A genomic toolkit for winged bean Psophocarpus tetragonolobus.

A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed 'the soybean for the tropics'. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.

Deciphering the molecular basis for photosynthetic parameters in Bambara groundnut (Vigna subterranea L. Verdc) under drought stress.

BACKGROUND: Assessment of segregating populations for their ability to withstand drought stress conditions is one of the best approaches to develop breeding lines and drought tolerant varieties. Bambara groundnut (Vigna subterranea L. Verdc.) is a leguminous crop, capable of growing in low-input agricultural systems in semi-arid areas. An F4 bi-parental segregating population obtained from S19-3 × DodR was developed to evaluate the effect of drought stress on photosynthetic parameters and identify QTLs associated with these traits under drought-stressed and well-watered conditions in a rainout shelter. RESULTS: Stomatal conductance (gs), photosynthesis rate (A), transpiration rate (E) and intracellular CO2 (Ci) were significantly reduced (p < 0.05) while water use efficiency (WUE) was significantly increased (p < 0.05) under drought-stressed conditions. A strong linear correlation was observed between gs, WUE, A, E and Ci under both water regimes. The variability between different water treatment, among individual lines and the interaction between lines and environment for photosynthetic parameters provides resources for superior lines selection and drought resistant variety improvement. Significant QTL for gs and FV/FM under well-watered conditions were mapped on LG5 and LG3, respectively, with more than 20% of the PVE, which could be considered as the major QTL to control these traits. Five clustered QTLs for photosynthetic traits under drought-stressed and well-watered conditions were mapped on LG5, LG6A, LG10 and LG11, respectively. CONCLUSIONS: Significant and putative QTLs associated with photosynthetic parameters and the effect of drought stress on these traits have been revealed by QTL linkage mapping and field experiment in the F4 segregating population derived from S19-3 × DodR in bambara groundnut. The study provides fundamental knowledge of how photosynthetic traits response to drought stress and how genetic features control these traits under drought-stressed and well-watered conditions in bambara groundnut.

Can cereal-legume intercrop systems contribute to household nutrition in semi-arid environments: A systematic review and meta-analysis.

Introduction: Intercropping cereals with legumes can intensify rainfed cereal monocropping for improved household food and nutritional security. However, there is scant literature confirming the associated nutritional benefits. Methodology: A systematic review and meta-analysis of nutritional water productivity (NWP) and nutrient contribution (NC) of selected cereal-legume intercrop systems was conducted through literature searches in Scopus, Web of Science and ScienceDirect databases. After the assessment, only nine articles written in English that were field experiments comprising grain cereal and legume intercrop systems were retained. Using the R statistical software (version 3.6.0), paired t-tests were used to determine if differences existed between the intercrop system and the corresponding cereal monocrop for yield (Y), water productivity (WP), NC, and NWP. Results: The intercropped cereal or legume yield was 10 to 35% lower than that for the corresponding monocrop system. In most instances, intercropping cereals with legumes improved NY, NWP, and NC due to their added nutrients. Substantial improvements were observed for calcium (Ca), where NY, NWP, and NC improved by 658, 82, and 256%, respectively. Discussion: Results showed that cereal-legume intercrop systems could improve nutrient yield in water-limited environments. Promoting cereal- legume intercrops that feature nutrient-dense legume component crops could contribute toward addressing the SDGs of Zero Hunger (SDG 3), Good Health and Well-3 (SDG 2) and Responsible consumption and production (SDG 12).

A multiscale mathematical model describing the growth and development of bambara groundnut.

