Crops for the Future

Semenyih, Malaysia

Crops for the Future

Semenyih, Malaysia
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Wong Q.N.,University of Nottingham Malaysia Campus | Tanzi A.S.,University of Nottingham Malaysia Campus | Ho W.K.,University of Nottingham Malaysia Campus | Malla S.,University of Nottingham | And 6 more authors.
Genes | Year: 2017

Winged bean (Psophocarpus tetragonolobus) is an herbaceous multipurpose legume grown in hot and humid countries as a pulse, vegetable (leaves and pods), or root tuber crop depending on local consumption preferences. In addition to its different nutrient-rich edible parts which could contribute to food and nutritional security, it is an efficient nitrogen fixer as a component of sustainable agricultural systems. Generating genetic resources and improved lines would help to accelerate the breeding improvement of this crop, as the lack of improved cultivars adapted to specific environments has been one of the limitations preventing wider use. A transcriptomic de novo assembly was constructed from four tissues: leaf, root, pod, and reproductive tissues from Malaysian accessions, comprising of 198,554 contigs with a N50 of 1462 bp. Of these, 138,958 (70.0%) could be annotated. Among 9682 genic simple sequence repeat (SSR) motifs identified (excluding monomer repeats), trinucleotide-repeats were the most abundant (4855), followed by di-nucleotide (4500) repeats. A total of 18 SSR markers targeting di- and tri-nucleotide repeats have been validated as polymorphic markers based on an initial assessment of nine genotypes originated from five countries. A cluster analysis revealed provisional clusters among this limited, yet diverse selection of germplasm. The developed assembly and validated genic SSRs in this study provide a foundation for a better understanding of the plant breeding system for the genetic improvement of winged bean. © 2017 by the authors. Licensee MDPI, Basel, Switzerland.

Khan F.,University of Nottingham | Chai H.H.,Crops for the Future | Ajmera I.,University of Nottingham | Hodgman C.,University of Nottingham | And 2 more authors.
Genes | Year: 2017

The ability to grow crops under low-water conditions is a significant advantage in relation to global food security. Bambara groundnut is an underutilised crop grown by subsistence farmers in Africa and is known to survive in regions of water deficit. This study focuses on the analysis of the transcriptomic changes in two bambara groundnut landraces in response to dehydration stress. A cross-species hybridisation approach based on the Soybean Affymetrix GeneChip array has been employed. The differential gene expression analysis of a water-limited treatment, however, showed that the two landraces responded with almost completely different sets of genes. Hence, both landraces with very similar genotypes (as assessed by the hybridisation of genomic DNA onto the Soybean Affymetrix GeneChip) showed contrasting transcriptional behaviour in response to dehydration stress. In addition, both genotypes showed a high expression of dehydration-associated genes, even under water-sufficient conditions. Several gene regulators were identified as potentially important. Some are already known, such as WRKY40, but others may also be considered, namely PRR7, ATAUX2-11, CONSTANS-like 1, MYB60, AGL-83, and a Zinc-finger protein. These data provide a basis for drought trait research in the bambara groundnut, which will facilitate functional genomics studies. An analysis of this dataset has identified that both genotypes appear to be in a dehydration-ready state, even in the absence of dehydration stress, and may have adapted in different ways to achieve drought resistance. This will help in understanding the mechanisms underlying the ability of crops to produce viable yields under drought conditions. In addition, cross-species hybridisation to the soybean microarray has been shown to be informative for investigating the bambara groundnut transcriptome. © 2017 by the authors. Licensee MDPI, Basel, Switzerland.

Ho W.K.,Crops For the Future | Ho W.K.,University of Nottingham Malaysia Campus | Chai H.H.,University of Nottingham Malaysia Campus | Kendabie P.,University of Nottingham | And 7 more authors.
BMC Genomics | Year: 2017

