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African yam bean (AYB; Sphenostylis stenocarpa) is an underutilized legume indigenous to Africa with great potential to enhance food security and offer nutritional and medicinal opportunities. However, low grain yield caused by fungal diseases, including pod blight and leaf tip dieback, deters farmers from large‐scale cultivation. To determine the prevalence of fungal diseases affecting leaves, pods and flowers of AYB, a survey was conducted in 2018 and 2019 in major AYB‐growing areas in Nigeria. Leaf tip dieback, flower bud rot and pod blight were the most common symptoms. Morphological and molecular assays were conducted to identify the causal agents of the observed diseases. In all the samples examined, fungi from eight genera were isolated from diseased leaves, buds and pods. Koch's postulates were fulfilled only for fungi belonging to the Colletotrichum genus. Fungi from the other seven genera did not produce disease symptoms in healthy AYB tissues. Several Colletotrichum isolates were characterized by sequencing the rDNA internal transcribed spacer (ITS), glyceraldehyde‐3‐phosphate dehydrogenase, calmodulin and ApMAT loci. A combined phylogenetic analysis revealed four Colletotrichum species: C. siamense, C. theobromicola and C. fructicola, which were recovered from diseased leaves, and C. truncatum, recovered from diseased pods and buds. Our results are useful to gear efforts to develop integrated management strategies to control diseases affecting AYB in Nigeria and elsewhere. Availability of such strategies may stimulate greater AYB cultivation, which can contribute to diet diversification, something repeatedly advocated by a range of stakeholders to increase food security and prosperity of smallholder farmers. [ABSTRACT FROM AUTHOR]

In plant roots, arbuscular mycorrhizal fungi (AMF) are the most prevalent microsymbionts, and thereby provide many key ecosystem services to natural and agricultural ecosystems. Despite AMF's significance for the environment and the economy, little is known about the mycorrhizal inoculum potential and diversity of AMF associated with orphan African cereal crops, specially fonio millet (Digitaria exilis stapf.) under field conditions. We hypothesized that the type of fonio millet agroecosystem influences the AMF density and distribution in soils. We therefore, assessed the inoculum potential, density and diversity of AMF spores and soil enzyme activities in five fonio millet agroecosystems belonging to three climatic zones (Sudanian, Sudano-Sahelian and Sudano-Guinean). By combining AMF spore identification from field-collected soils and trap culture, 20 species belonging to 8 genera (Acaulospora, Ambispora, Dendiscutata, Gigaspora, Glomus, Racocetra, Sclerocystis and Scutellospora) were identified. Glomus was the most represented genus with 8 species, followed by Gigaspora (5 species) and Acaulospora (2 species); the remaining genera were each represented by one species. Except for Ambispora which was not found in the Sudanian area, all genera occurred in the three climatic zones. The abundance and diversity of AMF species and FDA-hydrolytic and phosphatase activities varied between fonio millet agroecosystems as well as between climatic zones. Soil pH and soil texture were the variables that best explained the density and distribution of AMF spores. Our results contribute to paving the way towards the development of microbial engineering approaches for agronomic improvement of fonio millet. [ABSTRACT FROM AUTHOR]

In plant roots, arbuscular mycorrhizal fungi (AMF) are the most prevalent microsymbionts, and thereby provide many key ecosystem services to natural and agricultural ecosystems. Despite AMF’s significance for the environment and the economy, little is known about the mycorrhizal inoculum potential and diversity of AMF associated with orphan African cereal crops, specially fonio millet (Digitaria exilis stapf.) under field conditions. We hypothesized that the type of fonio millet agroecosystem influences the AMF density and distribution in soils. We therefore, assessed the inoculum potential, density and diversity of AMF spores and soil enzyme activities in five fonio millet agroecosystems belonging to three climatic zones (Sudanian, Sudano-Sahelian and Sudano-Guinean). By combining AMF spore identification from field-collected soils and trap culture, 20 species belonging to 8 genera (Acaulospora, Ambispora, Dendiscutata, Gigaspora, Glomus, Racocetra, Sclerocystis and Scutellospora) were identified. Glomus was the most represented genus with 8 species, followed by Gigaspora (5 species) and Acaulospora (2 species); the remaining genera were each represented by one species. Except for Ambispora which was not found in the Sudanian area, all genera occurred in the three climatic zones. The abundance and diversity of AMF species and FDA-hydrolytic and phosphatase activities varied between fonio millet agroecosystems as well as between climatic zones. Soil pH and soil texture were the variables that best explained the density and distribution of AMF spores. Our results contribute to paving the way towards the development of microbial engineering approaches for agronomic improvement of fonio millet.

Neglected and underutilized crop species (NUCS/NUS) are claimed to contribute to sustainable development. However, many scholars argue that enabling policies and appropriate governance are needed to operationalize such a potential contribution. Therefore, this systematic review analyzes the literature dealing with the relationships between policy and governance aspects and the promotion of NUS in West Africa. It draws upon 45 eligible articles identified through a search conducted on the Web of Science in December 2023. The existing literature focuses on Nigeria and a few NUS, especially cassava. The addressed policy domains include biodiversity conservation; subsidies; seed systems; food security, self-sufficiency and sovereignty; trade and import substitution; food safety and health; climate change and energy; land use; research, innovation and development; and support and assistance systems. Meanwhile, the main governance domains are (1) inclusiveness and participation and (2) institutional capacity. The analysis suggests that NUS development is also affected by sectoral policy coherence and consistency as well as the policy–governance interplay. Future studies should widen the scope in terms of geographical coverage in West Africa and NUS addressed to allow for more comparisons. Furthermore, there is a need for further research to understand the synergies and trade-offs between sectoral policies affecting NUS promotion and development. [ABSTRACT FROM AUTHOR]

Tef research has little benefited from omics due to neglect of the crop by the global scientific community. However, the few utilized tools showed promising results. Chromosome-scale assembly of the genome reveals the evolution of tef. The whole-genome sequencing of drought-resurrecting Eragrostis nindensis and desiccation-sensitive Eragrostis curvula shows genes that play key roles in drought responses. A few studies using omics tools have revealed differentially expressed genes, proteins, and metabolites in tef plants exposed to drought. Molecular markers have deciphered diversity in tef germplasm collected from diverse agroecologies in Ethiopia. The application of targeting induced local lesions in genomes resulted in mutant tef lines with a semidwarf stature, which were later bred to locally adapted and high-yielding varieties. Genome editing using 'Green Revolution' genes resulted in a semidwarf and lodging-tolerant tef plant. Tef or teff [ Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef's diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research. [ABSTRACT FROM AUTHOR]

