Metabolite profiling of yam (Dioscorea spp.) accessions for use in crop improvement programmes

Effects of Chinese Yam Polysaccharide on Intramuscular Fat and Fatty Acid Composition in Breast and Thigh Muscles of Broilers

The purpose of this study is to evaluate the influences of Chinese yam polysaccharide (CYP) dietary supplementation on the composition of intramuscular fat (IMF) and fatty acids (FA) in thigh and breast muscles of broilers. Three hundred and sixty healthy one-day-old broilers (the breed of Crossbred chicken is named 817) with gender-balanced and similar body weight (39 ± 1 g) were randomly allocated into four groups (control, CYP1, CYP2, and CYP3 groups). Broilers in the control group were only fed a basal diet, and broilers in CYP1 group were fed the same diets further supplemented with 250 mg/kg CYP, the CYP2 group was fed the same diets further supplemented with 500 mg/kg CYP, and the CYP3 group was fed the same diets further supplemented with 1000 mg/kg CYP, respectively. Each group consisted of three replicates and each replicate consisted of 30 birds. The feeding days were 48 days. The results observed that the CYP2 group (500 mg/kg) can up-regulate the mRNA expression levels of β-catenin in thigh muscle compared to the control group. At the same time, all CYP groups (CYP1, CYP2, and CYP3 groups) can up-regulate mRNA expression of Wnt1 and β-catenin in breast muscle, while mRNA expression of PPARγ and C/EBPα in breast and thigh muscles could be down-regulated (p < 0.05). In summary, 500 mg/kg of CYP dietary supplementation can reduce IMF content and improve the FAs composition, enhancing the nutritional value of chicken meat.

Lasiodiplodia iraniensis, a New Causal Agent of Tuber Rot on Yam (Dioscorea Species) Imported into the United States and Implications for Quarantine Decisions

One negative consequence of international trade of agricultural commodities is the inadvertent global spread of crop diseases. Yam (Dioscorea spp.) is a staple food crop in many countries and is traded globally. Most of the commercially traded yams in the United States are imported. In late 2020, samples of yam tubers from a commercial facility were submitted to the plant diagnostic clinic at the UF/IFAS Tropical Research and Education Center in Homestead, Florida. Samples showed rotten symptoms and were drawn from lots that were marked to be destroyed because the source of the rotting symptoms was unknown. Preliminary isolation showed that a fungus was consistently associated with the symptoms and was confirmed in the subsequent pathogenicity test as the causal agent. The fungus grew profusely on potato dextrose agar (PDA) with highly melanized hyphae. Matured conidia showed longitudinal striations. Based on its growth pattern and morphology, it was suspected that this fungus may be in the genus Lasiodiplodia. DNA-based identification using partial sequences of the internal transcribed spacer (ITS), β-tubulin (TUB2), 28S rDNA (LSU), and elongation factor alpha (EF1-α) genes confirmed the identity of the isolates as Lasiodiplodia iraniensis Abdollahz., Zare & A.J.L. Phillips (synonym: L. iranensis). This is the first report of L. iraniensis affecting yam and has implications for international trade. This finding will provide an important foundation for making quarantine decisions to prevent spread of this disease.

Molecular characterization of Cordyline virus 1 isolates infecting yam (Dioscorea spp)

Cordyline virus 1 (CoV1) is a velarivirus that has so far only been reported in ornamental Ti plants (Cordyline fruticosa). Using high-throughput sequencing, we identified CoV1 infection in yam accessions from Vanuatu. Using a specific RT-PCR assay, we found that CoV1 is also present and highly prevalent in Dioscorea alata, D. cayenensis, and D. trifida in Guadeloupe. Phylogenetic analysis showed that CoV1 isolates infecting yam in Guadeloupe display a low level of molecular diversity. These data provide insights into the transmission of CoV1 in yam in Guadeloupe.

