knowledge should be utilized in future educational interventions. Underfeeding babies of below 4 times daily was correlated substantially with poorer knowledge score. This could be viewed as reverse causality, as clearly more knowledgeable mothers are expected to stick to optimum feeding frequency. Recommendations. Communication channels between physicians and mothers need to be opened and widened through focused educational programmes. Poor knowledge is clearly associated with infant underfeeding and difficulties in recognizing weaning symptoms. Such points need to be emphasized in design of health education packages to nursing mothers. Research on knowledge about weaning should focus on its association with traditional weaning methods and bottle feeding.

Can Cross-Country Genomic Predictions Be a Reasonable Strategy to Support Germplasm Exchange? - A Case Study With Hydrogen Cyanide in Cassava

Genomic prediction (GP) offers great opportunities for accelerated genetic gains by optimizing the breeding pipeline. One of the key factors to be considered is how the training populations (TP) are composed in terms of genetic improvement, kinship/origin, and their impacts on GP. Hydrogen cyanide content (HCN) is a determinant trait to guide cassava's products usage and processing. This work aimed to achieve the following objectives: (i) evaluate the feasibility of using cross-country (CC) GP between germplasm's of Embrapa Mandioca e Fruticultura (Embrapa, Brazil) and The International Institute of Tropical Agriculture (IITA, Nigeria) for HCN; (ii) provide an assessment of population structure for the joint dataset; (iii) estimate the genetic parameters based on single nucleotide polymorphisms (SNPs) and a haplotype-approach. Datasets of HCN from Embrapa and IITA breeding programs were analyzed, separately and jointly, with 1,230, 590, and 1,820 clones, respectively. After quality control, ∼14K SNPs were used for GP. The genomic estimated breeding values (GEBVs) were predicted based on SNP effects from analyses with TP composed of the following: (i) Embrapa genotypic and phenotypic data, (ii) IITA genotypic and phenotypic data, and (iii) the joint datasets. Comparisons on GEBVs' estimation were made considering the hypothetical situation of not having the phenotypic characterization for a set of clones for a certain research institute/country and might need to use the markers' effects that were trained with data from other research institutes/country's germplasm to estimate their clones' GEBV. Fixation index (FST) among the genetic groups identified within the joint dataset ranged from 0.002 to 0.091. The joint dataset provided an improved accuracy (0.8-0.85) compared to the prediction accuracy of either germplasm's sources individually (0.51-0.67). CC GP proved to have potential use under the present study's scenario, the correlation between GEBVs predicted with TP from Embrapa and IITA was 0.55 for Embrapa's germplasm, whereas for IITA's it was 0.1. This seems to be among the first attempts to evaluate the CC GP in plants. As such, a lot of useful new information was provided on the subject, which can guide new research on this very important and emerging field.

When a knockout is an Achilles' heel: Resistance to one potyvirus species triggers hypersusceptibility to another one in Arabidopsis thaliana

The translation initiation factors 4E are a small family of major susceptibility factors to potyviruses. It has been suggested that knocking out these genes could provide genetic resistance in crops when natural resistance alleles, which encode functional eIF4E proteins, are not available. Here, using the well-characterized Arabidopsis thaliana-potyvirus pathosystem, we evaluate the resistance spectrum of plants knocked out for eIF4E1, the susceptibility factor to clover yellow vein virus (ClYVV). We show that besides resistance to ClYVV, the eIF4E1 loss of function is associated with hypersusceptibility to turnip mosaic virus (TuMV), a potyvirus known to rely on the paralog host factor eIFiso4E. On TuMV infection, plants knocked out for eIF4E1 display striking developmental defects such as early senescence and primordia development stoppage. This phenotype is coupled with a strong TuMV overaccumulation throughout the plant, while remarkably the levels of the viral target eIFiso4E remain uninfluenced. Our data suggest that this hypersusceptibility cannot be explained by virus evolution leading to a gain of TuMV aggressiveness. Furthermore, we report that a functional eIF4E1 resistance allele engineered by CRISPR/Cas9 base-editing technology successfully circumvents the increase of TuMV susceptibility conditioned by eIF4E1 disruption. These findings in Arabidopsis add to several previous findings in crops suggesting that resistance based on knocking out eIF4E factors should be avoided in plant breeding, as it could also expose the plant to the severe threat of potyviruses able to recruit alternative eIF4E copies. At the same time, it provides a simple model that can help understanding of the homeostasis among eIF4E proteins in the plant cell and what makes them available to potyviruses.

