Impacts of storage practices on the physical, culinary and sensory quality of Kponan yam (Dioscorea cayenensis-rotundata) from Côte d'Ivoire during storage

BACKGROUND

Kponan is the most popular yam (Dioscorea cayenensis-rotundata) variety in Côte d'Ivoire. Unfortunately, losses due to rotting during storage do not ensure a regular supply to markets. This study aimed to identify the impacts of cultivation and storage practices in the main production areas on physical, cooking and sensory characteristics of Kponan. To this end, yams grown in Bondoukou were stored in straw huts, those grown in Bouna in pits and those grown in Kouassi-Kouassikro in the open air, according to the practices of each producer.

RESULTS

Findings showed that yams grown in Kouassi-Kouassikro and stored in the open air recorded the highest rot rate (58.09%) compared to the rot rate of yams grown and stored in pits in Bouna (26.67%) and those grown and stored in straw huts in Bondoukou (53.34%). However, the weight losses were respectively 10.47% (Bouna), 28.57% (Kouassi-Kouassikro) and 36.19% (Bondoukou). Loss rates varied significantly from 43.80% (pits) to 100% (huts and open air). Furthermore, the browning indices were higher for yams grown in Kouassi-Kouassikro and freshly harvested (26.09) compared to the browning index recorded for yams grown and freshly harvested in Bouna (23.43) and in Bondoukou (24.73). Concerning the hardness of yams, it decreased during storage for yams grown and stored in pits in Bouna (38.94 to 25.20 N) and for those grown and stored in straw huts in Bondoukou (39. 39 to 26.42 N).

CONCLUSION

The shelf life and culinary and sensory characteristics of Kponan depend on the cultivation and storage practices of each producer. © 2023 Society of Chemical Industry.

Development and Application of an Atomic Absorption Spectrometry-Based Method to Quantify Magnesium in Leaves of Dioscorea polystachya

The Chinese yam (Dioscorea polystachya, DP) is known for the nutritional value of its tuber. Nevertheless, DP also has promising pharmacological properties. Compared with the tuber, the leaves of DP are still very little studied. However, it may be possible to draw conclusions about the plant quality based on the coloration of the leaves. Magnesium, as a component of chlorophyll, seems to play a role. Therefore, the aim of this research work was to develop an atomic absorption spectrometry-based method for the analysis of magnesium (285.2125 nm) in leaf extracts of DP following the graphite furnace sub-technique. The optimization of the pyrolysis and atomization temperatures resulted in 1500 °C and 1800 °C, respectively. The general presence of flavonoids in the extracts was detected and could explain the high pyrolysis temperature due to the potential complexation of magnesium. The elaborated method had linearity in a range of 1-10 µg L-1 (R2 = 0.9975). The limits of detection and quantification amounted to 0.23 µg L-1 and 2.00 µg L-1, respectively. The characteristic mass was 0.027 pg, and the recovery was 96.7-102.0%. Finally, the method was applied to extracts prepared from differently colored leaves of DP. Similar magnesium contents were obtained for extracts made of dried and fresh leaves. It is often assumed that the yellowing of the leaves is associated with reduced magnesium content. However, the results indicated that yellow leaves are not due to lower magnesium levels. This stimulates the future analysis of DP leaves considering other essential minerals such as molybdenum or manganese.

Prioritizing preferred traits in the yam value chain in Nigeria: a gender situation analysis

This study describes what did and did not work in the prioritization of preferred traits within the value chain of yam and associated food products (boiled and pounded yam) in Nigeria. Demand-led breeding protocols have enhanced participatory methods along gender lines to increase the clarity of information on the yam traits preferred by farmers and other end users. Drawing on the experience of the cross-cutting gender team at the National Root Crops Research Institute (NRCRI), Umudike, and partners, this study documents the successes and constraints in the use of gender-inclusive approaches for effective breeding. Methods in our gender studies involve critical assessment of the distinction between quantitative and qualitative research, with particular attention to measurement. Various techniques for data collection, such as interviews, observation, and archival studies, are assessed to locate their potential for constructing successful research projects. The methods used include participatory varietal selection, participatory plant breeding, focused discussions with farmer groups, value chain mapping, G+ tools, trait preferences (processing and consumption), triangulation of multi-disciplinary datasets, and social survey research. Yam production in southeast Nigeria is dominated by men, while women are the main processors. Gendered power play, access to resources, and decision-making have been found to constrain women's participation in yam production (and in yam research). Sex disaggregation was applied within the value chain studies to capture the complementarity and differences in the perceptions of women and men. The methods used facilitated the development and release to farmers in 2023 of three improved yam varieties with consumer-preferred characteristics such as high yield, high dry matter content, white tubers, and good boiling and pounding capability. The success stories also show that effective communication and cooperation within the gender cross-cutting team and farmer groups are important for better results. When gender specialists, food scientists, and breeders work together, innovations are created, challenges are overcome, and information is shared.

Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the Rapid and Sensitive Detection of Yam mosaic virus

Yam (Dioscorea spp.) productivity is constrained significantly by the lack of a formal seed system. Vegetative propagation, through tuber setts as 'seed' yams, encourages the recycling of virus-infected planting materials, contributing to high virus incidence and yield losses. Efforts are ongoing to increase the production of high-quality seed yams in a formal seed system to reduce virus-induced yield losses and enhance the crop's productivity and food security. Specific and sensitive diagnostic tests are imperative to prevent the multiplication of virus-infected materials contributing to a sustainable seed yam certification system. During routine indexing of yam accessions, discrepancies were observed between the results obtained from the reverse transcription loop-mediated isothermal amplification (RT-LAMP) test and those from reverse transcription polymerase chain reaction (RT-PCR); RT-LAMP failed to detect Yam mosaic virus (YMV) in some samples that tested positive by RT-PCR. This prompted the design of a new set of LAMP primers, YMV1-OPT primers. These primers detected as little as 0.1 fg/µL of purified RNA obtained from a YMV-infected plant, a sensitivity equivalent to that obtained with RT-PCR. RT-LAMP using YMV1-OPT primers is recommended for all future virus-indexing of seed yams for YMV, offering a rapid, sensitive, and cost-effective approach.

Varietal and environmental influences on organoleptic and cooking quality of water yam (Dioscorea alata) landraces

BACKGROUND

Yam is a major staple food that provides both energy (starch) and bioactive compounds. However, there is a lack of knowledge on its cooking quality. We have determined the cooking quality of five varieties of water yam (among those most appreciated by consumers), when they were steamed or boiled. The yams were grown in two contrasting locations with regard to pedoclimatic conditions.

RESULTS

Ratio of length to mean circumference of the tuber, difficulty to peel, cooking time, color attributes, hardness of steamed pulp, and dry matter (DM) and starch contents significantly varied among varieties. Cooking time and hardness of the cooked pulp, either steamed or boiled, were higher for tubers grown at the drier location, with vertisols, than at the rainy one, with a ferralitic soil. The raw pulp was richer in starch at the rainy location. We found no correlation between either textural properties or DM and the cooking time. A slight (r = 0.44) but significant correlation was recorded between the DM of the raw pulp and the hardness of the steamed product.