Datasets from harmonised metabolic phenotyping of root, tuber and banana crop

Biochemical characterisation of germplasm collections and crop wild relatives (CWRs) facilitates the assessment of biological potential and the selection of breeding lines for crop improvement. Data from the biochemical characterisation of staple root, tuber and banana (RTB) crops, i.e. banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas) and yam (Dioscorea spp.), using a metabolomics approach is presented. The data support the previously published research article “Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops” (Price et al., 2020) [1].

Diversity panels for each crop, which included a variety of species, accessions, landraces and CWRs, were characterised. The biochemical profile for potato was based on five elite lines under abiotic stress. Metabolites were extracted from the tissue of foliage and storage organs (tuber, root and banana pulp) via solvent partition. Extracts were analysed via a combination of liquid chromatography – mass spectrometry (LC-MS), gas chromatography (GC)-MS, high pressure liquid chromatography with photodiode array detector (HPLC-PDA) and ultra performance liquid chromatography (UPLC)-PDA. Metabolites were identified by mass spectral matching to in-house libraries comprised from authentic standards and comparison to databases or previously published literature.

Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security

Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

Metabolome Profiling of Eight Chinese Yam (Dioscorea polystachya Turcz.) Varieties Reveals Metabolite Diversity and Variety Specific Uses

The Chinese yam (Dioscorea polystachya Turcz.) is an underutilized orphan tuber crop. However, in China it has been used in traditional medicine and food for centuries due to the presence of high starch, protein, fiber, and biologically active compounds. Knowledge on the metabolomic profiles of Chinese yam varieties is needed to explore the underutilized metabolites and variety specific uses. Here, the metabolome of eight Chinese yam varieties that are cultivated in different Chinese regions was profiled. A total of 431 metabolites belonging to different biochemical classes was detected. The majority of detected metabolites were classified as amino acids and derivatives. The different yam varieties offer unique uses; e.g., Hebei Ma Yam, Henan Huai Yam, and Henan Wild Yam were the most metabolically enriched and suitable as food and medicine. Yams from Hubei region had comparable nutritional profiles, which is most probably due to their geographical origin. Specifically, Henan Wild Yam had the highest concentrations of diosgenin, vitamins, and polysaccharides. Overall, this study presents a metabolome reference for D. polystachya varieties.

The effect of β-cyclocitral treatment on the carotenoid content of transgenic Marsh grapefruit (Citrus paradisi Macf.) suspension-cultured cells

This work reports the development of suspension culture system of transgenic Marsh grapefruit (Citrus paradisi Macf., Rutaceae) callus overexpressing bacterial phytoene synthase; and the use of this suspension culture to investigate the effects of β-cyclocitral on carotenoid content and composition. At a β-cyclocitral concentration of 0.5 mM and after ten days cultivation, analysis of the carotenoids showed a significant increase in the content of β-, α-carotene, and phytoene predominantly. The maximal increase in total provitamin A carotenoids content following β-cyclocitral application was ~2-fold higher than the control, reaching 245.8 μg/g DW. The trend for increased transcript levels of biosynthetic genes PSY and ZDS correlated with the enhancement of the content of these carotenes following β-cyclocitral treatment and GC-MS based metabolite profiling showed significant changes of metabolite levels across intermediary metabolism. These findings suggest that β-cyclocitral can act as a chemical elicitor, to enhance the formation of carotenes in citrus suspension-cultured cells (SCC), which could be utilized in studying the regulation of carotenoid biosynthesis and biotechnological application to the renewable production of nutritional carotenoids.

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.

Assessment of metabolic variability and diversity present in leaf, peel and pulp tissue of diploid and triploid Musa spp

Banana (Musa spp.) plants produce many health promoting compounds in leaf, peel and pulp. For a robust metabolic analysis of these tissues, leaf at five developmental stages were compared to assess suitable sampling practices. Results confirmed that the common sampling practise of leaf 3 is applicable for metabolic comparisons. The developed work flow was applied to analyse the metabolite diversity present in 18 different Musa varieties, providing baseline levels of metabolites in leaf, peel and pulp tissue. Correlation analysis was then used to ascertain whether similar trends can be detected in the three plant tissues of the diversity panel. The genome group displayed a dominant role in the composition of the metabolome in all three tissues. This led to the conclusion that a correlation between tissues was only possible within a genome group as the different parental backgrounds caused too great a variation in the metabolomes. It also suggests the metabolome could be used to monitor the interaction/hybridisation of genomes during breeding programmes.