Gelatinization, pasting and retrogradation properties and molecular fine structure of starches from seven cassava cultivars

Genetic diversity in the physicochemical properties and fine structures of seven cassava starches samples was studied. The apparent amylose content ranged from 24.8 to 27.6%. The whole branched starches showed significant differences in average hydrodynamic radius, ranging from 53.35 to 58.45 nm, while debranched starch exhibited differences in degrees of polymerization and height of both amylose and amylopectin peaks. The molecular size of amylose and amylopectin was positively correlated. The amount of short chains fa (6 ≤ X ≤ 12) and fb1 (13 ≤ X ≤ 24) had significant differences among the cultivars. Structure-function relation analysis indicated that the CPV and SB were mainly determined by amylopectin fine structures, BD, PTi and Tp and retrogradation properties were mainly determined by the amylose fine structure, while PTe and To were mainly affected by both amylose and amylopectin fine structures. The current findings will be helpful to improve the understanding cassava starch quality for use in industrial starch applications.

RNA silencing of South African cassava mosaic virus in transgenic cassava expressing AC1/AC4 hp- RNA induces tolerance

Cassava mosaic disease (CMD), caused by geminiviruses, is a major hurdle to cassava production. Due to the heterozygous nature of cassava, breeding for virus resistance is difficult, but cassava has been shown to be a good candidate for genetic engineering using RNA interference (RNAi). T This study reports on the ability of a transgene-derived RNA hairpin, homologous to an overlapping region of the SACMV replication associated protein and putative virus suppressor of silencing protein (AC1/AC4), to confer tolerance in the CMD-susceptible model cassava cultivar 60444. Three of the fourteen transgenic lines expressing SACMV AC1/AC4 hairpin-derived siRNAs showed decreased symptoms and viral loads compared to untransformed control plants. Expression of SACMV AC1/AC4 homologous siRNAs showed that this tolerance is most likely associated with post-transcriptional gene silencing of the virus. This is the first report of targeting the overlapping AC1 and AC4 genes of SACMV conferring CMD tolerance in cassava.

Plant-Pathogen Warfare under Changing Climate Conditions

Global environmental changes caused by natural and human activities have accelerated in the past 200 years. The increase in greenhouse gases is predicted to continue to raise global temperature and change water availability in the 21^st century. In this Review, we explore the profound effect the environment has on plant diseases - a susceptible host will not be infected by a virulent pathogen if the environmental conditions are not conducive for disease. The change in CO₂ concentrations, temperature, and water availability can have positive, neutral, or negative effects on disease development, as each disease may respond differently to these variations. However, the concept of disease optima could potentially apply to all pathosystems. Plant resistance pathways, including pattern-triggered immunity to effector-triggered immunity, RNA interference, and defense hormone networks, are all affected by environmental factors. On the pathogen side, virulence mechanisms, such as the production of toxins and virulence proteins, as well as pathogen reproduction and survival are influenced by temperature and humidity. For practical reasons, most laboratory investigations into plant-pathogen interactions at the molecular level focus on well-established pathosystems and use a few static environmental conditions that capture only a fraction of the dynamic plant-pathogen-environment interactions that occur in nature. There is great need for future research to increasingly use dynamic environmental conditions in order to fully understand the multidimensional nature of plant-pathogen interactions and produce disease-resistant crop plants that are resilient to climate change.

Genome Editing, Gene Drives, and Synthetic Biology: Will They Contribute to Disease-Resistant Crops, and Who Will Benefit?

Genetically engineered crops have been grown for more than 20 years, resulting in widespread albeit variable benefits for farmers and consumers. We review current, likely, and potential genetic engineering (GE) applications for the development of disease-resistant crop cultivars. Gene editing, gene drives, and synthetic biology offer novel opportunities to control viral, bacterial, and fungal pathogens, parasitic weeds, and insect vectors of plant pathogens. We conclude that there will be no shortage of GE applications totackle disease resistance and other farmer and consumer priorities for agricultural crops. Beyond reviewing scientific prospects for genetically engineered crops, we address the social institutional forces that are commonly overlooked by biological scientists. Intellectual property regimes, technology regulatory frameworks, the balance of funding between public- and private-sector research, and advocacy by concerned civil society groups interact to define who uses which GE technologies, on which crops, and for the benefit of whom. Ensuring equitable access to the benefits of genetically engineered crops requires affirmative policies, targeted investments, and excellent science.