CONCLUSION

We propose a comprehensive multicriteria approach for determination of yam cooking quality, textural properties, color attributes and chemical composition, along with varietal and environmental influences. This approach takes into consideration the complexity of food quality, allows a better understanding of its determinants and provides a basis for useful guidelines for breeders. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Quantification of Allantoin in Yams (Dioscorea sp.) Using a 1H NMR Spectroscopic Method

Allantoin is an abundant component of yams and has been known as a skin protectant due to its pharmacological activities. In previous methods for allantoin determination using high-performance liquid chromatography (HPLC), the separation was unsatisfactory. We herein developed a ¹H quantitative nuclear magnetic resonance (qNMR) method for quantification of allantoin in the flesh and peel of yams. The method was carried out based on the relative ratio of signals integration of allantoin to a certain amount of the internal standard dimethyl sulfone (DMSO₂) and validated in terms of specificity, linearity (range 62.5-2000 μg/ml), sensitivity (limit of detection (LOD) and quantification (LOQ) 4.63 and 14.03 μg/ml, respectively), precision (RSD% 0.02-0.26), and recovery (86.35-92.11%). The method was then applied for the evaluation of allantoin in flesh and peel extracts of four different yams cultivated in Korea.

Structural analysis and inhibition capacity of dioscorin protein yam: Theoretical study by molecular docking and dynamic simulations

Proteases such as trypsins in the gut of Spodoptera frugiperda are responsible for breaking down dietary proteins into amino acids necessary for insect growth and development. In this study, we characterized the insecticidal potential of dioscorin, the storage protein of yam (Dioscorea alata), using molecular docking and molecular dynamics simulations to determine the interactions between trypsin enzymes and the protein inhibitor dioscorin. To achieve this, we used the three-dimensional structures of the trypsin-like digestive enzymes of S. frugiperda, a pest of corn and cotton, as receptors or target molecules. We performed protein-protein docking using Cluspro software, estimation of the binding free energy, and information on the dynamic and time-dependent behavior of dioscorin-trypsin complexes using the NAMD package. Our computational analysis showed that dioscorin can bind to the digestive trypsins of S. frugiperda, as confirmed by the affinity energy values (-1022.4 to -1236.9), stability of the complexes during the simulation trajectory, and binding free energy values between -57.3 and -66.9 kcal/mol. Additionally, dioscorin uses two reactive sites to bind trypsin, but the largest contribution to the interaction energy is made by amino acid residues between amino acid backbone positions 8-14 by hydrogen bonds, hydrophobic, and Van der Waals (VdW) interactions. VdW is the energy that makes the greatest contribution to the binding energy. Collectively, our findings demonstrate, for the first time, the binding capacity of the yam protein dioscorin to the digestive trypsin of S. frugiperda. These promising results suggest a possible bioinsecticide action of dioscorin.

Gender-Disaggregated Consumer Testing and Descriptive Sensory Analysis of Local and New Yam Varieties

Gender-disaggregated sensory evaluation has become an essential element that could enhance breeding activities by increasing the adoption of new varieties. The effect of age, sex and geographical location on descriptor preferences for boiled and pounded yam were studied using descriptive and consumer testing. Attributes with definitions and measurement scales were used to generate lexicons for boiled and pounded yam. Analytical tools employed for the inferential statistics were the independent t-test, analysis of variance, Kruskal-Wallis test, Mann-Whitney test and relative importance index (RII). Descriptive testing showed that all the D. rotundata varieties were good for boiling and pounding. The D. alata varieties afase soanyinto and afase biri were most liked, while afase pa and ahodenfo were disliked. Age had no significant effect on descriptor preferences. Being a female or male, however, influenced preferences for pounded yam descriptors such as mouldability, lumpiness and colour. The RII for the D. rotundata varieties (0.22-0.28) showed that they are all good varieties for boiling and pounding. The local D. alata varieties were still highly acceptable compared the new CRI varieties due to the aroma. Rural consumers preferred all the descriptors of boiled D. rotundata than urban consumers, whereas urban consumers liked the pounded yam varieties better than the rural consumers. Availability of the new yam varieties on local markets could therefore increase consumption and improve adoption.

with potential for biocontrol of yam anthracnose

Anthracnose disease caused by Colletotrichum gloeosporioides is one of the devastating diseases of yams (Dioscorea sp.) worldwide. In this study, we aimed to isolate endophytic actinobacteria from yam plants and to evaluate their potential for the control of yam anthracnose based on bioassays and genomic analyses. A total of 116 endophytic actinomycete strains were isolated from the surface-sterilized yam tissues from a yam orchard in Hainan Province, China. In total, 23 isolates showed antagonistic activity against C. gloeosporioides. An endophytic actinomycete, designated HNM0140^T, which exhibited strong antifungal activities, multiple biocontrol, and plant growth-promoting (PGP) traits was subsequently selected to colonize in the tissue-cultured seedlings of yam and was tested for its in vivo biocontrol potential on yam anthracnose. The results showed that treatment with strain HNM0140^T markedly reduced the severity and incidence of yam anthracnose under greenhouse conditions. Morphological and chemotaxonomic analyses showed that strain HNM0140^T was assigned to the genus Streptomyces. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain HNM0140^T formed a separate cluster together with Streptomyces lydicus ATCC 25470^T (99.45%), Streptomyces chattanoogensis NRRL ISP-5002^T (99.45%), and Streptomyces kronopolitis NEAU-ML8^T (98.97%). The phylogenomic tree also showed that strain HNM0140^T stably clustered with Streptomyces lydicus ATCC 25470^T. The ANI and dDDH between strain HNM0140^T and its closest related-type species were well below the recommended thresholds for species demarcation. Hence, based on the phylogenetic, genomic, and phenotypic analyses, strain HNM0140^T should represent a new streptomycete species named Streptomyces endophytica sp. nov. Genomic analysis revealed that strain HNM0140^T harbored 18 putative BGCs for secondary metabolites, some PGP-related genes, and several genes coding for antifungal enzymes. The presented results indicated that strain HNM0140^T was a promising biocontrol agent for yam anthracnose.

Overexpression of DoBAM1 from Yam (Dioscorea opposita Thunb.) Enhances Cold Tolerance in Transgenic Tobacco

β-amylase (BAM) plays an important role in plant development and response to abiotic stresses. In this study, 5 DoBAM members were identified in yam (Dioscorea opposita Thunb.). A novel β-amylase gene BAM1, (named DoBAM1), was isolated from yam varieties Bikeqi and Dahechangyu. The open reading frame (ORF) of DoBAM1 is 2806 bp and encodes 543 amino acids. Subcellular localization analysis indicates that DoBAM1 localizes to the cell membrane and cytoplasm. In the yam variety Dahechangyu, the starch content, β-amylase activity, and expression of DoBAM1 were characterized and found to all be higher than in Bikeqi. DoBAM1 overexpression in tobacco is shown to promote the accumulation of soluble sugar and chlorophyll content and to increase the activities of peroxidase (POD), superoxide dismutase (SOD), catalase (CAT), and β-amylase. Under cold treatment, we observed the induced upregulation of DoBAM1 and lower starch content and malondialdehyde (MDA) accumulation than in WT plants. In conclusion, these results demonstrate that DoBAM1 overexpression plays an advanced role in cold tolerance, at least in part by raising the levels of soluble sugars that are capable of acting as osmolytes or antioxidants.