A principal objective in agriculture is to maximise food production; this is particularly relevant with the added demands of an ever increasing population, coupled with the unpredictability that climate change brings. Further improvements in productivity can only be achieved with an increased understanding of plant and crop processes. In this respect, mathematical modelling of plants and crops plays an important role. In this paper we present a two-scale mathematical model of crop yield that accounts for plant growth and canopy interactions. A system of nonlinear ordinary differential equations (ODEs) is formulated to describe the growth of each individual plant, where equations are coupled via a term that describes plant competition via canopy-canopy interactions. A crop of greenhouse plants is then modelled via an agent based modelling approach in which the growth of each plant is described via our system of ODEs. The model is formulated for the African drought tolerant legume bambara groundnut (Vigna subterranea), which is currently being investigated as a food source in light of climate change and food insecurity challenges. Our model allows us to account for plant diversity and also investigate the effect of individual plant traits (e.g. plant canopy size and planting distance) on the yield of the overall crop. Informed with greenhouse data, model results show that plant positioning relative to other plants has a large impact on individual plant yield. Variation in physiological plant traits from genetic diversity and the environmental effects lead to experimentally observed variations in crop yield. These traits include plant height, plant carrying capacity, leaf accumulation rate and canopy spread. Of these traits plant height and ground cover growth rates are found to have the greatest impact on crop yield. We also consider a range of different planting arrangements (uniform grid, staggered grid, circular rings and random allocation) and find that the staggered grid leads to the greatest crop yield (6% more compared to uniform grid). Whilst formulated specifically for bambara groundnut, the generic formulation of our model means that with changes to certain parameter's, it may be extended to other crop species that form a canopy.

Genomic selection strategies to increase genetic gain in tea breeding programs.

Tea [Camellia sinensis (L.) O. Kuntze] is mainly grown in low- to middle-income countries (LMIC) and is a global commodity. Breeding programs in these countries face the challenge of increasing genetic gain because the accuracy of selecting superior genotypes is low and resources are limited. Phenotypic selection (PS) is traditionally the primary method of developing improved tea varieties and can take over 16 yr. Genomic selection (GS) can be used to improve the efficiency of tea breeding by increasing selection accuracy and shortening the generation interval and breeding cycle. Our main objective was to investigate the potential of implementing GS in tea-breeding programs to speed up genetic progress despite the low cost of PS in LMIC. We used stochastic simulations to compare three GS-breeding programs with a Pedigree and PS program. The PS program mimicked a practical commercial tea-breeding program over a 40-yr breeding period. All the GS programs achieved at least 1.65 times higher genetic gains than the PS program and 1.4 times compared with Seed-Ped program. Seed-GSc was the most cost-effective strategy of implementing GS in tea-breeding programs. It introduces GS at the seedlings stage to increase selection accuracy early in the program and reduced the generation interval to 2 yr. The Seed-Ped program outperformed PS by 1.2 times and could be implemented where it is not possible to use GS. Our results indicate that GS could be used to improve genetic gain per unit time and cost even in cost-constrained tea-breeding programs.

Genetic diversity analysis and marker-trait associations in Amaranthus species.

Amaranth (Amaranthus spp.) is a highly nutritious, underutilized vegetable and pseudo-cereal crop. It possesses diverse abiotic stress tolerance traits, is genetically diverse and highly phenotypically plastic, making it an ideal crop to thrive in a rapidly changing climate. Despite considerable genetic diversity there is a lack of detailed characterization of germplasm or population structures. The present study utilized the DArTSeq platform to determine the genetic relationships and population structure between 188 amaranth accessions from 18 agronomically important vegetable, grain, and weedy species. A total of 74, 303 SNP alleles were generated of which 63, 821 were physically mapped to the genome of the grain species A. hypochondriacus. Population structure was inferred in two steps. First, all 188 amaranth accessions comprised of 18 species and second, only 120 A. tricolor accessions. After SNP filtering, a total of 8,688 SNPs were generated on 181 amaranth accessions of 16 species and 9,789 SNPs generated on 118 A. tricolor accessions. Both SNP datasets produced three major sub-populations (K = 3) and generate consistent taxonomic classification of the amaranth sub-genera (Amaranthus Amaranthus, Amaranthus Acnida and Amaranthus albersia), although the accessions were poorly demarcated by geographical origin and morphological traits. A. tricolor accessions were well discriminated from other amaranth species. A genome-wide association study (GWAS) of 10 qualitative traits revealed an association between specific phenotypes and genetic variants within the genome and identified 22 marker trait associations (MTAs) and 100 MTAs (P≤0.01, P≤0.001) on 16 amaranth species and 118 A.tricolor datasets, respectively. The release of SNP markers from this panel has produced invaluable preliminary genetic information for phenotyping and cultivar improvement in amaranth species.