Background: Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for minor and underutilised crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata). From these comparisons we identify conserved synteny blocks corresponding to the Linkage Groups (LGs) in bambara groundnut genetic maps and evaluate the potential to identify genes in conserved syntenic locations in a sequenced genome that underlie a QTL position in the underutilised crop genome. Results: Two individual intraspecific linkage maps consisting of DArTseq markers were constructed in two bambara groundnut (2n = 2x = 22) segregating populations: 1) The genetic map of Population IA was derived from F2 lines (n = 263; IITA686 x Ankpa4) and covered 1,395.2 cM across 11 linkage groups; 2) The genetic map of Population TD was derived from F3 lines (n = 71; Tiga Nicuru x DipC) and covered 1,376.7 cM across 11 linkage groups. A total of 96 DArTseq markers from an initial pool of 142 pre-selected common markers were used. These were not only polymorphic in both populations but also each marker could be located using the unique sequence tag (at selected stringency) onto the common bean, adzuki bean and mung bean genomes, thus allowing the sequenced genomes to be used as an initial 'pseudo' physical map for bambara groundnut. A good correspondence was observed at the macro synteny level, particularly to the common bean genome. A test using the QTL location of an agronomic trait in one of the bambara groundnut maps allowed the corresponding flanking positions to be identified in common bean, mung bean and adzuki bean, demonstrating the possibility of identifying potential candidate genes underlying traits of interest through the conserved syntenic physical location of QTL in the well annotated genomes of closely related species. Conclusions: The approach of adding pre-selected common markers in both populations before genetic map construction has provided a translational framework for potential identification of candidate genes underlying a QTL of trait of interest in bambara groundnut by linking the positions of known genetic effects within the underutilised species to the physical maps of other well-annotated legume species, without the need for an existing whole genome sequence of the study species. Identifying the conserved synteny between underutilised species without complete genome sequences and the genomes of major crops and model species with genetic and trait data is an important step in the translation of resources and information from major crop and model species into the minor crop species. Such minor crops will be required to play an important role in future agriculture under the effects of climate change. © 2017 The Author(s).

Trognitz B.,AIT Austrian Institute of Technology | Scheldeman X.,Bioversity International | Hansel-Hohl K.,AIT Austrian Institute of Technology | Kuant A.,Pro Mundo Humano | And 2 more authors.
PLoS ONE | Year: 2011

Significant cocoa production in the municipality of Waslala, Nicaragua, began in 1961. Since the 1980s, its economic importance to rural smallholders increased, and the region now contributes more than 50% of national cocoa bean production. This research aimed to assist local farmers to develop production of high-value cocoa based on optimal use of cacao biodiversity. Using microsatellite markers, the allelic composition and genetic structure of cacao was assessed from 44 representative plantings and two unmanaged trees. The population at Waslala consists of only three putative founder genotype spectra (lineages). Two (B and R) were introduced during the past 50 years and occur in >95% of all trees sampled, indicating high rates of outcrossing. Based on intermediate allelic diversity, there was large farm-to-farm multilocus genotypic variation. GIS analysis revealed unequal distribution of the genotype spectra, with R being frequent within a 2 km corridor along roads, and B at more remote sites with lower precipitation. The third lineage, Y, was detected in the two forest trees. For explaining the spatial stratification of the genotype spectra, both human intervention and a combination of management and selection driven by environmental conditions, appear responsible. Genotypes of individual trees were highly diverse across plantings, thus enabling selection for farm-specific qualities. On-farm populations can currently be most clearly recognized by the degree of the contribution of the three genotype spectra. Of two possible strategies for future development of cacao in Waslala, i.e. introducing more unrelated germplasm, or working with existing on-site diversity, the latter seems most appropriate. Superior genotypes could be selected by their specific composite genotype spectra as soon as associations with desired quality traits are established, and clonally multiplied. The two Y trees from the forest share a single multilocus genotype, possibly representing the Mayan, 'ancient Criollo' cacao. © 2011 Trognitz et al.

Kahane R.,C o FAO AGPM | Kahane R.,CIRAD - Agricultural Research for Development | Hodgkin T.,Platform for Agrobiodiversity Research | Jaenicke H.,Burghof 26 | And 5 more authors.
Agronomy for Sustainable Development | Year: 2013