There are thousands of neglected and underutilized species (NUS) worldwide, but only a few make it to the mainstream and spotlight. The reason for that lies probably in the dynamics of the transition from a NUS to a major crop. However, there is no transition framework that specifically addresses NUS. To bridge the gap, this paper suggests a transition framework for NUS. This work was carried out within the project SUSTLIVES (Sustaining and improving local crop patrimony in Burkina Faso and Niger for better lives and ecosystems). It draws upon a search performed on the Web of Science in July 2022. The eligible articles were analysed using the Multi-Level Perspective (MLP) on socio-technical transitions and its three elements viz. niches, socio-technical regime and socio-technical landscape: Niches refer to NUS; the socio-technical regime relates to the incumbent, dominant system of major commercial staple crops, and includes factors hindering NUS integration; and the socio-technical landscape refers to policies and macro-trends affecting both the niche and the regime. The transition dynamics and success depend not only on the characteristics of the niche NUS (cf. strengths and weaknesses), regime and landscape, but also on the type, intensity and timing of interactions among them. The interaction of elements as well as transition speed are moderated by the levers of change that lie in the areas of policy, finance and market, technology and practices, culture, and science and innovation. Further work is needed to refine and test the framework in different contexts and on various NUS. [ABSTRACT FROM AUTHOR]

• White rust disease caused by wilsoniana bliti is a global concern in amaranths. • Advanced breeding lines (ABL) exhibiting high white rust resistance were identified. • Significant variability in ABLs for nutritional, antioxidant and minerals content. • Identified 5 locally preferable nutritious ABLs with enhanced white rust resistance. Identification and utilization of locally preferred vegetables and increasing dietary diversity are the most effective ways to sustainably prevent hidden hunger. Underutilized crops such as amaranth (Amaranthus spp. L.) can address the nutritional problem of society. However, its wide adoption and cultivation are restricted by a major fungal disease i.e., white rust caused by Wilsoniana bliti (Biv.) Thines (Syn. Albugo bliti) , especially in the tropical and subtropical regions of the world. As genetic improvement for the development of resistant varieties is the most sustainable approach, amaranth germplasm was explored and through individual plant selection and selfings, advanced breeding lines were developed in our study. Through field screening and artificial challenge inoculation, advanced breeding lines (ABLs) with high levels of white rust resistance were identified. Further evaluation for yield and quality traits indicated significant variability in the ABLs for nutritional components such as protein content (18.19–27.50%), total phenols (568.62–1220 mg GAE /100 g DW) and FRAP antioxidant activity (559.83–1531.17 mg AAE/100 g DW). The ABLs also differed in their mineral nutrient content in terms of N (2.91–4.40%), P (0.41–0.60 %), Ca (1.60–2.40 %), S (0.25–0.32 %), Fe (831.13–1168.48 ppm), Mn (285–1146.96 ppm) and Zn (133.85–206.29 ppm). Advanced breeding lines viz., IIHR-B-AM286–17–2–8 (A. dubius), IIHR-B-AM-08–13–5–2 (A. blitum), IIHR-B-AM276–3–9–4, IIHR-B-AM65–17–3–8 and IIHR-B-AM45–6–2 (A. tricolor) with good local consumer preference with enhanced resistance to white rust were identified. [ABSTRACT FROM AUTHOR]

With the establishment of human civilization, wild plant species were domesticated and cultivated at their centres of origin and further disseminated in different parts of the world. While being grown in the wild and on farms, innumerable mutations occurred over years creating new variations in their genome. Today's improved crop plants are the result of years of artificial selection for a few of those mutations, many times coupled with deliberate selection for desirable recombinants that originated in nature or developed through targeted breeding. Artificial phenotypic selection leaves footprints in the genome of crop species. Over the last three decades, researchers have identified numerous genes and causal mutations associated with domestication events, leading to a better understanding of how our forefathers and foremothers tinkered with plant development to meet their food and fodder needs. Our ability to script complex genetic information through efficient genome editing tools has enabled us to take a great leap forward to accelerate crop domestication. In this review, we have discussed how genome editing tools facilitate the domestication of wild and semi-domesticated species, the prerequisites for performing editing in wild genomes, and the potential future target loci for installing domestication syndrome rapidly in wild plant species. Genome editing technologies could help us bring wild and partially domesticated crop plants to mainstream agriculture to sustainably meet our current and future needs. [ABSTRACT FROM AUTHOR]

Context: Food security, integral to the UN sustainable development goals, has become a global priority. Only a handful of cultivated species meet 80% of dietary intake, and hence, in future, it may be inadequate to depend only on these crops. Aims: Wild germplasm is endowed with desirable traits of relevance to food, health and climate resilience and, hence, there is a need to intensify efforts for bringing wild edible plants into mainstream agriculture. Wild banana (Ensete spp.) is a staple food source besides having bioactive compounds, nutraceuticals and cosmeceuticals. Methods: Ensete species are cultivated in Asian and African countries, and its cultivation through superior clones is done through conventional methods and plant tissue culture techniques. Despite information on the ecological, social and economic features of Ensete spp., there has been no systematic assessment of their nutritional and other agronomic traits. Key results: Herein, we provide a comprehensive account of Ensete sp. conservation, domestication, nutritional profile and medicinal importance as well as documenting the biotechnological approaches and identifying research gaps and prospects of these underutilised species. Conclusion and implications: We believe this review could form a baseline resource to aid decision-making for improvement of the crop towards sustainable use and domestication of the species in the global context. Wild banana (Ensete spp.) is an important source of starchy food. In different geographical regions, it plays a significant role along with other wild crops in minimising the gap between supply and demand of food. Wild banana can tolerate and survive in severe drought conditions and, therefore, may emerge as future crops for regions experiencing changes in climate and water scarcity. This review highlights the current status and future prospects related to wild banana. [ABSTRACT FROM AUTHOR]

Yam is an important tuber crop with enormous potential to enhance rural sustenance and livelihood in DRC. However, studies to enhance its genetic improvement are very far from sufficient with only a handful of information available on the crop. Yam has been treated as an orphan crop compared to contemporary crops such as cassava and sweet potato which have adapted to different cropping systems and become widespread in production. The lack of research attention to address the major production challenges has further decreased the value and potential of the crop compared to its contemporaries. These production constraints include lack of adequate quality planting materials, low yield potential, poor resistance/tolerance to yam mosaic and anthracnose diseases and ultimately poor tuber quality attributes focusing on tuber taste, flesh oxidation and dry matter contents of the majority of the farmers preferred varieties. In this review, we evaluated the status of yam in DRC and presented the needful activities to be incorporated for its improvement. Diversity has however been maintained mainly through ennoblement efforts in house gardens and small farmlands using traditional farming methods. Studies from other nations where yam has been successful with prominence in characterization and genetic improvement brought to light the need for DRC to consider yam as a staple carbohydrate food source, even to the extent of modifications in food public policy. Reversal of the yam's current stigma is a challenge to the scientific community and the population in general. [ABSTRACT FROM AUTHOR]