Natural Genotypic Variation Underpins Root System Response to Drought Stress in Bambara Groundnut [Vigna subterranea (L.) Verdc.].

Bambara groundnut [Vigna subterranea (L.) Verdc.] is grown in rainfed production systems and suffers from periodic drought stress (DS), leading to yield reductions. Natural genotypic variation for root traits is essential for adaptation to water deficit conditions. However, root traits have not been fully utilised as selection criteria to improve DS in bambara groundnut. The present study explored the natural genotypic variation found in single genotypes of bambara groundnut derived from landraces to identify adaptive differences in tap root length (TRL) and root length density (RLD) in response to DS. A diverse core collection of eight bambara groundnut genotypes from various locations (namely, Gresik, LunT, IITA-686, DodR, S19-3, Tiga nicuru, and Ankpa-4, DipC1), were grown for two seasons (2018 and 2019) in polyvinyl chloride (PVC) columns with well-watered (WW) and 30-day DS treatments. Plant samples were collected at 55 days after emergence (DAE) (30 days of DS) and at 105 DAE (30 days of DS plus 50 days of recovery). Under DS, differential TRL among genotypes at 55 DAE was observed, with DodR recording the longest among genotypes with an increase (1% in 2018) in TRL under DS compared to WW, whereas LunT and IITA-686 showed significant (p < 0.001) decrease in TRL (27 and 25%, respectively, in 2018). Average RLD was observed to have the highest reduction under DS in the 90-110 cm layer (42 and 58%, respectively, in 2018 and 2019). Rainy habitat LunT had limited roots in 2018 and recorded the least (0.06 ± 0.013 cm-3) RLD in 2019. However, dry-habitat DodR showed an increase in the RLD (60-90 cm) under DS compared to WW, while dry-habitat S19-3 densely occupied all depths with RLD of 0.16 ± 0.05 and 0.18 ± 0.01 cm cm-3 in the deepest layer in both seasons, respectively. Reduced RLD under DS showed recovery when the plants were re-watered. These plants were additionally observed to have RLD that surpasses the density in WW at all soil depths at 105 DAE. Also, recovery was shown in Tiga nicuru and DodR (0-30 cm) and IITA-686 (90-110 cm) in 2019. Average RLD under DS treatment was associated with substantial grain yield advantage (R 2 = 0.27 and R 2 = 0.49, respectively) in 2018 and 2019. An increase in TRL allowed DodR to quickly explore water at a deeper soil depth in response to gradually declining soil water availability. High RLD in genotypes such as DodR, DipC1 and S19-3 also offered adaptive advantage over other genotypes under DS. Variation in intrinsic RLD in deeper soil depths in the studied genotypes determines root foraging capacity when facing DS. This suggests that different agroecological environments to which bambara groundnut is subjected in its natural habitat have promoted a phenotypic differentiation in root systems to adapt to ecotypic conditions, which may help offset the impact of DS. The natural genotypic variation exhibited, especially by DodR, could be exploited to identify potential quantitative trait loci (QTLs) that control deep rooting and root length density.

Peperomia pellucida (L.) Kunth and eye diseases: A review on phytochemistry, pharmacology and toxicology.

Peperomia pellucida (L.) Kunth is a medicinal plant used to manage inflammatory illnesses such as conjunctivitis, and gastrointestinal and respiratory tract disorders in tropical and subtropical regions. However, little is known about its pharmacological mechanism of action against eye diseases. This review aims to critically discuss the phytochemistry, pharmacology and toxicology of P. pellucida as well as its roles in the treatment of cataract, glaucoma and diabetic retinopathy. Recent developments in the uses of P. pellucida for healthcare and nutraceutical products by the pharmaceutical industry are also covered in this review. For this review, a literature search was performed with PubMed, ScienceDirect, SciFinder Scholar and Scopus databases, using relevant keywords. Among the various phytochemicals identified from P. pellucida, ß-caryophyllene, carotol, dillapiole, ellagic acid, pellucidin A, phytol and vitexin exhibit strong pharmacological activities within the mitogen-activated protein kinase and nuclear factor-κB signalling pathways in inflammatory eye diseases. The antihypertensive, anti-inflammatory, antioxidant, antihyperglycemic and anti-angiogenic activities displayed by P. pellucida extracts in many in vitro, in vivo and clinical studies suggest its potential role in the management of inflammatory eye diseases. P. pellucida extract was non-toxic against normal cell lines but displayed mild toxicity in animal models. The growing public interest in P. pellucida has inspired the nutraceutical and pharmaceutical industries to process the plant into health products. Although the potential pharmacological mechanisms against eye diseases have been summarized, further studies of the interactions among constituent phytochemicals from P. pellucida within various signalling pathways shall support the use of the plant as an alternative therapeutic source.