By the year 2050, agriculture will have to provide the food and nutrition requirements of some 9 billion people. Moreover, to maintain that level of productivity indefinitely it must do so using environmentally sustainable production systems. This task will be profoundly complicated by the effects of climate change, increasing competition for water resources and loss of productive lands. Agricultural production methods will also need to recognize and accommodate ongoing rural to urban migration and address a host of economic, ecological and social concerns about the 'high inputs/high outputs' model of present-day industrial agriculture. At the same time, there is a need to confront the unacceptable levels of continuing food and nutrition insecurity, greatest in the emerging economy countries of Africa and Asia where poverty, rapid population growth and climate change present additional challenges and where agriculture is practiced primarily by small-scale farmers. Within this context, we here review science-based evidence arguing that diversification with greater use of highly valuable but presently under-valorised crops and species should be an essential element of any model for sustainable smallholder agriculture. The major points of these development opportunity crops are presented in four sections: agricultural farming systems, health and nutrition, environmental sustainability and prosperity of the populations. For each section, these crops and their associated indigenous knowledge are reported to bring benefits and services when integrated with food systems. In this paper, we conclude that not only a change in policy is needed to influence behaviours and practices but also strong leadership able to synergize the various initiatives and implement an action plan. © 2013 INRA and Springer-Verlag France.

News Article | November 15, 2016

A multi-million dollar research group co-founded by the confectionery company Mars is set to publish the genetic maps to five traditional African crops as part of an ambitious project that it says could help end malnutrition on the continent. The project is applying modern biotechnology to African “orphan crops” – including finger millet and the “superfood” moringa – with the goal of breeding new versions that are more productive or more tolerant to drought or disease. It is one of several new initiatives to develop improved varieties of crops that have been grown by small-scale farmers for generations but long-overlooked by international researchers and industry focused on globally traded staples like wheat and maize. The researchers say they will publish the crops’ genome sequences online for anyone to download for free; they are also training hundreds of African plant breeders on how to use the data. At UN food talks in Rome last month, Howard-Yana Shapiro, chief agricultural officer Mars, one of the world’s largest food companies with revenues in 2015 of $33bn (£26.5bn), said the project will “significantly improve the nutrition of an entire continent”. Critics of the project say efforts to map the genetic data of crops are more likely to help private companies moving into new African seed markets rather than smallholder farmers. Mariam Mayet, director of the African Centre for Biodiversity, said: “What are farmers going to do with gene sequences? … These top-down, techno-fix solutions sound good, and sound like we’re entering the 21st century, but they’re not what small farmers need.” Patrick Mulvaney, at the UK Food Group, said that even if genetic data is freely available online, “the only ones that can really make use of it are the big companies”. He suggested corporations “want orphan crops too, to consolidate their control” of global food systems. “It won’t be too long before you can’t grow maize in southern France, because of climate change. Sorghum, cassava, yams – these are also backups if you’re in trouble,” added Pat Mooney, at the ETC Group, who also questioned corporate motives for work on these crops. Chikelu Mba, from the UN’s Food and Agriculture Organisation, said advanced biotechnology tools like genome sequencing could help develop “new, superior, more nutritious, drought tolerant varieties of these crops that very poor people need to survive”. But he stressed they are not a magic bullet. Small-scale farmers also need infrastructure and access to “quality seeds and planting materials at affordable prices”, he added. “It needs to be in people’s minds that downstream, some of the products may be restricted by intellectual property rights … which are supposed to encourage and reward innovation but can also be misused and/or abused,” Mba added. African countries, he said, must also support public sector crop development rather than leaving it to private initiative alone. “It is a worthwhile use of taxpayer resources to encourage work on these for the simple reason that they are food security crops.” The African Orphan Crops Consortium (AOCC), founded in 2011, has partners including Mars and Google, a Chinese research group, a Nairobi laboratory, and biotech firms. It calls itself a “public-private partnership” led by the New Partnership for Africa’s Development (NEPAD) arm of the African Union. The UN children’s agency, Unicef, is also listed as a partner to advocate and “raise support” for the project. Allen Van Deynze, a scientist at the University of California-Davis who is involved in the project, said it is worth about $40m-50m, but that most of this has come in-kind from the group’s partners contributing their own in-house staff time and facilities. The project has listed 101 focus crops including some that already have more obvious commercial value like coconut, avocado and oil palm along with others including spiderplant and breadfruit. The first major data release, expected within the next two months, will be genetic maps to finger millet, African eggplant, acacia, and moringa – a tree with leaves unusually rich in iron, protein and vitamins. “Making nutritious crops productive – that’s the mission, and then getting them to the people who need them,” said Van Deynze. “For me, that’s the way out of poverty – feed people properly … Give everyone the resources that they need, mentally and physically.” But the science behind using genomics to develop crops is complex and it’s not expected that small farmers will use this data themselves – seed companies are likely to be involved. Most seeds in Africa are saved and traded by farmers themselves in informal systems, though several countries have adopted controversial new laws and policies to encourage commercial investment, protect intellectual property and develop regional seed markets. Elizabeth Mpofu, general coordinator of the global peasants’ movement La Vía Campesina, said this is not what small farmers like her need. “We really need to protect our own indigenous seeds.” Mpofu, who grows groundnut and sorghum in Zimbabwe, said she is concerned about increasing corporate interest in “crops that we farmers have grown for ages and ages … These are perfect organic crops. Why should we tamper with these?” The AOCC is making its data free online to users who agree not to patent the genome sequences. But companies can still use this information to develop improved commercial varieties to sell. “We’re saying our information is free. We’re not saying [that] you have to give your varieties away for free – that’s very different. If we were to say that, we would be doomed,” said Van Deynze. “There has to be a business model around everything.” The project is itself focusing on speeding up conventional crop breeding but it also leaves the door open to more controversial techniques where genes are cut, spliced or moved between species. “All DNA technology could be used for synthetic biology, transgenics, conventional breeding, gene editing, so it’s open,” said Van Deynze. He said he doubts companies will develop genetically modified crops using the data because of regulatory issues and consumer opposition. But earlier this year, the African Biodiversity Centre found field trials of GM crops were already under way in seven African countries. It said these “will undoubtedly be accompanied by intellectual property laws, seed regulations, and other products and practices amenable to agribusiness”. “The GM industry appears to be expanding its grasp over traditional subsistence crops which had, until recently, been disregarded,” it said. Agrochemical giant Monsanto is involved in work to genetically engineer new versions of cowpea with the African Agricultural Technology Foundation, set up in part with US and UK aid money. DuPont Pioneer is a partner in a “biofortified” sorghum project supported by the Bill and Melinda Gates Foundation. The Syngenta Foundation is backing research on tef, a gluten-free “ancient grain” grown in Ethiopia. An international project called DivSeek, meanwhile, aims to sequence and publish genetic data on crops with samples in the world’s seed banks. Sean Mayes, a British geneticist involved in the separate Crops for the Future initiative, said concern over climate change, the need to feed a growing global population, and rising demand in rich countries for more varied foods are fuelling new interest in these plants. All of these crops, he said, have “potential to increase yields, nutrition … but the work hasn’t been done, because there hasn’t been that commercial drive”.