Summary: Finger millet (Eleusine coracana) is a staple crop for subsistence farmers and is primarily cultivated in arid and semi-arid regions. Nevertheless, there are limited data available on the occurrence of plant-parasitic nematodes that specifically target finger millet, and the damage arising from such infections. In this study, we investigated the population dynamics, damage threshold and tolerance of the lesion nematode, Pratylenchus n. sp., and the root-knot nematode, Meloidogyne javanica , on finger millet 'P-224'. We used 11 initial population densities (P i) of second-stage juveniles (J2): 0, 0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32 and 64 J2 (g soil)−1 for M. javanica and the same densities of mixed life-stages for Pratylenchus n. sp. The logistic growth model, Seinhorst yield loss and population dynamic models were fitted to the shoot height, plant biomass and final nematode population density. Based on the population dynamics model parameters, maximum multiplication rates and maximum population densities for each nematode species were estimated. The maximum multiplication rates (a) were 32.39 and 17.46, whilst the maximum population densities (M) were 18.83 nematodes (g soil)−1 and 19.78 J2 (g soil)−1 for Pratylenchus n. sp. and M. javanica respectively. The maximum height reached (C) was negatively affected by increasing P i for both nematode genera, while the rate of growth (B) and the time to reach 0.5 × C was not affected based on the logistic model. A tolerance limit (T) of 1.70 nematodes (g soil)−1 and 0.65 J2 (g soil)−1; relative minimum grain yield (m) of 0.23 and 0.40 for Pratylenchus n. sp. and M. javanica was found, respectively. The results indicate that 'P-224' is a good host for both Pratylenchus n. sp. and M. javanica , which significantly reduce yield. These findings can be used as a base to develop effective nematode management strategies for finger millet. [ABSTRACT FROM AUTHOR]

Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid. [ABSTRACT FROM AUTHOR]

Amaranths (Amaranthus L.) are multi-use crop species renowned for their nutritional quality and their tolerance to biotic and abiotic stresses. Since the soil salinity of croplands is a growing problem worldwide, we tested the salinity tolerance of six grain and two leaf cultivars of Amaranthus cruentus L. The plants were grown for 53 days under hydroponic conditions at 0, 50 and 100 mM NaCl. We investigated the growth rate, photosynthetic activity, mineral content, pigments and biochemical compounds involved in oxidative stress. Although 100 mM NaCl always decreased biomass production, we highlighted Don Leon and K91 as tolerant cultivars under moderate salt stress (50 mM NaCl). Under salinity, sodium accumulated more in the shoots than in the roots, particularly in the stems. Sodium accumulation in the plants decreased the net photosynthetic rate, transpiration rate and stomatal conductance but increased water use efficiency, and it decreased chlorophyll, betalain and polyphenol content in the leaves. It also decreased the foliar content of calcium, magnesium and potassium but not the iron and zinc content. The physiological parameters responded differently to sodium accumulation depending on the cultivar, suggesting a different relative importance of ionic and osmotic phases of salt stress among cultivars. Our results allowed us to identify the morpho-physiological traits of the cultivars with different salt tolerance levels. [ABSTRACT FROM AUTHOR]

Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid.

Although there exist over 7000 crop species, only a few are commercially valuable and grown on a large scale in monocultures worldwide. However, underutilised crops (also called orphan crops) have significant potential for food security and Telfairia occidentalis Hook. F. (Cucurbitaceae) is one such orphan crop grown in West Africa for its nutritious leaves, oil and protein-rich seeds. In this dioecious crop, farmers like to eliminate male plants and keep mostly females to increase their yield. However, they face the challenge of determining sex due to limited morphological differences between females and males before flowering. This study used double digested restriction site-associated DNA sequencing data (ddRADseq) to examine the genetic diversity within and among landraces of T. occidentalis, identify common sex-determining loci, and establish reliable assays to characterize the sex of immature plants in the vegetative state. To differentiate males from females of T. occidentalis, two molecular assays were thereupon developed based on polymerase chain reaction (PCR) to genotype sex-specific sequence variation either through restriction by Mfe1 or the direct use of sex-specific primers. Both assays require standard laboratory conditions to reach a certainty of 94.3% for females and 95.7% for males from the studied samples. With the inclusion of additional landraces, medium to largescale farms growing T. occidentalis as a crop can readily benefit from an early determination of the sex of plants. [ABSTRACT FROM AUTHOR]

There are different approaches and frameworks for the assessment of sustainability in agriculture and food systems, but only a few of them focus on crops. This gap is even more evident when it comes to the so-called neglected and underutilised species (NUS). To bridge this gap, the present paper describes an approach for the assessment of the environmental, social and economic sustainability of NUS developed within the project SUSTLIVES (Sustaining and improving local crop patrimony in Burkina Faso and Niger for better lives and ecosystems). The indicators identified through a literature review, based on the Web of Science, have been integrated with other indicators used for sustainability evaluation in the agrifood sector. Based on that, a sustainability assessment approach (list of indicators, evaluation methods and units; scoring system and mode of aggregation of scores; reference crops for the selected NUS) was developed. Then, two workshops were organized in Niamey (January 2023) and Ouagadougou (February 2023) to validate the sustainability assessment approach. The validated sustainability assessment matrix contains 27 indicators divided into different themes covering the three dimensions of sustainability: environmental (environmental integrity, agronomic performance and productivity), social (cultural importance and relevance, nutritional quality and diversity, employment, equity and accessibility) and economic (competitiveness, profitability). A scoring system was proposed for each indicator; from 0 (unsustainable) to 10 (very sustainable) with 5 corresponding to the sustainability benchmark value. Besides sustainability assessment, the developed approach allows selecting the NUS with the highest potential in view of their promotion and the development of their value chains. [ABSTRACT FROM AUTHOR]

Amaranths (Amaranthus L.) are multi-use crop species renowned for their nutritional quality and their tolerance to biotic and abiotic stresses. Since the soil salinity of croplands is a growing problem worldwide, we tested the salinity tolerance of six grain and two leaf cultivars of Amaranthus cruentus L. The plants were grown for 53 days under hydroponic conditions at 0, 50 and 100 mM NaCl. We investigated the growth rate, photosynthetic activity, mineral content, pigments and biochemical compounds involved in oxidative stress. Although 100 mM NaCl always decreased biomass production, we highlighted Don Leon and K91 as tolerant cultivars under moderate salt stress (50 mM NaCl). Under salinity, sodium accumulated more in the shoots than in the roots, particularly in the stems. Sodium accumulation in the plants decreased the net photosynthetic rate, transpiration rate and stomatal conductance but increased water use efficiency, and it decreased chlorophyll, betalain and polyphenol content in the leaves. It also decreased the foliar content of calcium, magnesium and potassium but not the iron and zinc content. The physiological parameters responded differently to sodium accumulation depending on the cultivar, suggesting a different relative importance of ionic and osmotic phases of salt stress among cultivars. Our results allowed us to identify the morpho-physiological traits of the cultivars with different salt tolerance levels.