Development and Validation of Quantitative Analysis Method for Phenanthrenes in Peels of the Dioscorea Genus

Phenanthrenes are bioactive phenolic compounds found in genus Dioscorea, in which they are distributed more in peel than in flesh. Recent studies on phenanthrenes from Dioscorea sp. peels have revealed the potential for valuable biomaterials. Herein, an analytical method using high-performance liquid chromatography (HPLC) for quantitation of bioactive phenanthrenes was developed and validated. The calibration curves were obtained using the phenanthrenes (1-3) previously isolated from Dioscorea batatas concentrations in the range of 0.625-20.00 μg/ml with a satisfactory coefficient of determination (R²) of 0.999. The limit of detection (LOD) and the limit of quantification (LOQ) values of the isolated phenanthrenes ranged from 0.78-0.89 and 2.38-2.71 μg/ml, respectively. The intraday and interday precision ranged from 0.25-7.58%. The recoveries of the isolated phenanthrenes were from 95 to 100% at concentrations of 1.25, 2.5, and 5.0 μg/ml. Additionally, phenanthrenes (1-3) were found in all investigated peel extracts. Hence, the developed method was encouraging for the quantitative analysis of phenanthrenes in genus Dioscorea.

Green Crop Yam-Derived Carbons: Off-Plane Active Sites for Oxygen Electroreduction Identified by First-Principles

Plant-derived nonprecious metal catalysts are considered one of the promising candidates of platinum for oxygen reduction reaction (ORR). In this work, the typical microscopic morphology of fresh green crop yam is first detected by cryoscanning electronic microscopy. Using the green and widely sourced yam with spherical starch in nature as a precursor, well-defined spherical carbons are prepared via hypersaline-assisted hydrothermal carbonization and NH₃activation, featuring a high heteroatom doping level and a hierarchical porous structure. Experimental results and density functional theory (DFT) calculations reveal that diverse off-plane Fe-N_x-C_y ensembles on the spherical carbons trigger the high performance that exceeds state-of-art Pt/C and most reported carbon catalysts toward ORR in a KOH solution. The increased charge density and the bond length of Fe coordinated in the sites should be responsible for the significantly improved property. The easily editing of off-plane active sites from the simple carbon morphology may shed light on optimizing nonprecious carbons as next-generation catalysts for ORR.

Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm

Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera Badnavirus, Petuvirus and Cavemovirus has been described. Such endogenous badnaviral elements pose challenges to the development of nucleic acid-based diagnostic methods for episomal virus infections and decisions on health certification for international movement of germplasm and seed. One major food security crop affected is yam (Dioscorea spp.). A diverse range of Dioscorea bacilliform viruses (DBVs), and endogenous DBV (eDBV) sequences have been found to be widespread in yams cultivated in West Africa and other parts of the world. This study outlines the development of multiplex PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE) to assist in the detection and analysis of eDBVs, through the example of analysing yam germplasm from Nigeria and Ghana. Primers targeting the three most prevalent DBV monophyletic species groups in West Africa were designed to improve DGGE resolution of complex eDBV sequence fingerprints. Multiplex PCR-DGGE with the addition of a tailor-made DGGE sequence marker enables rapid comparison of endogenous badnaviral sequence diversity across germplasm, as illustrated in this study for eDBV diversity in yam.

[Status of soil fertility, nutrient balance, and environmental risk assessment in yam production of North China Plain]

Taking the main production area of yam in North China Plain as the research area, we analyzed the status of soil fertility and fertilizer application in yam production through field investigation and tracking monitoring, examined soil nutrient balance using the input-output model of nutrients in agricultural system, and assessed the environmental risks in the yam planting system. The results showed that: 1) the contents of soil organic matter and total N were extremely low, and the contents of available P and available Zn were both low; both nitrate and available Cu contents were at the middle level, the contents of soil slowly available K, available S, and exchangeable Ca and Mg were all extremely high, the contents of available K, available Fe, and available Mn were all at high level; 2) The nitrogen (N), phosphorus (P₂O₅), and potassium (K₂O) inputs were 575-943 kg·hm^-2, 341-981 kg·hm^-2, and 655-1219 kg·hm^-2 during the whole growth period of yam, with chemical fertilizer accounting for 83.0%, 88.6%, and 91.3%, respectively; The input imbalance between organic and inorganic fertilizer, as well as the excessive nutrients input were prominent; 3) The surplus rate of soil nitrogen, phosphorus and potassium reached 271.14 kg·hm^-2, 466.34 kg·hm^-2, and 739.97 kg·hm^-2, with corresponding surplus ratio of 48.7%, 258.1%, and 324.5%, respectively, which all exceeded the environmental safety threshold and were classified as moderate risk, severe risk, and severe risk, respectively. The overall environmental risk caused by chemical fertilizer application in yam production had reached severe risk level.

Strategies to combat the problem of yam anthracnose disease: Status and prospects

Yam (Dioscorea spp.) anthracnose, caused by Colletotrichum alatae, is the most devastating fungal disease of yam in West Africa, leading to 50%-90% of tuber yield losses in severe cases. In some instances, plants die without producing any tubers or each shoot may produce several small tubers before it dies if the disease strikes early. C. alatae affects all parts of the yam plant at all stages of development, including leaves, stems, tubers, and seeds of yams, and it is highly prevalent in the yam belt region and other yam-producing countries in the world. Traditional methods adopted by farmers to control the disease have not been very successful. Fungicides have also failed to provide long-lasting control. Although conventional breeding and genomics-assisted breeding have been used to develop some level of resistance to anthracnose in Dioscorea alata, the appearance of new and more virulent strains makes the development of improved varieties with broad-spectrum and durable resistance critical. These shortcomings, coupled with interspecific incompatibility, dioecy, polyploidy, poor flowering, and the long breeding cycle of the crop, have prompted researchers to explore biotechnological techniques to complement conventional breeding to speed up crop improvement. Modern biotechnological tools have the potential of producing fungus-resistant cultivars, thereby bypassing the natural bottlenecks of traditional breeding. This article reviews the existing biotechnological strategies and proposes several approaches that could be adopted to develop anthracnose-resistant yam varieties for improved food security in West Africa.

Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor

A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA-DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).