Resistance Against Cassava Brown Streak Viruses From Africa in Cassava Germplasm From South America

Cassava brown streak disease (CBSD) is a severe virus disease of cassava and prevalent in the eastern regions of Africa. The disease is characterized by distinct vein chlorosis and streak symptoms on leaves and stems and necrosis of storage roots. This necrosis can encompass large areas of the root, rendering it inedible so that the entire cassava harvest can be lost. African cassava varieties are susceptible to either of the two viruses causing the disease, cassava brown streak virus (CBSV) and Uganda cassava brown streak virus, and while there are less sensitive varieties, all cassava eventually succumb to the disease. The lack of CBSD resistance in African cassava varieties prompted this search for new sources of virus resistance in the diversity of South American cassava germplasm held in the collection at International Center for Tropical Agriculture, Columbia. Our search for CBSD resistance in South American cassava germplasm accessions revealed that most of the 238 South American cassava lines infected with CBSV established systemic virus infections with moderate to severe disease symptoms on leaves and stems. Fifteen cassava accessions did not become virus infected, remained free of symptoms, and CBSV was undetected by qRT-PCR. When tuberous roots of those lines were examined, necrotic tissue was found in eight lines and CBSV was detected. The remaining seven cassava accessions remained clear of symptoms on all tissues and organs and were virus free. A broad spectrum of virus resistance also including other virus isolates was confirmed for the breeding lines DSC167 and DSC118. While detailed infection experiments with other cassava lines selected for resistance are still ongoing, this indicates that the resistance identified may also hold against a broader diversity of CBSVs. Taken together, we present the results of a comprehensive study on CBSV resistance and susceptibility in cassava germplasm accessions from South America. The virus resistance in cassava germplasm identified provides compelling evidence for the invaluable contribution of germplasm collections to supply the genetic resources for the improvement of our crops.

Evaluation of resistance to cassava mosaic disease in selected African cassava cultivars using combined molecular and greenhouse grafting tools

Cassava mosaic disease (CMD) threatens cassava (Manihot esculenta) production in Africa. A total of 24 selected cultivars were screened against CMD using combined molecular and greenhouse grafting tools. Disease severity was recorded for 10 weeks after inoculation and the molecular markers associated with CMD2 were detected by PCR. CMD severity significantly differed (P < 0.0001) among cultivars. Twelve cultivars were morphologically resistant and eight of these possessed CMD2 and four did not. These results suggest that there are several CMD-resistant cassava cultivars that could be recommended for on-farm production and for conservation and breeding programs.

Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance in plants

To infect plants, viruses rely heavily on their host's machinery. Plant genetic resistances based on host factor modifications can be found among existing natural variability and are widely used for some but not all crops. While biotechnology can supply for the lack of natural resistance alleles, new strategies need to be developed to increase resistance spectra and durability without impairing plant development. Here, we assess how the targeted allele modification of the Arabidopsis thaliana translation initiation factor eIF4E1 can lead to broad and efficient resistance to the major group of potyviruses. A synthetic Arabidopsis thaliana eIF4E1 allele was designed by introducing multiple amino acid changes associated with resistance to potyvirus in naturally occurring Pisum sativum alleles. This new allele encodes a functional protein while maintaining plant resistance to a potyvirus isolate that usually hijacks eIF4E1. Due to its biological functionality, this synthetic allele allows, at no developmental cost, the pyramiding of resistances to potyviruses that selectively use the two major translation initiation factors, eIF4E1 or its isoform eIFiso4E. Moreover, this combination extends the resistance spectrum to potyvirus isolates for which no efficient resistance has so far been found, including resistance-breaking isolates and an unrelated virus belonging to the Luteoviridae family. This study is a proof-of-concept for the efficiency of gene engineering combined with knowledge of natural variation to generate trans-species virus resistance at no developmental cost to the plant. This has implications for breeding of crops with broad-spectrum and high durability resistance using recent genome editing techniques.

Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges

The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.

Utilization of engineered resistance to viruses in crops of the developing world, with emphasis on sub-Saharan Africa

Viral diseases in crop plants constitute a major obstacle to food security in the developing world. Subsistence crops, including cassava, sweetpotato, potato, banana, papaya, common bean, rice and maize are often infected with RNA and/or DNA viruses that cannot be controlled with pesticides. Hence, healthy planting materials and virus-resistant cultivars are essential for high yields of good quality. However, resistance genes are not available for all viral diseases of crop plants. Therefore, virus resistance engineered in plants using modern biotechnology methods is an important addition to the crop production toolbox.