Climate change causes environmental variation worldwide, which is one of the most serious threats to global food security. In addition, more than 2 billion people in the world are reported to suffer from serious malnutrition, referred to as 'hidden hunger.' Dependence on only a few crops could lead to the loss of genetic diversity and high fragility of crop breeding in systems adapting to global scale climate change. The exploitation of underutilized species and genetic resources, referred to as orphan crops, could be a useful approach for resolving the issue of adaptability to environmental alteration, biodiversity preservation, and improvement of nutrient quality and quantity to ensure food security. Moreover, the use of these alternative crops will help to increase the human health benefits and the income of farmers in developing countries. In this review, we highlight the potential of orphan crops, especially amaranths, for use as vegetables and health-promoting nutritional components. This review highlights promising diversified sources of amaranth germplasms, their tolerance to abiotic stresses, and their nutritional, phytochemical, and antioxidant values for vegetable purposes. Betalains (betacyanins and betaxanthins), unique antioxidant components in amaranth vegetables, are also highlighted regarding their chemodiversity across amaranth germplasms and their stability and degradation. In addition, we discuss the physiological functions, antioxidant, antilipidemic, anticancer, and antimicrobial activities, as well as the biosynthesis pathway, molecular, biochemical, genetics, and genomic mechanisms of betalains in detail. [Display omitted] • Prospect of orphan crops and amaranth species for future food systems. • Adaptation to the environment and nutrition of orphan crops and amaranth species. • Diverse physiological functions of betalains. • Biosynthesis pathway and molecular, biochemical and genomic mechanisms of betalains. [ABSTRACT FROM AUTHOR]

Societal Impact Statement Using Taro (Colocasia esculenta) as a case study, we examine how perception gaps contribute to negative feedback loops that create or maintain the orphan status of certain crops. For students and researchers seeking uncrowded areas for study, orphan crops and crop‐wild‐relatives offer large open spaces, figuratively and literally. Learning how to see what has not been seen may in turn help us to reduce our global dependence on very few crops, and the risks that follow from this. The combination of climate change and variability and increasing population has painted a dark picture of future food security for many regions in the world where resources are scarce. The key to future food and nutrition security may very well lie in unlocking the untapped potential of orphan and overlooked crops. Summary The present distribution of taro (Colocasia esculenta), as a cultivated food plant, extends from southern to northern Africa, western Asia to eastern Asia, throughout Southeast Asia and the Pacific Islands, and through the Americas, from the USA to Brazil. Despite its vast geographical range, high nutritional value, and considerable trade as a fresh and processed crop, there has been relatively little interest in taro and its wild relatives among research funding agencies, and little effective or large‐scale assessment of production, trade and usage. Given the proven ability of this crop to grow under diverse climatic regimes, from the equatorial tropics to northern and southern temperate zones it may be useful to consider perception gaps that contribute to disregard of the crop. Here we suggest and discuss a range of perception gaps that together may explain the status of taro as an orphan crop. Perception gaps exist because of many factors: dogma, linguistic diversity, social biases, under‐research, limited physical visibility of living wild populations, poor archaeological visibility, missing production numbers and inaccurate distribution maps. These contributing factors are shared, to lesser or greater extent, by many other orphan crops, but the disjunction between actual utilization (significant) and research effort (minimal) may be greater for taro than for most other “orphans”.

• Colocasia esculenta is a future food crop with enormous nutritional and pharmaceutical potential. • Breeding advancement and biofortification as a way forward from orphan to adoption. • Comprehensive insight for understanding taro as zero wastage orphan food crop. • Screening diverse genotypes for bioactive compounds using the omics-based intervention. Taro (Colocasia esculenta) is one of the traditional crops with enormous nutritional and pharmaceutical potential as compared to the other tuber crops. It is evident from the available literature that different plant part of taro contains a combination of bioactive compounds such as tarin, polysaccharides (TPS1 and TPS2), alkaloids, polyphenols, and saponins. Anti-carcinogenic, anti-compulsive, anti-hyperglycemia, anti-hypertensive, anti-inflammatory, hepatoprotective, immunoprotective, and neuroprotective properties have been demonstrated for these bioactive compounds. Taro's unique characteristics, such as the presence of small-sized starch granules, resistant starch type, and hypoallergenic properties, have the potential to elevate its status from underutilized to wonder future crop. Poi is a traditionally processed product of taro that has medicinal properties. Other processed products of taro are taro flour, cookies, noodles, achu and it is also a major constituent of baby food products due to its easily digestible nature. The documentation of traditional uses of taro food products in rural communities, as well as the quantification of bioactive compounds, demonstrate taro's vast potential as functional food products and in drug development. Hence, screening diverse genotypes for bioactive compounds from different continents could aid breeding efforts directed at taro biofortification. Commercialization of taro usage should be considered as a dietary intervention strategy for addressing malnutrition and hidden hunger in poor communities worldwide. In this review, we have comprehensively highlighted the scope of taro as a future food crop with enormous nutritional and antioxidant potential, biotechnological advancements, and the scope for breeding biofortified taro. [ABSTRACT FROM AUTHOR]

Tef is a highly nutritious gluten-free Ethiopian cereal with food-feed potential. However, its productivity is affected by lodging, weed infestation, terminal drought, small seed size, and shattering. Following the recent availability of tef genome sequences, we highlight the need to harness the benefits that this underutilised crop offers to improve food security. [ABSTRACT FROM AUTHOR]

Herbaceous vines, including the neglected crop Telfairia pedata, play a key role in small-holder livelihoods of Eastern Africa. Despite this species’ importance in enhancing agro-biodiversity, little is known about its distribution and growth performance in relation to environmental variables. We collected biophysical and environmental data, i.e., on climate and elevation, for 346 T. pedata vines across four districts of Northern Tanzania from September, 2019, to February, 2020. The four sites included Same, Lushoto, Muheza and Arumeru districts. We found that plants of T. pedata were mainly grown in elevations ranging between 900 to 1800 m above sea level with annual rainfall regimes of 1000 to 1400 mm. We recorded large abundance of T. pedata in Lushoto (46%) and Arumeru (28%) and observed that the number of fruits and fruit diameter were both positively correlated with elevation across the study districts. There was a significant effect of elevation on number of seeds, with Same district having more seeds across the studied districts. Rainfall had a significant effect on fruit diameter and number of seeds in the study districts. Furthermore, the tree species Albizia schimperiana was most commonly (in 40% of the cases) associated with T. pedata, followed by Persea americana (14%), and Croton macrostachyus (9%). We highlight that mountainous regions are ideal for this highly nutritious crop, and that native trees are of high importance for enriching this vine to current agro-ecosystems. Our findings will increase awareness on the importance of raising T. pedata crop, livelihood diversification, and increasing biodiversity through production of this orphan crop in small-holder farms.

