The literature in recent times lacks adequate report on the utilization and genetic improvement programmes on Dioscorea dumetorum. Despite the wide application of this yam species in agriculture and medicine, it suffers neglect while other species are becoming increasingly popular. Therefore, it is pertinent to focus on research that will bring this species to the limelight. The aim of the present study was to evaluate the ploidy levels, morphological traits and secondary metabolite profile of 53 accessions of D. dumetorum from six countries in West and Central Africa. Ploidy levels were determined using flow cytometry. Overall, 18 morphological traits were recorded from the above- and underground parts of the plant. The 53 accessions were subjected to statistical analyses using the data on ploidy levels, morphological traits and qualitative phytochemical screening. A total of 15 accessions from the generated clusters were selected for thin layer chromatographic and quantitative phytochemical analyses. The analyses revealed diploid (2x) and triploid (3x) levels in these accessions. The pruned dendrogram derived from agglomerative hierarchical clustering based on the distance matrix revealed three main groups, showing a relationship between sex and ploidy level in the accessions and exhibiting sufficient cluster variability that may be important in designing breeding programmes. The crop was also shown to possess metabolites such as alkaloids, saponins and flavonoids, which are known to be useful in the application of phytomedicine. Genetic variability observed among the yam accessions in this study can be used for breeding purposes and to broaden the genetic basis of the crop for efficient utilization of the genetic potential possessed by this species.

Sesame (Sesamum indicum L.) is one of the oldest and most nutritional oilseed crops, of which domestication history has been poorly understood. This study suggested that sesame has undergone domestication bottleneck during its use for a long time. In this investigation, the molecular analysis included 4.4 Mbp of the genomic DNA of sesame comprising stearoyl acyl desaturase (sad), fatty acid desaturase 2 (fad2) and omega 3 fatty acid desaturase (o3fad) genes in 99 accessions of four populations of sesame germplasm namely: wild species, landraces, improved cultivars and introgressed lines. Results indicated that the improved cultivars and landraces lost 46.6 and 36.7% of nucleotide diversity, respectively, which indicate that the genetic diversity of the crop had been eroded due to selection after domestication. However, there was no significant reduction in genetic diversity of improved cultivars compared with landraces, indicating that unique improved cultivars generated through crosses were of less frequency in this population. Moreover, introgressed lines retained only 17.77% (π) and 4.57% (θ) of landrace diversity. To evaluate the impact of selection across fatty acid biosynthetic pathway, individual nucleotide diversity at three major genes involved in the pathway was surveyed. The analysis between wild and improved cultivars supported positive selection in fad2 and o3fad loci. Though locus-to-locus sequence variation was observed, positive results with two most important loci supported selection after domestication. Reduced diversity in these critical quality governing genes in improved cultivars suggested that future sesame cultivation would benefit from the incorporation of alleles from sesame's wild relatives.

Microsatellites or simple sequence repeats (SSRs) are useful molecular markers allowing for efficient conservation and sustainable use of genetic resources of plant species. Development of SSR marker system for new species is a very expensive task and time consuming. Cross-species amplification of microsatellite loci is considered as a cost-effective approach for developing microsatellite markers for new species. The aim of this work was to examine the transferability of some SSR markers of two Arecaceae species (Astrocaryum aculeatum and Elaeis oleifera), in Acrocomia aculeata. Out of the total markers analysed 44% of the markers successfully amplified the genomic DNA in A. aculeata, of which 26% were polymorphic detecting a range of three to eight alleles with an average of 4.5 per locus. High average percentage of polymorphic loci (P= 71.2%) per provenance was obtained within a range of 57–100% detecting genetic variation in A. aculeata germplasm collections. The polymorphic markers detected a positive inbreeding coefficient (F>0) per locus revealing heterozygote deficiency in the accessions that were analysed. As the cross-amplification was at family level, in which the taxonomic distance is relatively wider between the sources (A. aculeatum and E. oleifera) and the target (A. aculeata) species, the amplification success was relatively low. However, the results are promising and implicated that high cross-amplification success could be achieved at species or genus level in A. aculeata. The markers will contribute towards the domestication of the potential macaw palm through realizing various studies such as population genetics, germplasm characterization, genetic improvement and conservation.

This article links the concept of access and benefit-sharing as it pertains to crop genetic resources to climate change adaptation and argues that systems for access and benefit-sharing can, and should, be designed to contribute to climate change adaptation for agriculture. The access and benefit-sharing provisions of the two international agreements that together provide the international legal framework for access and benefit-sharing – the Convention on Biological Diversity (with its Nagoya Protocol) and the International Treaty on Plant Genetic Resources for Food and Agriculture – are presented and analysed. How these agreements are implemented is central to adaptation, as the effects of climate change threaten crop genetic resources and future adaptive capacity, and, if properly maintained and utilized, crop genetic resources will be essential to climate change adaptation across the globe. This article, therefore, argues that an important adaptation strategy linked to such implementation is to direct benefit-sharing for crop genetic resources towards adaptation efforts and to ensure facilitated and efficient access to crop genetic resources for adaptation purposes. Some options for how this can be pursued at both the international and national level are offered.