Bambara Groundnut: An Underutilized Leguminous Crop for Global Food Security and Nutrition.

Rapid population growth, climate change, intensive monoculture farming, and resource depletion are among the challenges that threaten the increasingly vulnerable global agri-food system. Heavy reliance on a few major crops is also linked to a monotonous diet, poor dietary habits, and micronutrient deficiencies, which are often associated with diet-related diseases. Diversification-of both agricultural production systems and diet-is a practical and sustainable approach to address these challenges and to improve global food and nutritional security. This strategy is aligned with the recommendations from the EAT-Lancet report, which highlighted the urgent need for increased consumption of plant-based foods to sustain population and planetary health. Bambara groundnut (Vigna subterranea (L.) Verdc.), an underutilized African legume, has the potential to contribute to improved food and nutrition security, while providing solutions for environmental sustainability and equity in food availability and affordability. This paper discusses the potential role of Bambara groundnut in diversifying agri-food systems and contributing to enhanced dietary and planetary sustainability, with emphasis on areas that span the value chain: from genetics, agroecology, nutrition, processing, and utilization, through to its socioeconomic potential. Bambara groundnut is a sustainable, low-cost source of complex carbohydrates, plant-based protein, unsaturated fatty acids, and essential minerals (magnesium, iron, zinc, and potassium), especially for those living in arid and semi-arid regions. As a legume, Bambara groundnut fixes atmospheric nitrogen to improve soil fertility. It is resilient to adverse environmental conditions and can yield on poor soil. Despite its impressive nutritional and agroecological profile, the potential of Bambara groundnut in improving the global food system is undermined by several factors, including resource limitation, knowledge gap, social stigma, and lack of policy incentives. Multiple research efforts to address these hurdles have led to a more promising outlook for Bambara groundnut; however, there is an urgent need to continue research to realize its full potential.

An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily.

Oil palm (Elaeis guineensis Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of E. guineensis that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by assigning an additional 1968 originally unplaced scaffolds that were available publicly into the physical genome. By integrating three ultra-dense linkage maps and using them to place genomic scaffolds, the 16 pseudomolecules were extended. As we show, the improved genome has enhanced the mapping resolution for genome-wide association studies (GWAS) and permitted further identification of candidate genes/protein-coding regions (CDSs) and any non-coding RNA that may be associated with them for further studies. We then employed the new physical map in a comparative genomics study against two other agriculturally and economically important palm species-date palm (Phoenix dactylifera L.) and coconut palm (Cocos nucifera L.)-confirming the high level of conserved synteny among these palm species. We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map. The improved genome of oil palm will enable molecular breeding approaches to expedite crop improvement, especially in the largest subfamily of Arecoideae, which consists of 107 species belonging to Arecaceae.

Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm.

Evaluation of transcriptome data in combination with QTL information has been applied in many crops to study the expression of genes responsible for specific phenotypes. In oil palm, the mesocarp oil extracted from E. oleifera × E. guineensis interspecific hybrids is known to have lower palmitic acid (C16:0) content compared to pure African palms. The present study demonstrates the effectiveness of transcriptome data in revealing the expression profiles of genes in the fatty acid (FA) and triacylglycerol (TAG) biosynthesis processes in interspecific hybrids. The transcriptome assembly yielded 43,920 putative genes of which a large proportion were homologous to known genes in the public databases. Most of the genes encoding key enzymes involved in the FA and TAG synthesis pathways were identified. Of these, 27, including two candidate genes located within the QTL associated with C16:0 content, showed differential expression between developmental stages, populations and/or palms with contrasting C16:0 content. Further evaluation using quantitative real-time PCR revealed that differentially expressed patterns are generally consistent with those observed in the transcriptome data. Our results also suggest that different isoforms are likely to be responsible for some of the variation observed in FA composition of interspecific hybrids.