Socio-demographic factors are often responsible for the persistent neglect of orphan crops such as Kersting's groundnut (Macrotyloma geocarpum) in sub-Saharan Africa. The objective of this study was to investigate the influence of socio-demographic factors on production of Kersting's groundnut (KG), as a basis for informing policy and development efforts in Benin. Data were collected from 305 randomly selected respondents from three major KG growing areas of Benin (Zou, Collines and Plateau). Descriptive statistics, analysis of variance, ordered logit models and Kendall's coefficient of concordance were used to analyse data, rank and prioritise production constraints across sociodemographic clusters. Factors such as land tenure, farm size, farming experience, education level, age and location had significant positive influence on cultivated KG plot size. Similarly, gender, education level and membership to cooperative groups had positive effects on farmer-reported yield. Furthermore, location in the department of Zou had a negative effect on reported yield. Production activities (sowing and harvesting) were significantly influenced by gender and education level. The most significant constraints were damage due to transhumance, lack of quality seed, changing rainfall patterns, production complexity and poor access to credit and land. Strategic actions for boosting KG productivity should include use of improved varieties, sustainable seed system, appropriate crop management practices, and improved access to credit. [ABSTRACT FROM AUTHOR]

Kersting's groundnut (Macrotyloma geocarpum (Harms) Maréchal & Baudet) is an important source of protein and essential nutrients that contribute to food security in West Africa. However, the crop is still underexploited by the populations and under-researched by the scientific community. This study aimed to investigate the genetic diversity and population structure of 217 Kersting's groundnut accessions from five origins using 886 DArTseq markers. Gene diversity was low and ranged from 0.049 to 0.064. The number of private alleles greatly varied among populations (42–192) and morphotypes (40–339). Moderate to very high levels of selfing and inbreeding were observed among populations (s = 56–85%, FIS = 0.389–0.736) and morphotypes (s = 57–82%, FIS = 0.400–0.691). Moreover, little to very high genetic differentiations were observed among populations (0.006 ≤ FIS ≤ 0.371) and morphotypes (0.029 ≤ FIS ≤ 0.307). Analysis of molecular variance partitioned 38.5% of the genetic variation among and 48.7% within populations (P < 0.001). Significant isolation by distance was detected between populations (R2 = 0.612, P = 0.011) and accessions (R2 = 0.499, P < 0.001). Discriminant analysis of principal components and neighbour joining consistently distinguished eight distinct clusters. These data provide a global picture of the existing genetic diversity for Kersting's groundnut and will guide the choice of breeding strategies to increase production. [ABSTRACT FROM AUTHOR]

Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop's genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology. [ABSTRACT FROM AUTHOR]

Background: Scarlet eggplant (Solanum aethiopicum gr. gilo) is a part of African indigenous vegetables and acknowledged as a source of variations in the breeding of Brinjal. Since its genetic diversity is still largely unexplored, therefore genetic diversity and population structure of this plant were investigated in this study. Methods and results: Scarlet eggplant germplasm made of fifty-two accessions originated from two districts of Rwanda was assessed by employing the iPBS-retrotransposon markers system. Twelve most polymorphic primers were employed for molecular characterization and they yielded 329 total bands whereupon 85.03% were polymorphic. The recorded mean polymorphism information content was 0.363 and other diversity indices such as; mean the effective number of alleles, mean Shannon's information index and gene diversity with the following values; 1.298, 0.300 and 0.187 respectively. A superior level of diversity was noticed among accessions from Musanze district. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) gathered scarlet germplasm in a divergence manner to their collection district. Analysis of molecular variance (AMOVA) displayed that the utmost variations (81%) in scarlet eggplant germplasm are resulting in differences within populations. Conclusions: The extensive diversity of scarlet eggplant in Rwanda might be used to form the base and genetic resource of an exhaustive breeding program of this economically important African indigenous vegetable. For instance, accessions MZE53 and GKE11 might be proposed as parent candidates due to their high relative genetic distance (0.6781). [ABSTRACT FROM AUTHOR]

Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop’s genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology.

Enset (Ensete ventricosum), is a perennial herbaceous plant belonging to the family Musaceae, along with banana and plantain. Despite wild populations occurring in eastern, central and southern Africa, it is only in Ethiopia that the crop has been domesticated, where it is culturally and agriculturally symbolic as a food security crop. Although an under-researched orphan crop, enset serves as a staple food for about 20% of the Ethiopian population, comprising more than 20 million people, demonstrating its value in the country. Similar to banana and plantain, enset is heavily affected by plant-parasitic nematodes, with recent studies indicating record levels of infection by the root lesion nematode Pratylenchus goodeyi. Enset is propagated vegetatively using suckers that are purposely initiated from the mother corm. However, while banana and plantain suckers have proven to be a key source of nematode infection and spread, knowledge on the infection levels and role of enset suckers in nematode dissemination is lacking. Given the high levels of plant-parasitic nematodes reported in previous surveys, it is therefore speculated that planting material may act as a key source of nematode dissemination. To address this lack of information, we assessed enset planting material in four key enset growing zones in Ethiopia. A total of 340 enset sucker samples were collected from farmers and markets and analyzed for the presence of nematodes. Nematodes were extracted using a modified Baermann method over a period of 48 h. The root lesion nematode P. goodeyi was present in 100% of the samples, at various levels of infection. These conclusive results show that planting material is indeed a key source of nematode infection in enset, hence measures taken to ensure clean suckers for planting will certainly mitigate nematode infection and spread. The effect of nematode infection on yield and quality on enset remains to be investigated and would be a way forward to complement the nematode/disease studies conducted so far and add valuable knowledge to the current poorly known impact of pests and diseases.