Metabolite Profiling of Dioscorea (Yam) Leaves to Identify Bioactive Compounds Reveals Their Potential as Renewable Resources

Yams (Dioscorea spp.) are cultivated and consumed as edible tubers, while their leaves are discarded as waste or burned with negative environmental impact. Herein, the metabolites of two yam species (Danma, DAN; Dunggeunma, DUN), harvested in June, July, and August, were profiled using GC-TOF-MS and UHPLC-LTQ-Orbitrap-MS/MS and the antioxidant activity of the extracts was evaluated to stimulate the utilization of yam leaves as a by-product. We observed that the relative levels of amino acids, organic acids, sugars, and saponins decreased linearly with prolonged harvest time, while fatty acid, phenanthrene, and flavonoid levels gradually increased. Furthermore, the leaf extracts obtained in August exhibited the highest antioxidant activity. To determine the antioxidant-contributing metabolites, OPLS-DA was performed for the leaf metabolites of DAN and DUN leaves harvested in August. Hydroxytyrosol-glucoside, apigenin-rhamnoside, and rutin were more abundant in DUN, while luteolin, phenanthrene derivatives, epicatechin, and kaempferide were relatively higher in DAN and their respective metabolites were positively correlated with the antioxidant activity. Moreover, secondary metabolites were more abundant in the leaves than in the roots, and consequently, the antioxidant activity of the former was also higher. Overall, the potential value of yam leaves as a renewable source of bioactive compounds is proposed.

Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing

Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or "drip" tips filled with extracellular bacteria of the species Orrella dioscoreae.¹ This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and underground tubers, which also contain a small population of O. dioscoreae.^2,3 Despite apparent vertical transmission, the genome of O. dioscoreae does not show any of the hallmarks of genome erosion often found in hereditary symbionts (e.g., small genome size and accumulation of pseudogenes).^4-6 We investigated here the range and distribution of leaf symbiosis between D. sansibarensis and O. dioscoreae using preserved leaf samples from herbarium collections that were originally collected from various locations in Africa. We recovered DNA from the extracellular symbiont in all samples, showing that the symbiosis is widespread throughout continental Africa and Madagascar. Despite the degraded nature of this DNA, we constructed 17 symbiont genomes using de novo methods without relying on a reference. Phylogenetic and genomic analyses revealed that horizontal transmission of symbionts and horizontal gene transfer have shaped the evolution of the symbiont. These mechanisms could help explain lack of signs of reductive genome evolution despite an obligate host-associated lifestyle. Furthermore, phylogenetic analysis of D. sansibarensis based on plastid genomes revealed a strong geographical clustering of samples and provided evidence that the symbiosis originated at least 13 mya, earlier than previously estimated.³.

Variation in the Physical and Functional Properties of Yam (Dioscorea spp.) Flour Produced by Different Processing Techniques

Research on the processing of yam (Dioscorea spp.) into flour is aimed at optimizing techniques to obtain a material with high physicochemical and functional properties. The present study investigates the effect of the processing techniques on the levels of inulin, organic acids, total phenolics (TP), antioxidant capacity, and polyphenol oxidase (PPO) and peroxidase (POD) activities, as well as on the physicochemical properties of flour derived from two yam species-Dioscorea esculenta and Dioscorea bulbifera. All tubers were peeled and sliced, then subjected to different processing techniques through blanching, soaking, and drying. The results revealed that freeze-drying appears to be the best technique in achieving the highest whiteness index of yam flour. This coincided well with the low phenolics content and POD activity, which suggests a reduced enzymatic browning reaction in the freeze-dried yam flour. On the other hand, chemical analyses showed that D. esculenta and D. bulbifera flours have the highest levels of inulin (23.0 and 27.8 g/100 g DW, respectively) and succinic acid (7.96 and 7.65 g/100 g DW, respectively) in the samples subjected to direct oven-drying. Oven drying without pretreatment neither blanching nor water steeping maintained antioxidant activity in the flour derived from both D. esculenta and D. bulbifera.

Cultivation and possible domestication of feral and possibly wild yams (Dioscorea spp.) in Southwest Ethiopia: ethnobotanical and morphological evidence

The far Southwest Ethiopians transplant wild plant species to their gardens. One of such plant is the Dioscorea that we studied to assess the knowledge of wild yam and process of domestication. The study links two types of evidence to obtain insight about the process of yam domestication. We analyze two data sets derived from (1) ethnobotanical survey using 231 semi-structured interviews; and (2) morphological study in 47 yam accessions. Our study revealed that domestication is still active in some villages. Knowledge of yam domestication was shared by 44% of the farmers' even by those that have never practiced its domestication. Farmers who can describe the trend of domestication and the morphotypes of domesticate represented 21 and 28%, respectively. Farmers who have recent transplants in their garden varied from 4% in Bench to 10% in Sheko. The domestication process described by the two ethnic groups is similar. The duration of domestication can take up to six years, but with most of the individuals, it only takes three to five years. By linking the two types of evidence, two evolutionary processes are distinguished: (1) populations of recent domesticate expressing a domestication syndrome possibly belongs to the wild D. abyssinica or D. praehensilis, and (2) plants of incipient domesticate that might be derived from volunteers or diverse types of hybrids. Each of these processes can lead to integration of wild genotypes into the cultivated gene pool, and hence, enhance genetic diversity of cultivated yams. The domestication practices of traditional farmers should thus be taken into account if yam conservation and improvement plans need to be established.

Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum

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.

Near-infrared spectroscopy applications for high-throughput phenotyping for cassava and yam: A review

The review aimed to identify the different high‐throughput phenotyping (HTP) techniques that used for quality evaluation in cassava and yam breeding programmes, and this has provided insights towards the development of metrics and their application in cassava and yam improvements. A systematic review of the published research articles involved the use of NIRS in analysing the quality traits of cassava and yam was carried out, and Scopus, Science Direct, Web of Sciences and Google Scholar were searched. The results of the review established that NIRS could be used in understanding the chemical constituents (carbohydrate, protein, vitamins, minerals, carotenoids, moisture, starch, etc.) for high‐throughput phenotyping. This study provides preliminary evidence of the application of NIRS as an efficient and affordable procedure for HTP. However, the feasibility of using mid‐infrared spectroscopy (MIRS) and hyperspectral imaging (HSI) in combination with the NIRS could be further studied for quality traits phenotyping.

A review of varietal change in roots, tubers and bananas: consumer preferences and other drivers of adoption and implications for breeding

This review of the literature on varietal change in sub-Saharan Africa looks in detail at adoption of new varieties of bananas in Uganda, cassava in Nigeria, potato in Kenya, sweetpotato in Uganda and yams in Côte d'Ivoire. The review explored three hypotheses about drivers of varietal change. There was a strong confirmation for the hypothesis that insufficient priority given to consumer-preferred traits by breeding programmes contributes to the limited uptake of modern varieties (MVs) and low varietal turnover. Lack of evidence meant the second hypothesis of insufficient attention to understanding and responding to gender differences in consumer preferences for quality and post-harvest traits was unresolved. The evidence on the third hypothesis about the informal seed system contributing to slow uptake of MVs was mixed. In some cases, the informal system has contributed to rapid uptake of MVs, but often it appears to be a barrier with inconsistent varietal naming a major challenge.

Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)

BACKGROUND AND AIMS

Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample.