Major QTLs for Trunk Height and Correlated Agronomic Traits Provide Insights into Multiple Trait Integration in Oil Palm Breeding.

Superior oil yield is always the top priority of the oil palm industry. Short trunk height (THT) and compactness traits have become increasingly important to improve harvesting efficiency since the industry started to suffer yield losses due to labor shortages. Breeding populations with low THT and short frond length (FL) are actually available, such as Dumpy AVROS pisifera (DAV) and Gunung Melayu dura (GM). However, multiple trait stacking still remains a challenge for oil palm breeding, which usually requires 12-20 years to complete a breeding cycle. In this study, yield and height increment in the GM × GM (GM-3341) and the GM × DAV (GM-DAV-3461) crossing programs were evaluated and palms with good yield and smaller height increment were identified. In the GM-3341 family, non-linear THT growth between THT_2008 (seven years old) and THT_2014 (13 years old) was revealed by a moderate correlation, suggesting that inter-palm competition becomes increasingly important. In total, 19 quantitative trait loci (QTLs) for THT_2008 (8), oil per palm (O/P) (7) and FL (4) were localized on the GM-3341 linkage map, with an average mapping interval of 2.01 cM. Three major QTLs for THT_2008, O/P and FL are co-located on chromosome 11 and reflect the correlation of THT_2008 with O/P and FL. Multiple trait selection for high O/P and low THT (based on the cumulative effects of positive alleles per trait) identified one palm from 100 palms, but with a large starting population of 1000-1500 seedling per cross, this low frequency could be easily compensated for during breeding selection.

Root Foraging Capacity in Bambara Groundnut (Vigna Subterranea (L.) Verdc.) Core Parental Lines Depends on the Root System Architecture during the Pre-Flowering Stage.

Characterizing the morphological variability in root system architecture (RSA) during the sensitive pre-flowering growth stage is important for crop performance. To assess this variation, eight bambara groundnut single genotypes derived from landraces of contrasting geographic origin were selected for root system architecture and rooting distribution studies. Plants were grown in a polyvinyl chloride (PVC) column system under controlled water and nutrient availability in a rainout shelter. Days to 50% plant emergence was characterized during the first two weeks after sowing, while taproot length (TRL), root length (RL), root length density (RLD), branching number (BN), branching density (BD) and intensity (BI), surface area (SA), root volume (RV), root diameter (RDia), root dry weight (RDW), shoot dry weight (SDW), and shoot height (SH) were determined at the end of the experiment, i.e., 35 days after emergence. Genotypes S19-3 and DipC1 sourced from drier regions of sub-Saharan Africa generally had longer taproots and greater root length distribution in deeper (60 to 90 cm) soil depths. In contrast, bambara groundnut genotypes from wetter regions (i.e., Gresik, Lunt, and IITA-686) in Southeast Asia and West Africa exhibited relatively shallow and highly branched root growth closer to the soil surface. Genotypes at the pre-flowering growth stage showed differential root foraging patterns and branching habits with two extremes, i.e., deep-cheap rooting in the genotypes sourced from dry regions and a shallow-costly rooting system in genotypes adapted to higher rainfall areas with shallow soils. We propose specific bambara groundnut genotype as donors in root trait driven breeding programs to improve water capture and use efficiency.

Bambara groundnut: an exemplar underutilised legume for resilience under climate change.