The oyster nut, Telfairia pedata, a vine that grows on tall trees, is native only to Tanzania and Uganda. Its nuts are valued by the local population mainly because of their lactogenic properties. Despite its nutritional, economic, and environmental benefits and its low management demands, little is known about why this species has almost disappeared from local markets and farmlands. We selected 187 publications that described the current nutritional, environmental, and commercialization potential of Telfairia species as well as their socioeconomic importance, domestication, and utilization in East Africa. Most studies (60%) mentioned the nutritional and health benefits of Telfairia species, while 40% described their socioeconomic and environmental potentials. Almost half of the studies (47%) cited lack of alternative propagation methods to seeds, including cuttings, tissue culture, and grafting, as a constraint for oyster nut development. We conclude that studies on oyster nut production are rare despite its potential to contribute to food security, environmental conservation, and commercialization. The future of oyster nut production depends on the efforts by agriculturalists, conservationists, and nutritionists to conduct collaborative research and outreach programmes on this underutilized crop to diversify livelihoods of Tanzania's smallholder farmers. [ABSTRACT FROM AUTHOR]

Enset (Ensete ventricosum), is a perennial herbaceous plant belonging to the family Musaceae, along with banana and plantain. Despite wild populations occurring in eastern, central and southern Africa, it is only in Ethiopia that the crop has been domesticated, where it is culturally and agriculturally symbolic as a food security crop. Although an under-researched orphan crop, enset serves as a staple food for about 20% of the Ethiopian population, comprising more than 20 million people, demonstrating its value in the country. Similar to banana and plantain, enset is heavily affected by plant-parasitic nematodes, with recent studies indicating record levels of infection by the root lesion nematode Pratylenchus goodeyi. Enset is propagated vegetatively using suckers that are purposely initiated from the mother corm. However, while banana and plantain suckers have proven to be a key source of nematode infection and spread, knowledge on the infection levels and role of enset suckers in nematode dissemination is lacking. Given the high levels of plant-parasitic nematodes reported in previous surveys, it is therefore speculated that planting material may act as a key source of nematode dissemination. To address this lack of information, we assessed enset planting material in four key enset growing zones in Ethiopia. A total of 340 enset sucker samples were collected from farmers and markets and analyzed for the presence of nematodes. Nematodes were extracted using a modified Baermann method over a period of 48 h. The root lesion nematode P. goodeyi was present in 100% of the samples, at various levels of infection. These conclusive results show that planting material is indeed a key source of nematode infection in enset, hence measures taken to ensure clean suckers for planting will certainly mitigate nematode infection and spread. The effect of nematode infection on yield and quality on enset remains to be investigated and would be a way forward to complement the nematode/disease studies conducted so far and add valuable knowledge to the current poorly known impact of pests and diseases. [ABSTRACT FROM AUTHOR]

The combination of genomic, physiological, and population genetic research has accelerated the understanding and improvement of numerous crops. For nonmodel crops, the lack of interdisciplinary research hinders their improvement. Grain amaranth is an ancient nutritious pseudocereal that has been domesticated three times in different regions of the Americas. We present and employ PopAmaranth, a population genetic genome browser, which provides an accessible representation of the genetic variation of the threegrain amaranth species (Amaranthus hypochondriacus, Amaranthus cruentus, and Amaranthus caudatus) and two wild relatives (Amaranthus hybridus and Amaranthus quitensis) along the A. hypochondriacus reference sequence. We performed population-scale diversity and selection analysis from whole-genome sequencing data of 88 curated genetically and taxonomically unambiguously classified accessions. We employ the platform to show that genetic diversity in the water stress-related MIF1 gene declined during amaranth domestication and provide evidence for convergent saponin reduction between amaranth and quinoa. PopAmaranth is available through amaranthGDB at amaranthgdb.org/popamaranth.html. [ABSTRACT FROM AUTHOR]

Pearl millet [Pennisetum glaucum (L.) R. Br.] is an underutilized small grain, nutrient-rich cereal crop cultivated in the arid and semiarid tropics of Asia and Africa. However, several barriers exist that preclude the full exploitation of the crop such as low yield, inadequate processing technologies, lack of extension support and limited productive varieties. Furthermore, anti-nutritional factors in the grain such as polyphenols reduce digestibility, palatability and bio-availability of other nutrients. Reduction or elimination of these antinutritional factors through pre-treatments like boiling, cooking, roasting, soaking improves the nutritional quality of the grain. Underutilized pearl millet genetic resources and processing has the potential to contribute towards sustainable agriculture particularly in drought prone and marginal areas of Africa. This review focuses on nutritional value, pearl millet cultivation and utilization challenges, processing and value addition interventions to improve crop adoption and productivity in sub-Saharan Africa. [ABSTRACT FROM AUTHOR]

Tef is the most important and well adapted cereal crop in Ethiopia and grows better than other cereals both in biotic and abiotic stress conditions. In this study 93 tef accessions representative of various agro-ecologies of Ethiopia along with four improved varieties, one local check and six wild relatives were studied. The materials were genotyped with 12 simple sequence repeat markers (SSRs) to investigate the extent and structure of the genetic diversity of tef. A total of 152 alleles were detected indicating high polymorphism in the studied accessions. The number of alleles per polymorphic loci ranged from seven for CNLT 538 to 29 for CNLT150 with an average of 12.67. High average polymorphic information content (0.82) and average expected heterozygosity (0.86) also signifies the suitability and efficiency of SSR markers to discriminate among tef genotypes. Cluster, principal coordinate and structure analyses grouped the 98 tef genotypes and six wild relatives into four distinct classes. The groupings showed no special pattern despite the different regions of origins for the accessions; however, the five wild relatives were grouped together. The analysis of molecular variance and fixation index showed low genetic differentiation and high gene flow between regions revealing that much of the variability was attributed to within populations variation. Generally, the present study showed that there is high genetic variability with unstructured genetic pattern among the studied tef genotypes which implies the vitality of conserved tef germplasms at Ethiopian Biodiversity Institute and the impact of the seed exchange system on tef breeding activities in Ethiopia. [ABSTRACT FROM AUTHOR]