METHODS

We characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach.

KEY RESULTS

Diploid genotypes were more frequent than triploids and tetraploids worldwide. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. The genetic make-up of triploids and tetraploids suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced to the Caribbean region.

CONCLUSIONS

Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation.

A review of root, tuber and banana crops in developing countries: past, present and future

For many of the developing world's poorest farmers and food‐insecure people, roots, tubers, bananas and plantain crops (RTBs) serve as a critical source of food, nutrition and cash income. RTBs have been particularly important in areas where local agri‐food systems are under stress. Under such circumstances, growers, processors and traders often see opportunities to improve food security or increase their incomes with those crops due to shifting tastes and preferences for food and non‐food products. Since the early 1990s, cassava output surged in sub‐Saharan Africa, while potato production expanded rapidly in Asia. RTBs are consumed by over three billion people in developing countries with a market value of US$ 339 billion. This paper analyses the major changes in production, utilisation and trade of RTBs over the last six decades, assesses estimates of their future trajectory and offers recommendations so that they might achieve their full potential.

Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange

Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.

The Dioscorea Genus (Yam)-An Appraisal of Nutritional and Therapeutic Potentials

The quest for a food secure and safe world has led to continuous effort toward improvements of global food and health systems. While the developed countries seem to have these systems stabilized, some parts of the world still face enormous challenges. Yam (Dioscorea species) is an orphan crop, widely distributed globally; and has contributed enormously to food security especially in sub-Saharan Africa because of its role in providing nutritional benefits and income. Additionally, yam has non-nutritional components called bioactive compounds, which offer numerous health benefits ranging from prevention to treatment of degenerative diseases. Pharmaceutical application of diosgenin and dioscorin, among other compounds isolated from yam, has shown more prospects recently. Despite the benefits embedded in yam, reports on the nutritional and therapeutic potentials of yam have been fragmented and the diversity within the genus has led to much confusion. An overview of the nutritional and health importance of yam will harness the crop to meet its potential towards combating hunger and malnutrition, while improving global health. This review makes a conscious attempt to provide an overview regarding the nutritional, bioactive compositions and therapeutic potentials of yam diversity. Insights on how to increase its utilization for a greater impact are elucidated.

nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species)

This study investigated endophytic nitrogen-fixing bacteria isolated from two species of yam (water yam, Dioscorea alata L.; lesser yam, Dioscorea esculenta L.) grown in nutrient-poor alkaline soil conditions on Miyako Island, Okinawa, Japan. Two bacterial strains of the genus Rhizobium, S-93^T and S-62, were isolated. The phylogenetic tree, based on the almost-complete 16S rRNA gene sequences (1476 bp for each strain), placed them in a distinct clade, with Rhizobium miluonense CCBAU 41251^T, Rhizobium hainanense I66^T, Rhizobium multihospitium HAMBI 2975^T, Rhizobium freirei PRF 81^T and Rhizobium tropici CIAT 899^T being their closest species. Their bacterial fatty acid profile, with major components of C_19 : 0 cyclo ω8c and summed feature 8, as well as other phenotypic characteristics and DNA G+C content (59.65 mol%) indicated that the novel strains belong to the genus Rhizobium. Pairwise average nucleotide identity analyses separated the novel strains from their most closely related species with similarity values of 90.5, 88.9, 88.5, 84.5 and 84.4 % for R. multihospitium HAMBI 2975^T, R. tropici CIAT 899^T, R. hainanense CCBAU 57015^T, R. miluonense HAMBI 2971^T and R. freirei PRF 81^T, respectively; digital DNA–DNA hybridization values were in the range of 26–42 %. Considering the phenotypic characteristics as well as the genomic data, it is suggested that strains S-93^T and S-62 represent a new species, for which the name Rhizobium dioscoreae is proposed. The type strain is S-93^T (=NRIC 0988^T=NBRC 114257^T=DSM 110498^T).

High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing

Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. A total of 35,269 protein-encoding gene models as well as 9941 non-coding RNA genes were predicted, and functional annotations were assigned.

Influence of Adding Chinese Yam (Dioscorea opposita Thunb.) Flour on Dough Rheology, Gluten Structure, Baking Performance, and Antioxidant Properties of Bread

Impacts of wheat flour substituted with various levels of Chinese yam (Dioscorea opposita Thunb.) flour (from 0% to 25%) on the dough rheological characteristics, gluten structure, baking performance, and antioxidant properties of bread were investigated. The water absorption increased significantly (p < 0.05), while development time and stability decreased remarkably (p < 0.05) as the proportion of yam flour increased. SEM results indicated that the addition of yam flour destroyed the gluten network structure in the dough. Fourier Transform Infrared Spectroscopy (FTIR) spectra showed that addition of yam flour decreased the content of α-helix and β-sheet in gluten. With the increase in the proportion of yam flour, the specific volume and overall acceptability decreased (p < 0.05) whereas the total phenolics content (TPC), polysaccharides content, total flavonoids content (TFC), allantoin content, The 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging capability, fractal dimension, and hardness increased (p < 0.05). Overall, breads made of wheat flour replacement with no more than 15% Guihuai number 2 yam flour were of a high quality and had more antioxidant properties. These showed that Guihuai number 2 had broad application prospects in baked products.

Glyphosate in yam from Ghana

Glyphosate is used in Ghana on many crops including yam. There is the suspicion that there could be residue problems in the yam crop. Glyphosate as a polar compound is noted for its difficulty to be analysed in biological matrices. In this study, the method for glyphosate analysis based on FMOC-Cl derivatization was modified with a clean-up (CH2Cl2) step and validated to analyse glyphosate in yam by LC-MS/MS. The results showed that the validated method was efficient for the analysis of glyphosate in yam, with recoveries of 34%, linearity of 0.997, RSD of 7%, LOD of 0.04 mg kg-1, and LOQ of 0.12 mg kg-1. Out of 68 samples analysed from a field experiment and from markets, glyphosate was detected in 14 samples, but at levels below the LOQ. It is concluded that the yam contained glyphosate residues at very low levels which may not pose threat to human health.

Development of a cost-effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections

Using genome-wide single nucleotide polymorphism (SNP) discovery in greater yam (Discorea alata L.), 4,593 good quality SNPs were identified in 40 accessions. One hundred ninety six of these SNPs were selected to represent the overall dataset and used to design a competitive allele specific PCR array (KASPar). This array was validated on 141 accessions from the Tropical Plants Biological Resources Centre (CRB-PT) and CIRAD collections that encompass worldwide D. alata diversity. Overall, 129 SNPs were successfully converted as cost-effective genotyping tools. The results showed that the ploidy levels of accessions could be accurately estimated using this array. The rate of redundant accessions within the collections was high in agreement with the low genetic diversity of D. alata and its diversification by somatic clone selection. The overall diversity resulting from these 129 polymorphic SNPs was consistent with the findings of previously published studies. This KASPar array will be useful in collection management, ploidy level inference, while complementing accurate agro-morphological descriptions.