Hermann M.,Crops for the Future | Kwek M.J.,Crops for the Future | Khoo T.K.,Crops for the Future | Amaya K.,Bioversity International
Acta Horticulturae | Year: 2013

The disproportionate use of crops - with a few species accounting for most of global food production - is being re-enforced by the considerable research, breeding and development efforts that make global crops so competitive vis-à-vis "neglected and underutilised species" (NUS). NUS promotional rhetoric, preaching to the converted, complaints about the discrimination of the "food of the poor" and the loss of traditional dietary habits are unlikely to revert the neglect of the vast majority of crop species. We need to lessen the supply and demand constraints that affect the production and consumption of NUS. NUS attributes relevant to consumers, nutrition and climate change need to be substantiated, demand for NUS stimulated, discriminating agricultural and trade policies amended, and donors convinced to make greater investments in NUS research and development. Much fascinating NUS research and development is underway, but much of this is dissipated amongst countries, institutions and taxa. Researchers operate in unsupportive environments and are often unaware of each other's work. Their efforts remain unrecognised as addressing global concerns. We suggest that the much-needed enhancement of NUS knowledge management should be at the centre of collective efforts of the NUS community. This will underpin future research and development advances as well as inform the formulation and advocacy of policies. This paper recommends that the NUS community make greater use of Internet knowledge repositories to deposit research results, publications and images into the public domain. As examples for such a low-cost approach, we assess the usefulness of Wikipedia, Google Books and Wikimedia Commons for the documentation and dissemination of NUS knowledge. We urge donors and administrators to promote and encourage the use of these and other public and electronically accessible repositories as sources of verification for the achievement of project and research outputs.