Finger millet (FM; Eleusine coracana (L.) Gaertn.) is becoming increasingly vulnerable to various climate-induced stresses, because of which the genetic and genomic resources will be important for improving the crop in the 21st century. Currently, sizable-untapped genetic resources exists that offer promise for FM improvement to biotic and abiotic stresses. Also, earlier reports elaborate on the potential FM genomic resources, such as molecular markers, genetic maps, and DNA sequence, but the data are scanty to support the efficient and accelerated delivery of the climate-smart FM varieties. This is partly attributable to the delayed availability of complete genome sequence (CGS) of FM. Following the latest developments in FM genomic research, based on the CGS, a diversity of genomic resources have been reported. The review, therefore, provided a detailed analysis on the FM genetic and genomic resources-aided interventions that could contribute to the three pillars of Climate-smart agriculture (CSA) for addressing FM production challenges under changing climate. Exceptionally, it presented enriched information on additional useful sources of variation within FM genetic resources that have been screened for improving FM tolerance to various climate-induced stresses. Also, it presents the novel opportunities for CSA that could come as a result of the recent availability of CGS data for revolutionizing the development of cutting-edge-molecular breeding tools. Specifically, emphasis was placed on genome-wide-based technologies, such as genomic selection (GS), gene pyramiding, and gene expression with the second-generation genomic biotechnologies, such as TILLING and EcoTILLING that are wanting and have received little attention. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Using Taro (Colocasia esculenta) as a case study, we examine how perception gaps contribute to negative feedback loops that create or maintain the orphan status of certain crops. For students and researchers seeking uncrowded areas for study, orphan crops and crop‐wild‐relatives offer large open spaces, figuratively and literally. Learning how to see what has not been seen may in turn help us to reduce our global dependence on very few crops, and the risks that follow from this. The combination of climate change and variability and increasing population has painted a dark picture of future food security for many regions in the world where resources are scarce. The key to future food and nutrition security may very well lie in unlocking the untapped potential of orphan and overlooked crops. Summary: The present distribution of taro (Colocasia esculenta), as a cultivated food plant, extends from southern to northern Africa, western Asia to eastern Asia, throughout Southeast Asia and the Pacific Islands, and through the Americas, from the USA to Brazil. Despite its vast geographical range, high nutritional value, and considerable trade as a fresh and processed crop, there has been relatively little interest in taro and its wild relatives among research funding agencies, and little effective or large‐scale assessment of production, trade and usage. Given the proven ability of this crop to grow under diverse climatic regimes, from the equatorial tropics to northern and southern temperate zones it may be useful to consider perception gaps that contribute to disregard of the crop. Here we suggest and discuss a range of perception gaps that together may explain the status of taro as an orphan crop. Perception gaps exist because of many factors: dogma, linguistic diversity, social biases, under‐research, limited physical visibility of living wild populations, poor archaeological visibility, missing production numbers and inaccurate distribution maps. These contributing factors are shared, to lesser or greater extent, by many other orphan crops, but the disjunction between actual utilization (significant) and research effort (minimal) may be greater for taro than for most other "orphans". [ABSTRACT FROM AUTHOR]

More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although orphan crops and their wild relatives have received little attentions from researchers for many years, genomic studies have recently been performed on these plants. Here, we provide an overview of genomic studies on orphan crops, with a focus on orphan cereals and their wild relatives. The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced. In addition to genomic benefits for orphan crop breeding, we discuss the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives (including weeds) and provide perspectives on genetic improvement of both orphan and major crops (including de novo domestication of orphan crops) in the coming genomic era. Orphan crops play important roles in global food and nutrition security and represent a broad gene pool. This article provides an overview of genomic studies on orphan crops and their wild relatives (including weeds) and discusses the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives. [ABSTRACT FROM AUTHOR]

Atriplex hortensis (2n = 2x = 18, 1C genome size ∼1.1 gigabases), also known as garden orach and mountain-spinach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae alliance (Chenopodiaceae sensu stricto, subfam. Chenopodioideae) that has spread in cultivation from its native primary domestication area in Eurasia to other temperate and subtropical regions worldwide. Atriplex L. is a highly complex but, as understood now, a monophyletic group of mainly halophytic and/or xerophytic plants, of which A. hortensis has been a vegetable of minor importance in some areas of Eurasia (from Central Asia to the Mediterranean) at least since antiquity. Nonetheless, it is a crop with tremendous nutritional potential due primarily to its exceptional leaf and seed protein quantities (approaching 30%) and quality (high levels of lysine). Although there is some literature describing the taxonomy and production of A. hortensis, there is a general lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic positioning, and future potential of the species. Here, we report the assembly of the first high-quality, chromosome-scale reference genome for A. hortensis cv. “Golden.” Long-read data from Oxford Nanopore’s MinION DNA sequencer was assembled with the program Canu and polished with Illumina short reads. Contigs were scaffolded to chromosome scale using chromatin-proximity maps (Hi-C) yielding a final assembly containing 1,325 scaffolds with a N50 of 98.9 Mb – with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-six percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy-(32%) and Copia-like (11%) long-terminal repeats. The annotation was completed using MAKER which identified 37,083 gene models and 2,555 tRNA genes. Completeness of the genome, assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) metric, identified 97.5% of the conserved orthologs as complete, with only 2.2% being duplicated, reflecting the diploid nature of A. hortensis. A resequencing panel of 21 wild, unimproved and cultivated A. hortensis accessions revealed three distinct populations with little variation within subpopulations. These resources provide vital information to better understand A. hortensis and facilitate future study.

Main conclusion: The diversification of food crops can improve our diets and address the effects of climate change, and in this context the orphan crop Chinese yam shows significant potential as a functional food. As the effects of climate change become increasingly visible even in temperate regions, there is an urgent need to diversify our crops in order to address hunger and malnutrition. This has led to the re-evaluation of neglected species such as Chinese yam (Dioscorea polystachya Turcz.), which has been cultivated for centuries in East Asia as a food crop and as a widely-used ingredient in traditional Chinese medicine. The tubers are rich in nutrients, but also contain bioactive metabolites such as resistant starches, steroidal sapogenins (like diosgenin), the storage protein dioscorin, and mucilage polysaccharides. These health-promoting products can help to prevent cardiovascular disease, diabetes, and disorders of the gut microbiome. Whereas most edible yams are tropical species, Chinese yam could be cultivated widely in Europe and other temperate regions to take advantage of its nutritional and bioactive properties. However, this is a laborious process and agronomic knowledge is fragmented. The underground tubers contain most of the starch, but are vulnerable to breaking and thus difficult to harvest. Breeding to improve tuber shape is complex given the dioecious nature of the species, the mostly vegetative reproduction via bulbils, and the presence of more than 100 chromosomes. Protocols have yet to be established for in vitro cultivation and genetic transformation, which limits the scope of research. This article summarizes the sparse research landscape and evaluates the nutritional and medical applications of Chinese yam. By highlighting the potential of Chinese yam tubers, we aim to encourage the adoption of this orphan crop as a novel functional food. [ABSTRACT FROM AUTHOR]

Atriplex hortensis (2 n = 2 x = 18, 1C genome size ∼1.1 gigabases), also known as garden orach and mountain-spinach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae alliance (Chenopodiaceae sensu stricto, subfam. Chenopodioideae) that has spread in cultivation from its native primary domestication area in Eurasia to other temperate and subtropical regions worldwide. Atriplex L. is a highly complex but, as understood now, a monophyletic group of mainly halophytic and/or xerophytic plants, of which A. hortensis has been a vegetable of minor importance in some areas of Eurasia (from Central Asia to the Mediterranean) at least since antiquity. Nonetheless, it is a crop with tremendous nutritional potential due primarily to its exceptional leaf and seed protein quantities (approaching 30%) and quality (high levels of lysine). Although there is some literature describing the taxonomy and production of A. hortensis , there is a general lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic positioning, and future potential of the species. Here, we report the assembly of the first high-quality, chromosome-scale reference genome for A. hortensis cv. "Golden." Long-read data from Oxford Nanopore's MinION DNA sequencer was assembled with the program Canu and polished with Illumina short reads. Contigs were scaffolded to chromosome scale using chromatin-proximity maps (Hi-C) yielding a final assembly containing 1,325 scaffolds with a N50 of 98.9 Mb – with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-six percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy-(32%) and Copia-like (11%) long-terminal repeats. The annotation was completed using MAKER which identified 37,083 gene models and 2,555 tRNA genes. Completeness of the genome, assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) metric, identified 97.5% of the conserved orthologs as complete, with only 2.2% being duplicated, reflecting the diploid nature of A. hortensis. A resequencing panel of 21 wild, unimproved and cultivated A. hortensis accessions revealed three distinct populations with little variation within subpopulations. These resources provide vital information to better understand A. hortensis and facilitate future study. [ABSTRACT FROM AUTHOR]