Nondairy ice cream based on fermented yam (Dioscorea sp.)

BACKGROUND

The demand for industrialized foods that contribute to health and well-being has characterized the new generation of consumers. Yam (Dioscorea sp.) is a nutritious food; however, it is not used very much in industrial food processes. The objective of this study was to develop and to characterize a truly dairy-free low-fat ice cream prepared from unfermented and fermented with yam dough.

RESULTS

The fermentation was conducted by Leuconostoc lactic CCMA 0415 remained viable (107 CFU/g) during 90 days of storage. The fermentation process reduced the starch concentration from 26.82% to 22.35% and the protein concentration from 4.68% to 3.99% and increased the concentration of some minerals (K, S, Cu, Mn, Zn, and Fe). The total phenolic contents for fermented and unfermented ice creams were 51 and 54 mg, respectively. The radical scavenging activity were 18% and 10% with the 1,1-diphenyl-2-picrylhydrazyl method and 44% and 26% with the 2,2'-azino-bis (3 ethylbenzo-thiazoline-6-sulfonic acid) method for the unfermented and fermented samples, respectively. The fermented and unfermented ice creams were both characterized as non-Newtonian fluids exhibiting pseudoplastic behaviors.

CONCLUSIONS

These results indicated that yam is a suitable substitute for milk, thus making it an option to produce edible lactose-free ice cream with low fat.

Root Branching and Nutrient Efficiency: Status and Way Forward in Root and Tuber Crops

Plants are immobile organisms that require roots to efficiently and cost-effectively exploit their habitat for water and nutrients. Plant root systems are dynamic structures capable of altering root branching, root angle, and root growth rates determining overall architecture. This plasticity involves belowground plant-root mediated synergies coupled through a continuum of environmental interactions and endogenous developmental processes facilitating plants to adapt to favorable or adverse soil conditions. Plant root branching is paramount to ensure adequate access to soil water and nutrients. Although substantial resources have been devoted toward this goal, significant knowledge gaps exist. In well-studied systems such as rice and maize, it has become evident that root branching plays a significant role in the acquisition of nutrients and other soil-based resources. In these crop species, specific root branching traits that confer enhanced nutrient acquisition are well-characterized and are already being incorporated into breeding populations. In contrast, the understanding of root branching in root and tuber crop productivity has lagged behind. In this review article, we highlight what is known about root branching in root and tuber crops (RTCs) and mark new research directions, such as the use novel phenotyping methods, examining the changes in root morphology and anatomy under nutrient stress, and germplasm screening with enhanced root architecture for more efficient nutrient capture. These directions will permit a better understanding of the interaction between root branching and nutrient acquisition in these globally important crop species.

Safety of Yam-Derived (Dioscorea rotundata) Foodstuffs-Chips, Flakes and Flour: Effect of Processing and Post-Processing Conditions

The production of yam-derived (Dioscorea rotundata) foodstuffs is mainly performed by small and medium scale processors that employ old traditional methods. This can lead to differences in quality from processor to processor, and from location to location, with consequent safety concerns. As such, the effects of processing and post-processing phases (i.e., storage, transport, etc.) on the safety of some yam-derived foodstuffs-namely chips, flakes, and flour-has been evaluated, with a focus on bacterial and fungal contamination, aflatoxins, pesticides, and heavy metals (Pb, Ni, Cd and Hg). Yams harvested and processed in Nigeria were screened, being that the country is the largest producer of the tuber, with 70⁻75% of the world production. Results highlighted no presence of pesticides, however, many samples showed high levels of bacterial and fungal contamination, together with heavy metal concentrations above the recommended safety levels. No trend was observed between the items considered; it was noticed, however, that samples purchased from the markets showed higher contamination levels than those freshly produced, especially regarding bacterial and aflatoxins presence. The processing stage was identified as the most critical, especially drying. Nonetheless, post-processing steps such as storage and handling at the point of sale also contributed for chemical contamination, such as aflatoxin and heavy metals. The results suggested that both the processing and post-processing phases have an impact on the safety of yam chips, flakes, and flour.

Effects of yam/leguminous crops intercropping on soil chemical and biological properties of yam field

We investigated the effects of yam/leguminous crops intercropping on soil chemical and biological properties as well as soil comprehensive fertility in a field experiment. Results showed that compared with the monoculture, both yam/alfalfa and yam/clover intercropping increased the concentrations of nitrate nitrogen (N), available phosphorus (P) and available potassium (K) in the 0-20 cm and 20-40 cm soil layers, while reduced soil pH and electrical conductivity (EC) in early growth period and rhizome rapid expansion period of yam. Intercropping with leguminous crops enhanced the activities of urease, alkaline phosphatase and catalase, and also enhanced soil basal respiration in the 0-20 cm and 20-40 cm soil layers during the whole growth period of yam. There was no influence of intercropping on soil sucrase activity and dehydrogenase activity. The effects of intercropping with leguminous crops on soil fertility at yam harvest were further analyzed by combining the membership function model and principal component analysis. Results showed that intercropping with leguminous crops could significantly increase the soil comprehensive fertility in the 0-20 cm and 20-40 cm soil layers. Therefore, it might be an effective measure to improve soil fertility and environmental quality, as well as alleviate continuous cropping obstacles of yam by yam/leguminous crops intercropping through enhancing soil biological diversity.

Effects of Planting and Processing Modes on the Degradation of Dithianon and Pyraclostrobin in Chinese Yam (Dioscorea spp.)

The yam (Dioscorea spp.) is widely cultivated in China. The degradation of dithianon and pyraclostrobin in yams with different planting and processing treatments was investigated in this article. An analytical method for two pesticides in yam and yam plant was developed, and recoveries were between 77% and 93%, with relative standard deviations from 0.8% to 7.4%, respectively. On the basis of this method, half-lives for plants grown on stakes versus plants grown without stakes were compared. The results indicated that the half-life for pesticide residues for plants grown on stakes versus plants grown without stakes differed as 6.7 versus 3.1 days for dithianon and 5.4 versus 5.2 days for pyraclostrobin. Dithianon was significantly influenced by planting mode because of its low stability under sunlight. The processing factors of various processing treatments (hot air-drying, vacuum freeze-drying, microwave vacuum-drying, infrared-drying, steaming, and boiling) were all <1, indicating that those processes can reduce residues of two pesticides at different levels. Significant amounts of residues were removed during the boiling treatment, whereas the others showed less effect.