MAIN CONCLUSION: Bambara groundnut has the potential to be used to contribute more the climate change ready agriculture. The requirement for nitrogen fixing, stress tolerant legumes is clear, particularly in low input agriculture. However, ensuring that existing negative traits are tackled and demand is stimulated through the development of markets and products still represents a challenge to making greater use of this legume. World agriculture is currently based on very limited numbers of crops, representing a significant risk to food supplies, particularly in the face of climate change which is expected to increase the frequency of extreme events. Minor and underutilised crops can help to develop a more resilient and nutritionally dense future agriculture. Bambara groundnut [Vigna subterranea (L.) Verdc.[, as a drought resistant, nitrogen-fixing, legume has a role to play. However, as with most underutilised crops, there are significant gaps in knowledge and also negative traits such as 'hard-to-cook' and 'photoperiod sensitivity to pod filling' associated with the crop which future breeding programmes and processing methods need to tackle, to allow it to make a significant contribution to the well-being of future generations. The current review assesses these factors and also considers what are the next steps towards realising the potential of this crop.

Crops For the Future (CFF): an overview of research efforts in the adoption of underutilised species.

MAIN CONCLUSION: Crops For the Future (CFF), as an entity, has established a broad range of research activities to promote the improvement and adoption of currently underutilised crops. This paper summarises selected research activities at Crops For the Future (CFF) in pursuit of its mission 'to develop solutions for diversifying future agriculture using underutilised crops'. CFF is a research company focussed on the improvement of underutilised crops, so that they might be grown and consumed more widely with benefits to human food and nutritional security; its founding guarantors were the Government of Malaysia and the University of Nottingham. From its base in Malaysia, it engages in research around the world with a focus on species and system diversification. CFF has adopted a food system approach that adds value by delivering prototype food, feed and knowledge products. Bambara groundnut (Vigna subterranea) was adopted as an exemplar crop around which to develop CFF's food system approach with emphasis on the short-day photoperiod requirement for pod-filling and the hard-to-cook trait. Selective breeding has allowed the development of lines that are less susceptible to photoperiod but also provided a range of tools and approaches that are now being exploited in other crops such as winged bean (Psophocarpus tetragonolobus), amaranth (Amaranthus spp.), moringa (Moringa oleifera) and proso (Panicum miliaceum) and foxtail (Setaria italica) millets. CFF has developed and tested new food products and demonstrated that several crops can be used as feed for black soldier fly which can, in turn, be used to feed fish thereby reducing the need for fishmeal. Information about underutilised crops is widely dispersed; so, a major effort has been made to develop a knowledge base that can be interrogated and used to answer practical questions about potential exploitation of plant and nutritional characteristics. Future research will build on the success with Bambara groundnut and include topics such as urban agriculture, rural development and diversification, and the development of novel foods.

Linkage-based genome assembly improvement of oil palm (Elaeis guineensis).

Meiotic crossovers in outbred species, such as oil palm (Elaeis guineensis Jacq., 2n = 32) contribute to allelic re-assortment in the genome. Such genetic variation is usually exploited in breeding to combine positive alleles for trait superiority. A good quality reference genome is essential for identifying the genetic factors underlying traits of interest through linkage or association studies. At the moment, an AVROS pisifera genome is publicly available for oil palm. Distribution and frequency of crossovers throughout chromosomes in different origins of oil palm are still unclear. Hence, an ultrahigh-density genomic linkage map of a commercial Deli dura x AVROS pisifera family was constructed using the OP200K SNP array, to evaluate the genetic alignment with the genome assembly. A total of 27,890 linked SNP markers generated a total map length of 1,151.7 cM and an average mapping interval of 0.04 cM. Nineteen linkage groups represented 16 pseudo-chromosomes of oil palm, with 61.7% of the mapped SNPs present in the published genome. Meanwhile, the physical map was also successfully extended from 658 Mb to 969 Mb by assigning unplaced scaffolds to the pseudo-chromosomes. A genic linkage map with major representation of sugar and lipid biosynthesis pathways was subsequently built for future studies on oil related quantitative trait loci (QTL). This study improves the current physical genome of the commercial oil palm, and provides important insights into its recombination landscape, eventually unlocking the full potential genome sequence-enabled biology for oil palm.

Prospects of orphan crops in climate change.