A Transdisciplinary Approach for the Development of Sustainable Yam (Dioscorea sp.) Production in West Africa

Yam (Dioscorea sp.) is an understudied tuber crop despite its importance for food security, income generation, culture, and health in West Africa. Traditional yam cropping practices in West Africa deliver low yields and lead to environmental degradation. In the context of a ‘research for development’ project, we developed and implemented a participatory and transdisciplinary research approach as a means to derive more sustainable yam production practices. We identified and studied different soil and plant management technologies adapted to varying biophysical and socio-economic contexts. For this purpose, we established innovation platforms (IPs) in four yam growing regions of West Africa, to validate the new technologies and to promote their adoption. These co-developed technologies were set up and tested first in researcher-managed plots before doing the same in farmer-managed plots. The new technologies resulted in a significant increase in yam productivity compared to conventional practices. The results discussed in the IPs gained interest from regional stakeholders and were shared through the media at local and national levels. Overall, this development-focused research approach showcases the relevance of purposeful stakeholder involvement to improve agricultural research outcomes.

Potential of Neglected and Underutilized Yams (Dioscorea spp.) for Improving Nutritional Security and Health Benefits

Food and nutritional security are the major concerns in many countries of the world and may have potential to contribute to sustainable food systems under climate change. To address the food and nutritional insecurity, it has become extremely important to diversify the present-day agricultural system as well as to search for alternative food and feed ingredients. Some wild root and tuber crops occupy a remarkable position toward food security of the developing world due to their high calorific value and superior carbohydrate content. Yam (Dioscorea spp.) provides food and medicines to millions of people in the world especially in the tropics and sub tropics. It is recognized as the fourth most important tuber crop after potatoes, cassava, and sweet potatoes. It contributes about 10% of the total root and tubers production around the world. Yams also considered as famine food and plays a prime role in the food habit of small and marginal rural families and forest-dwelling communities during the food scarcity periods. These species are unique for their food, medicinal and economic values but their wider utilization is limited due to the presence of anti-nutritional compositions. This paper describes the ethnobotany of yam species in relation to their nutritional, anti-nutritional and pharmacological properties and highlights the potentiality for food and nutritional security for combating the “hidden hunger” caused by micronutrient deficiencies.

Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops

Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the available diversity due to lack of efficient germplasm characterization and structure. In recent years large-scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics-based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on-going genomic and phenotypic studies will enhance 'omics-wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization.

Metabolite profiling characterises chemotypes of Musa diploids and triploids at juvenile and pre-flowering growth stages

Bananas (Musa spp.) are consumed worldwide as dessert and cooking types. Edible banana varieties are for the most part seedless and sterile and therefore vegetatively propagated. This confers difficulties for breeding approaches against pressing biotic and abiotic threats and for the nutritional enhancement of banana pulp. A panel of banana accessions, representative of the diversity of wild and cultivated bananas, was analysed to assess the range of chemotypes available globally. The focus of this assessment was banana leaves at two growth stages (juvenile and pre-flowering), to see when during the plant growth metabolic differences can be established. The metabolic data corresponded to genomic trends reported in previous studies and demonstrated a link between metabolites/pathways and the genomes of M. acuminata and M. balbisiana. Furthermore, the vigour and resistance traits of M. balbisiana was connected to the phenolic composition and showed differences with the number of B genes in the hybrid accessions. Differences in the juvenile and pre-flowering data led to low correlation between the growth stages for prediction purposes.

Crop metabolomics: from diagnostics to assisted breeding

BACKGROUND

Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding.

AIM OF REVIEW

We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Translational metabolomics applied to crop breeding programs.