A Risk Assessment Framework for Seed Degeneration: Informing an Integrated Seed Health Strategy for Vegetatively Propagated Crops

Pathogen buildup in vegetative planting material, termed seed degeneration, is a major problem in many low-income countries. When smallholder farmers use seed produced on-farm or acquired outside certified programs, it is often infected. We introduce a risk assessment framework for seed degeneration, evaluating the relative performance of individual and combined components of an integrated seed health strategy. The frequency distribution of management performance outcomes was evaluated for models incorporating biological and environmental heterogeneity, with the following results. (1) On-farm seed selection can perform as well as certified seed, if the rate of success in selecting healthy plants for seed production is high; (2) when choosing among within-season management strategies, external inoculum can determine the relative usefulness of 'incidence-altering management' (affecting the proportion of diseased plants/seeds) and 'rate-altering management' (affecting the rate of disease transmission in the field); (3) under severe disease scenarios, where it is difficult to implement management components at high levels of effectiveness, combining management components can be synergistic and keep seed degeneration below a threshold; (4) combining management components can also close the yield gap between average and worst-case scenarios. We also illustrate the potential for expert elicitation to provide parameter estimates when empirical data are unavailable. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Diversity of Root-knot Nematodes Associated with Tubers of Yam (Dioscorea spp.) Established Using Isozyme Analysis and Mitochondrial DNA-based Identification

The root-knot nematodes (RKN), Meloidogyne spp., represent an important threat to yam (Dioscorea spp.) production in West Africa. With the aim to establish the diversity of RKN species affecting yam tubers, for control and resistance screening purposes, surveys were conducted in the main yam producing areas of Nigeria. Galled tubers (N = 48) were collected from farmers' stores and markets in nine states in Nigeria and in one district in Ghana. RKN isolated from yam tubers were identified using enzyme phenotyping (esterase and malate dehydrogenase) and mitochondrial DNA (mtDNA) NADH dehydrogenase subunit 5 (Nad5) barcoding. Examination of 48 populations revealed that yam tubers were infested by Meloidogyne incognita (69%), followed by M. javanica (13%), M. enterolobii (2%), and M. arenaria (2%). Most of the tubers sampled (86%) were infected by a single species, and multiple species of RKN were detected in 14% of the samples. Results of both identification methods revealed the same species, confirming their accuracy for the identification of these tropical RKN species. In addition to M. incognita, M. javanica, and M. enterolobii, we report for the first time M. arenaria infecting yam tubers in Nigeria. This finding extends the list of yam pests and calls for caution when developing practices for yam pest management.

PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm

Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex ‘fingerprints’ composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm.

Cassava (Manihot esculenta Crantz) and Yam (Dioscorea spp.) Crops and Their Derived Foodstuffs: Safety, Security and Nutritional Value

Cassava (Manihot esculenta Crantz) and yam (Dioscorea spp.) are tropical crops consumed by ca. 2 billion people and represent the main source of carbohydrate and energy for the approximately 700 million people living in the tropical and sub-tropical areas. They are a guarantee of food security for developing countries. The production of these crops and the transformation into food-derived commodities is increasing, it represents a profitable business and farmers generate substantial income from their market. However, there are some important concerns related to the food safety and food security. The high post-harvest losses, mainly for yam, the contamination by endogenous toxic compounds, mainly for cassava, and the contamination by external agents (such as micotoxins, pesticides, and heavy metal) represent a depletion of economic value and income. The loss in the raw crops or the impossibility to market the derived foodstuffs, due to incompliance with food regulations, can seriously limit all yam tubers and the cassava roots processors, from farmers to household, from small-medium to large enterprises. One of the greatest challenges to overcome those concerns is the transformation of traditional or indigenous processing methods into modern industrial operations, from the crop storage to the adequate package of each derived foodstuff.

Evaluation of anti-inflammatory activity and standardisation of hydro-methanol extract of underground tuber of Dioscorea alata

Context The underground edible tuber of Dioscorea alata L. (Dioscoreaceae) is a functional food with high nutritive value and therapeutic potential. The tuber is known to possess anti-inflammatory properties in traditional medicine. Objective The present study explores the anti-inflammatory activity and standardisation of D. alata tuber hydromethanol extract. Materials and methods Hydromethanol extract (70%) of D. alata tuber was chemically characterised using HPLC and GC-MS techniques. Murine lymphocytes were cultured for 48 h with six different concentrations (0-80 μg/mL) of the extract. The expression of nitric oxide (NO), TNF-α, COX-1, COX-2, and PGE2 were evaluated using colorimetric and ELISA methods. Results Dioscorea alata extract inhibited the expression of NO and TNF-α with an IC50 value of 134.51 ± 6.75 and 113.30 ± 7.44 μg/mL, respectively. The IC50 values for inhibition of total COX, COX-1, COX-2 activities and PGE2 level were 41.96 ± 3.07, 141.41 ± 8.99, 32.50 ± 1.69, and 186.34 ± 15.36 μg/mL, respectively. Inhibition of PGE2 level and COX-2 activity was positively correlated (R(2) = 0.9393). Gallic acid (GA), 4-hydroxy benzoic acid (4HBA), syringic acid (SYA), p-coumaric acid (PCA), and myricetin (MY) were identified and quantified using HPLC. GC-MS analysis revealed the presence of 13 different phytocompounds such as hexadecanoic acid, methyl stearate, cinnamyl cinnamate, and squalene. Conclusion The D. alata extract significantly down-regulated the pro-inflammatory signals in a gradual manner compared with control (0 μg/mL). Different bioactive phytocompounds individually possessing anti-inflammatory activities contributed to the overall bioactivity of the D. alata tuber extract.

A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses

Yam (Dioscorea spp.) plants are potentially hosts to a diverse range of badnavirus species (genus Badnavirus, family Caulimoviridae), but their detection is complicated by the existence of integrated badnavirus sequences in some yam genomes. To date, only two badnavirus genomes have been characterised, namely, Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform SN virus (DBSNV). A further 10 tentative species in yam have been described based on their partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences, generically referred to here as Dioscorea bacilliform viruses (DBVs). Further characterisation of DBV species is necessary to determine which represent episomal viruses and which are only present as integrated badnavirus sequences in some yam genomes. In this study, a sequence-independent multiply-primed rolling circle amplification (RCA) method was evaluated for selective amplification of episomal DBV genomes. This resulted in the identification and characterisation of nine complete genomic sequences (7.4-7.7 kbp) of existing and previously undescribed DBV phylogenetic groups from Dioscorea alata and Dioscorea rotundata accessions. These new yam badnavirus genomes expand our understanding of the diversity and genomic organisation of DBVs, and assist the development of improved diagnostic tools. Our findings also suggest that mixed badnavirus infections occur relatively often in West African yam germplasm.

Therapeutic effects of Dioscorea on post-menopause-induced cardiac apoptosis in rats

OBJECTIVE

To evaluate the effects of Dioscorea on bilateral ovariectomies-induced cardiac Fasdependent and mitochondria-dependent apoptotic pathways.

METHODS

Forty-eight female Wistar rats at 6-7 months of age were equally divided into a sham-operated group, and a bilateral ovariectomized (OVX) group for 2 months, and the rats in the OVX group were further fed with 0, 250 or 750 mL/kg Dioscorea spp. daily in the 2nd month. The excised hearts were measured by positive terminal deoxynucleotidyltransferase UTP nick end labeling (TUNEL) assays, western blotting and reverse transcription-polymerase chain reaction.