MAIN CONCLUSION: Orphan crops can contribute to building resilience of marginal cropping systems as a climate chnage adaptation strategy. Orphan crops play an important role in global food and nutrition security, and may have potential to contribute to sustainable food systems under climate change. Owing to reports of their potential under water scarcity, there is an argument to promote them to sustainably address challenges such as increasing drought and water scarcity, food and nutrition insecurity, environmental degradation, and employment creation under climate change. We conducted a scoping review using online databases to identify the prospects of orphan crops to contribute to (1) sustainable and healthy food systems, (2) genetic resources for future crop improvement, and (3) improving agricultural sustainability under climate change. The review found that, as a product of generations of landrace agriculture, several orphan crops are nutritious, resilient, and adapted to niche marginal agricultural environments. Including such orphan crops in the existing monocultural cropping systems could support more sustainable, nutritious, and diverse food systems in marginalised agricultural environments. Orphan crops also represent a broad gene pool for future crop improvement. The reduction in arable land due to climate change offers opportunities to expand the area under their production. Their suitability to marginal niche and low-input environments offers opportunities for low greenhouse gas (GHG) emissions from an agro-ecosystems, production, and processing perspective. This, together with their status as a sub-set of agro-biodiversity, offers opportunities to address socio-economic and environmental challenges under climate change. With research and development, and policy to support them, orphan crops could play an important role in climate-change adaptation, especially in the global south.

Winged bean (Psophocarpus tetragonolobus (L.) DC.) for food and nutritional security: synthesis of past research and future direction.

MAIN CONCLUSION: Winged bean is popularly known as "One Species Supermarket" for its nutrient-dense green pods, immature seeds, tubers, leaves, and mature seeds. This underutilised crop has potential beneficial traits related to its biological nitrogen-fixation to support low-input farming. Drawing from past knowledge, and based on current technologies, we propose a roadmap for research and development of winged bean for sustainable food systems. Reliance on a handful of "major" crops has led to decreased diversity in crop species, agricultural systems and human diets. To reverse this trend, we need to encourage the greater use of minor, "orphan", underutilised species. These could contribute to an increase in crop diversity within agricultural systems, to improve human diets, and to support more sustainable and resilient food production systems. Among these underutilised species, winged bean (Psophocarpus tetragonolobus) has long been proposed as a crop for expanded use particularly in the humid tropics. It is an herbaceous perennial legume of equatorial environments and has been identified as a rich source of protein, with most parts of the plant being edible when appropriately prepared. However, to date, limited progress in structured improvement programmes has restricted the expansion of winged bean beyond its traditional confines. In this paper, we discuss the reasons for this and recommend approaches for better use of its genetic resources and related Psophocarpus species in developing improved varieties. We review studies on the growth, phenology, nodulation and nitrogen-fixation activity, breeding programmes, and molecular analyses. We then discuss prospects for the crop based on the greater understanding that these studies have provided and considering modern plant-breeding technologies and approaches. We propose a more targeted and structured research approach to fulfil the potential of winged bean to contribute to food security.

High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations.

Oil palm (Elaeis guineensis Jacq.) is an outbreeding perennial tree crop with long breeding cycles, typically 12 years. Molecular marker technologies can greatly improve the breeding efficiency of oil palm. This study reports the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations, namely AA0768 and AA0769 with 48 and 58 progeny respectively. Genetic maps were constructed using the DArT and SNP markers generated in combination with anchor SSR markers. Both maps consisted of 16 major independent linkage groups (2n = 2× = 32) with 1399 and 1466 mapped markers for the AA0768 and AA0769 populations, respectively, including the morphological trait "shell-thickness" (Sh). The map lengths were 1873.7 and 1720.6 cM with an average marker density of 1.34 and 1.17 cM, respectively. The integrated map was 1803.1 cM long with 2066 mapped markers and average marker density of 0.87 cM. A total of 82% of the DArTseq marker sequence tags identified a single site in the published genome sequence, suggesting preferential targeting of gene-rich regions by DArTseq markers. Map integration of higher density focused around the Sh region identified closely linked markers to the Sh, with D.15322 marker 0.24 cM away from the morphological trait and 5071 bp from the transcriptional start of the published SHELL gene. Identification of the Sh marker demonstrates the robustness of using the DArTseq platform to generate high density genetic maps of oil palm with good genome coverage. Both genetic maps and integrated maps will be useful for quantitative trait loci analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences.

Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment.

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.