Edmond Moeletsi M.,The Water Council | Edmond Moeletsi M.,University of Limpopo | Phumlani Shabalala Z.,The Water Council | De Nysschen G.,The Water Council | Walker S.,Crops for the Future
Water SA | Year: 2016

Climate data recorded by national meteorological agencies is either incomplete or faulty for some periods due to a number of reasons. Multi-functional utilization of climate data in complete form necessitates the filling of these gaps. In this study an inverse distance weighting (IDW) method was used to estimate rainfall utilizing neighbouring station data in the Free State Province of South Africa. Six weather stations evenly distributed across the province, and with data for 1950 to 2008, were used to evaluate this patching IDW approach at daily and dekadal time steps. Coefficient of determination (r2), mean absolute error (MAE) and mean bias error (MBE) were the statistics used in the assessment. Firstly, the study conducted a sensitivity analysis of the IDW exponent (p) which showed that the best results are obtained when p is either 2 or 2.5. The estimated values at all six stations were highly correlated with the measured rainfall data with an overall r2 value exceeding 0.70 for both daily and dekadal estimates. MAE showed low miscalculations with values with an average of 1 mm per day and 4.4 mm per dekad. MBE was very low for both daily and dekadal evaluations but the disaggregated data showed underestimation of the IDW mostly for daily rainfall exceeding 10 mm. Thus, IDW methodology proved to be an acceptable approach for estimating both daily and dekadal rainfall in the Free State Province. © 2016, South African Water Research Commission. All rights reserved.

PubMed | University of Nottingham Malaysia Campus, Crops For the Future, Plant and Crop science and University of Nottingham
Type: Journal Article | Journal: PloS one | Year: 2016

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an African legume and is a promising underutilized crop with good seed nutritional values. Low temperature stress in a number of African countries at night, such as Botswana, can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. Analyses of the bambara groundnut transcriptome using cross-species gene expression data resulted in the identification of 375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23C) and very sub-optimal (18C) temperatures, respectively, of which 110 genes are commonly shared between the two stress conditions. The construction of a Highest Reciprocal Rank-based gene co-expression network, followed by its partition using a Heuristic Cluster Chiseling Algorithm resulted in 6 and 7 gene modules in sub-optimal and very sub-optimal temperature stresses being identified, respectively. Modules of sub-optimal temperature stress are principally enriched with carbohydrate and lipid metabolic processes, while most of the modules of very sub-optimal temperature stress are significantly enriched with responses to stimuli and various metabolic processes. Several transcription factors (from MYB, NAC, WRKY, WHIRLY & GATA classes) that may regulate the downstream genes involved in response to stimulus in order for the plant to withstand very sub-optimal temperature stress were highlighted. The identified gene modules could be useful in breeding for low-temperature stress tolerant bambara groundnut varieties.

Chai H.H.,University of Nottingham Malaysia Campus | Massawe F.,University of Nottingham Malaysia Campus | Mayes S.,Crops For the Future | Mayes S.,University of Nottingham
Euphytica | Year: 2016

Bambara groundnut (Vigna subterranea (L) Verdc.) is a drought tolerant underutilised indigenous African legume. The present study aimed to examine the response of bambara groundnut under increasing drought stress and the effects of cumulative mild drought on final yields. The components of morpho-physiological traits were measured for a small F5 breeding cross of bambara groundnut exposed to progressive mild drought in controlled-environment tropical glasshouses. Drought stress reduced stomatal conductance significantly (F(1,130) = 2259.59, p < 0.01), with variation observed between lines of the segregating population (F(64,130) = 16.27, p < 0.01). Higher stomatal density and reduced leaf area were observed in drought treatment plants (p < 0.01). Mild drought stress negatively influenced 100-seed weight (F(1,258) = 19.4, p < 0.01) and harvest index (F(1,258) = 12.87, p < 0.01) by 8 and 15.6 %, compared to the control irrigated treatment, respectively. Bambara groundnut used a combination of mechanisms to tolerate drought stress, including stomatal regulation of gas exchange, reduction of leaf area and maintenance of a relatively high leaf water status and relatively high levels of photosynthesis. Strong genotypic variation observed for many traits in the F5 segregating population allows individual lines with potentially greater tolerance for drought, combined with higher yielding characteristics, to be selected for future breeding programmes in bambara groundnut. © 2015, Springer Science+Business Media Dordrecht.

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