RESULTS

Dioscorea spp. decreased OVX-induced cardiac TUNEL-positive apoptotic cells; decreased OVX-induced TNF-alpha, Fas ligand, Fas death receptors, Fas-associated death domain, activated caspase-8, and -3 (Fas pathways); decreased OVX-induced Bad, Bax, Bax-to-Bcl2 ratio, activated caspase-9, and -3 (mitochondria pathway).

CONCLUSIONS

Dioscorea spp. prevented ovariectomy-induced cardiac Fas-dependent and mitochondriadependent apoptotic pathways in rat models. The fifi ndings may provide possible therapeutic effects of dioscorea for potentially preventing cardiac apoptosis after ovariectomy or post-menopause.

Characterizing diversity based on nutritional and bioactive compositions of yam germplasm (Dioscorea spp.) commonly cultivated in China

Yams (Dioscorea spp.) are widely cultivated as edible resources and medical materials in China. Characterizing chemical compositions in yam germplasm is crucial to determine their diversity and suitability for food and medicine applications. In this study, a core germplasm containing 25 yam landraces was used to create an effective classification of usage by characterizing their nutritive and medicinal compositions. All studied landraces exhibited high contents of starch from 60.7% to 80.6% dry weight (DW), protein (6.3–12.2% DW), minerals (especially Mg 326.8–544.7 mg/kg DW), and essential amino acids. Allantoin and dioscin varied considerably, with values of 0.62–1.49% DW and 0.032–0.092% DW, respectively. The quality variability of 25 yam landraces was clearly separated in light of UPGMA clustering and principal component analysis (PCA). Using an eigenvalue ≥1 as the cutoff, the first three principal components accounted for most of the total variability (62.33%). Classification was achieved based on the results of the measured parameters and principal component analysis scores. The results are of great help in determining appropriate application strategies for yam germplasm in China.

Root System Architecture and Abiotic Stress Tolerance: Current Knowledge in Root and Tuber Crops

The challenge to produce more food for a rising global population on diminishing agricultural land is complicated by the effects of climate change on agricultural productivity. Although great progress has been made in crop improvement, so far most efforts have targeted above-ground traits. Roots are essential for plant adaptation and productivity, but are less studied due to the difficulty of observing them during the plant life cycle. Root system architecture (RSA), made up of structural features like root length, spread, number, and length of lateral roots, among others, exhibits great plasticity in response to environmental changes, and could be critical to developing crops with more efficient roots. Much of the research on root traits has thus far focused on the most common cereal crops and model plants. As cereal yields have reached their yield potential in some regions, understanding their root system may help overcome these plateaus. However, root and tuber crops (RTCs) such as potato, sweetpotato, cassava, and yam may hold more potential for providing food security in the future, and knowledge of their root system additionally focuses directly on the edible portion. Root-trait modeling for multiple stress scenarios, together with high-throughput phenotyping and genotyping techniques, robust databases, and data analytical pipelines, may provide a valuable base for a truly inclusive 'green revolution.' In the current review, we discuss RSA with special reference to RTCs, and how knowledge on genetics of RSA can be manipulated to improve their tolerance to abiotic stresses.

Effect of species, pretreatments, and drying methods on the functional and pasting properties of high-quality yam flour

The study investigated the functional properties of HQYF (high-quality yam flour) from tubers of four dioscorea species. The tubers were processed into HQYF using two pretreatments (potassium metabisulphite: 0.28%, 15 min; blanching: 70°C, 15 min) and drying methods (cabinet: 60°C, 48 h; sun drying: 3 days). Significant differences (P < 0.05) were observed in pasting characteristics of flours among the four species. The drying method significantly affected only the peak viscosity. The interactive effect of species, pretreatment, and drying methods on the functional properties was significant (P < 0.05) except for emulsification capacity, angle of repose, and least gelation concentration. The significant variation observed in most of the functional properties of the HQYF could contribute significantly to breeding programs of the yam species for diverse food applications. The pastes of flour from Dioscorea dumetorum pretreated with potassium metabisulphite and dried under a cabinet dryer were stable compared to other samples, hence will have better applications in products requiring lower retrogradation during freeze/thaw cycles.

The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed

Endogenous viral sequences are essentially 'fossil records' that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. The best studied of these events are those which yielded the geminivirus-related DNA elements found within the nuclear genomes of various Nicotiana species. Although other ssDNA virus-like sequences are included within the draft genomes of various plant species, it is not entirely certain that these are not contaminants. The Nicotiana geminivirus-related DNA elements therefore remain the only definitively proven instances of endogenous plant ssDNA virus sequences. Here, we characterize two new classes of endogenous plant virus sequence that are also apparently derived from ancient geminiviruses in the genus Begomovirus. These two endogenous geminivirus-like elements (EGV1 and EGV2) are present in the Dioscorea spp. of the Enantiophyllum clade. We used fluorescence in situ hybridization to confirm that the EGV1 sequences are integrated in the D. alata genome and showed that one or two ancestral EGV sequences likely became integrated more than 1.4 million years ago during or before the diversification of the Asian and African Enantiophyllum Dioscorea spp. Unexpectedly, we found evidence of natural selection actively favouring the maintenance of EGV-expressed replication-associated protein (Rep) amino acid sequences, which clearly indicates that functional EGV Rep proteins were probably expressed for prolonged periods following endogenization. Further, the detection in D. alata of EGV gene transcripts, small 21-24 nt RNAs that are apparently derived from these transcripts, and expressed Rep proteins, provides evidence that some EGV genes are possibly still functionally expressed in at least some of the Enantiophyllum clade species.

Clarifying the Dioscoreabuchananii Benth. species complex: a new potentially extinct subspecies for South Africa

The Dioscoreabuchananii complex is shown to comprise three species, one of which is divided into two subspecies, based on morphological data. Two species, Dioscorearupicola Kunth and Dioscoreamultiloba Kunth, are endemic or subendemic to South Africa and of widespread occurrence in KwaZulu Natal. They differ markedly from each other in inflorescence and floral morphology and appear to be ecologically differentiated. The third species, Dioscoreabuchananii Benth., is primarily found in southeastern tropical Africa, but a small number of specimens collected in South Africa in the late 19(th) and early 20(th) centuries are placed in an endemic subspecies, Dioscoreabuchananiisubsp.undatiloba (Baker) Wilkin. The latter taxon is a high priority in terms of rediscovery and conservation. Keys, descriptions, supporting information and illustrations are provided and made available online through eMonocot biodiversity informatics tools. Three nomenclatural acts are undertaken: two names are placed in synonymy and a new combination made.

The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct Badnavirus species

Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis-rotundata complex. We propose that these sequences should be termed 'endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resulting in a mosaic structure that is typical of most EPRVs characterized to date. Using complementary molecular approaches, we show that eDBVs belong to at least four distinct Badnavirus species, indicating multiple, independent, endogenization events. Phylogenetic analyses of eDBVs support and enrich the current taxonomy of yam badnaviruses and lead to the characterization of a new Badnavirus species in yam. The impact of eDBVs on diagnosis, yam germplasm conservation and movement, and breeding is discussed.