Thousands of plants have been selected as crops; yet, only a few are fully domesticated. The lack of adaptation to agroecological environments of many crop plants with few characteristic domestication traits potentially has genetic causes. Here, we investigate the incomplete domestication of an ancient grain from the Americas, amaranth. Although three grain amaranth species have been cultivated as crop for millennia, all three lack key domestication traits. We sequenced 121 crop and wild individuals to investigate the genomic signature of repeated incomplete adaptation. Our analysis shows that grain amaranth has been domesticated three times from a single wild ancestor. One trait that has been selected during domestication in all three grain species is the seed color, which changed from dark seeds to white seeds. We were able to map the genetic control of the seed color adaptation to two genomic regions on chromosomes 3 and 9, employing three independent mapping populations. Within the locus on chromosome 9, we identify an MYB-like transcription factor gene, a known regulator for seed color variation in other plant species. We identify a soft selective sweep in this genomic region in one of the crop species but not in the other two species. The demographic analysis of wild and domesticated amaranths revealed a population bottleneck predating the domestication of grain amaranth. Our results indicate that a reduced level of ancestral genetic variation did not prevent the selection of traits with a simple genetic architecture but may have limited the adaptation of complex domestication traits. [ABSTRACT FROM AUTHOR]

Storage ability of trifoliate yam (Dioscorea dumetorum) is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in D. dumetorum. To the best of our knowledge, the candidate genes responsible for the hardening of D. dumetorum have not been identified. Here, transcriptome analyses of D. dumetorum tubers were performed in yam tubers of four developmental stages: 4 months after emergence (4MAE), immediately after harvest (AH), 3 days after harvest (3DAH) and 14 days after harvest (14DAH) of four accessions (Bangou 1, Bayangam 2, Fonkouankem 1, and Ibo sweet 3) using RNA-Seq. In total, between AH and 3DAH, 165, 199, 128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3, respectively. Functional analysis of DEGs revealed that genes encoding for CELLULOSE SYNTHASE A (CESA), XYLAN O-ACETYLTRANSFERASE (XOAT), CHLOROPHYLL A/B BINDING PROTEIN1, 2, 3, 4 (LHCB1, LHCB2, LHCB3, and LCH4) and an MYB transcription factor were predominantly and significantly up-regulated 3DAH, implying that these genes were potentially involved in the PHH as confirmed by qRT-PCR. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into gene expression in yam tubers after harvest and valuable information for molecular breeding against the PHH.

Main conclusion: Required genetic resources for the improvement of agronomic, nutritional and economic value of rice bean are available in the world collection. International cooperative effort is required to utilize and conserve them. Rice bean [Vigna umbellata (Thunb.) Ohwi and Ohashi], a lesser known pulse among the Asiatic Vigna, has long been considered as a food security crop of small and marginal farmers of Southeast Asia. Considered as a nutritionally rich food and fodder, it is also a source of genes for biotic and abiotic stress tolerance including drought, soil acidity and storage pest. Although it spread from its centre of domestication in the Indo-China region to other parts around the world, it never became an important crop anywhere probably because of agronomic disadvantages. Crop improvement for determinate nature, good yield, less variable seed colour, pleasant organoleptic properties and lower antinutrients is required. Scanning of scientific literature indicates that genetic resources with desirable agronomic and nutritional traits exist within the current collection but are spread across countries. Genomic studies in the species indicate that except for insect resistance and aluminium toxicity tolerance, not much attention has been paid to decipher and utilize other stress tolerance and nutritional quality traits. Collaborative efforts towards improving farming, food, trade value and off-farm conservation of rice bean would not only help marginal farmers but will also help to preserve the yet to be explored genomic resources available in this sturdy pulse. [ABSTRACT FROM AUTHOR]

Introduction: Tef [Eragrostis tef (Zucc.) Trotter] is the major food crop in Ethiopia where it is annually cultivated on about 30% of the total area allocated to cereals. The productivity of tef is, however, significantly reduced by drought which can occur at either the early or the late developmental stage of the crop. Methodology: A total of 10,000 EMS (ethyl methane sulfonate) mutagenized M2 tef populations were screened first for early and second for terminal drought tolerance. The performance of candidate lines was investigated using diverse agronomical and physiological parameters. Results and discussion: Several promising lines were obtained for both early and terminal drought tolerance. Among these, genotypes with outstanding performance were found for two drought tolerant tef lines targeting early drought tolerance (dtt2 and dtt13) and three terminal drought tolerant lines targeting terminal drought tolerance (tdt9, tdt15 and tdt19). Conclusions: Candidate lines for both early and terminal drought tolerance will play vital roles in developing drought tolerance in tef improvement. [ABSTRACT FROM AUTHOR]

BACKGROUND Sand rice (Agriophyllum squarrosum) is an underutilized pseudocereal bearing edible seeds. In this study, the phenolics and antioxidant activity of sand rice seeds after cooking and in vitro digestion were extensively investigated. RESULTS: Total phenolic content (TPC) of the sand rice seeds was slightly increased whereas total flavonoid content (TFC) decreased after boiling. Furthermore, nine compounds were detected in the uncooked seeds, with hyperoside (169.19 ± 6.59 µg g−1 dry weight (DW)), protocatechuic acid (167.46 ± 7.21 µg g−1 DW), and rutin (83.15 ± 3.26 µg g−1 DW) as the major components. Apart from the bioaccessible phenolics in the aqueous fraction, these compounds retained in the solid residue of the porridge were released to varying degrees during simulated digestion. In addition, these phenolic extracts also exerted considerable antioxidant potency, which was positively correlated with their corresponding TPC, TFC, and phenolic profiles. CONCLUSION: These results indicated that both boiling and in vitro digestive treatments could considerably enhance the release of bioactive compounds and thus contribute antioxidant properties to sand rice porridge. These findings suggest that sand rice seed is a potential functional food and an excellent natural antioxidant source. © 2019 Society of Chemical Industry [ABSTRACT FROM AUTHOR]