Efficient CRISPR/Cas9 Genome Editing of Phytoene desaturase in Cassava

CRISPR/Cas9 has become a powerful genome-editing tool for introducing genetic changes into crop species. In order to develop capacity for CRISPR/Cas9 technology in the tropical staple cassava (Manihot esculenta), the Phytoene desaturase (MePDS) gene was targeted in two cultivars using constructs carrying gRNAs targeting two sequences within MePDS exon 13. After Agrobacterium-mediated delivery of CRISPR/Cas9 reagents into cassava cells, both constructs induced visible albino phenotypes within cotyledon-stage somatic embryos regenerating on selection medium and the plants regenerated therefrom. A total of 58 (cv. 60444) and 25 (cv. TME 204) plant lines were recovered, of which 38 plant lines (19 from each cultivar) were analyzed for mutagenesis. The frequency of plant lines showing albino phenotype was high, ranging from 90 to 100% in cv. TME 204. Observed albino phenotypes were comprised of full albinos devoid of green tissue and chimeras containing a mixture of white and green tissues. Sequence analysis revealed that 38/38 (100%) of the plant lines examined carried mutations at the targeted MePDS site, with insertions, deletions, and substitutions recorded. One putatively mono-allelic homozygous line (1/19) was found from cv. 60444, while 1 (1/19) and 4 (4/19) putatively bi-allelic homozygous lines were found in 60444 and TME204, respectively. The remaining plant lines, comprised mostly of the chimeras, were found to be putatively heterozygous. We observed minor (1 bp) nucleotide substitutions and or deletions upstream of the 5' and or downstream of the 3' targeted MePDS region. The data reported demonstrates that CRISPR/Cas9-mediated genome editing of cassava is highly efficient and relatively simple, generating multi-allelic mutations in both cultivars studied. Modification of MePDS described here generates visually detectable mutated events in a relatively short time frame of 6-8 weeks, and does not require sequencing to confirm editing at the target. It therefore provides a valuable platform to facilitate rapid assessment and optimization of CRISPR/Cas9 and other genome-editing technologies in cassava.

Efficient CRISPR/Cas9 Genome Editing of Phytoene desaturase in Cassava

CRISPR/Cas9 has become a powerful genome-editing tool for introducing genetic changes into crop species. In order to develop capacity for CRISPR/Cas9 technology in the tropical staple cassava (Manihot esculenta), the Phytoene desaturase (MePDS) gene was targeted in two cultivars using constructs carrying gRNAs targeting two sequences within MePDS exon 13. After Agrobacterium-mediated delivery of CRISPR/Cas9 reagents into cassava cells, both constructs induced visible albino phenotypes within cotyledon-stage somatic embryos regenerating on selection medium and the plants regenerated therefrom. A total of 58 (cv. 60444) and 25 (cv. TME 204) plant lines were recovered, of which 38 plant lines (19 from each cultivar) were analyzed for mutagenesis. The frequency of plant lines showing albino phenotype was high, ranging from 90 to 100% in cv. TME 204. Observed albino phenotypes were comprised of full albinos devoid of green tissue and chimeras containing a mixture of white and green tissues. Sequence analysis revealed that 38/38 (100%) of the plant lines examined carried mutations at the targeted MePDS site, with insertions, deletions, and substitutions recorded. One putatively mono-allelic homozygous line (1/19) was found from cv. 60444, while 1 (1/19) and 4 (4/19) putatively bi-allelic homozygous lines were found in 60444 and TME204, respectively. The remaining plant lines, comprised mostly of the chimeras, were found to be putatively heterozygous. We observed minor (1 bp) nucleotide substitutions and or deletions upstream of the 5' and or downstream of the 3' targeted MePDS region. The data reported demonstrates that CRISPR/Cas9-mediated genome editing of cassava is highly efficient and relatively simple, generating multi-allelic mutations in both cultivars studied. Modification of MePDS described here generates visually detectable mutated events in a relatively short time frame of 6-8 weeks, and does not require sequencing to confirm editing at the target. It therefore provides a valuable platform to facilitate rapid assessment and optimization of CRISPR/Cas9 and other genome-editing technologies in cassava.