Low-temperature stress is an important factor affecting the growth and development of rice in temperate and high-elevation areas. In this study, 220 germplasm lines were used for screening of tolerant genotypes, validation of molecular markers and identification of robust markers for seedling-stage chilling stress tolerance to be used in marker-assisted breeding (MAS) programme. The temperature regimes imposed in the growth chamber simulated cold-stress injuries at the seedling stages of the germplasm lines. The genotypes were classified into six classes: those having susceptible genotypes were classified into moderately and highly susceptible types, while tolerant types into moderately tolerant, tolerant, highly tolerant and very highly tolerant classes. Genotypes namely Langma, Umleng-1 and Geetanjali showed survival up to 25 d, which were better than the positive check Kalinga-III surviving up to 20 d under chilling stress. Ten simple sequence repeat (SSR) markers were tested for differentiation of genotypes. Individual use of SSR markers like RM284, RM286, RM85, RM341 and RM5746 can be applied in MAS breeding including combination use of non-pair markers like RM284, RM239 and RM85, which was even better than the combined use of RM284 and RM85. However, combined use of all ten markers can most effectively be employed for cold tolerance through MAS breeding.

Bioprospecting is the search for valuable products from natural sources. Given that most species are poorly known, a key question is where to search. Ethnodirected bioprospecting approaches use traditional knowledge in the process of selecting plants to screen for desired properties. A complementary approach is to utilize phylogenetic analyses based on traditional uses or known chemistry to identify lineages in which desired properties are most likely to be found. Novel discoveries of plant bioactivity from these approaches can aid the development of treatments for diseases with unmet medical needs. For example, neurological disorders are a growing concern, and psychoactive plants used in traditional medicine may provide botanical sources for bioactivity relevant for treating diseases related to the brain and nervous system. However, no systematic study has explored the diversity and phylogenetic distribution of psychoactive plants. We compiled a database of 501 psychoactive plant species and their properties from published sources. We mapped these plant attributes on a phylogenetic tree of all land plant genera and showed that psychoactive properties are not randomly distributed on the phylogeny of land plants; instead certain plant lineages show overabundance of psychoactive properties. Furthermore, employing a ‘hot nodes’ approach to identify these lineages, we can narrow down our search for novel psychoactive plants to 8.5% of all plant genera for psychoactivity in general and 1–4% for specific categories of psychoactivity investigated. Our results showcase the potential of using a phylogenetic approach to bioprospect plants for psychoactivity and can serve as foundation for future investigations.

Climate change-induced events are causing salinization of many rice-growing areas, requiring the identification of new sources of genetic variation for salt tolerance in plant genetic resources since commonly grown cultivars are sensitive to salt. To identify the level of salt tolerance across a wide range of genotypes, we used a multivariate screening method using multiple growth and physiological traits simultaneously. For this purpose, four indica, two japonica and two wild rice genotypes were grown hydroponically under 40 and 80 mM NaCl stresses; fourteen different growth, qualitative and physiological traits, e.g. plant height, biomass, root and shoot elongation rates, and tissue ion accumulation, were recorded. In general, indica varieties performed better than both japonica and wild species. Our approach identified the existence of qualitatively different mechanisms of salt tolerance across the genotypes. For example, Pokkali, a salt-tolerant indica variety, displayed both ‘Na exclusion’ and ‘ion balance’ mechanisms, whereas PSBRc50 and IR58 showed only ‘Na exclusion’, and the Japonica genotypes Banikat and Nipponbare showed only ‘ion balance’. The results demonstrated that the tolerance is dependent on the level of stress and that this varies between genotypes; Nipponbare is moderately tolerant to 40 mM NaCl but not to 80 mM. We also suggest that the use of multivariate analyses can simplify the complex salinity tolerance picture and can effectively reveal the salinity tolerant genotype from a wide range of germplasm. The results reported here identify different physiological mechanism of tolerance across the genotypes and provide a sound basis for future studies examining their underlying molecular mechanisms.

Root-knot nematodes (RKNs), Meloidogyne spp., are considered, worldwide, as one of the main pathogens of solanaceous crops, including pepper (Capsicum spp.). Restrictions on the use of standard nematicides have motivated the development and use of resistant cultivars and rootstocks. Three genes in pepper, called Me1, Me3 and N, confer resistance to the three main RKN species (Meloidogyne incognita, Meloidogyne javanica and Meloidogyne arenaria). However, their effectiveness seems to be limited because nematode populations that have overcome the resistance have been found, leading to a search for new sources of resistance and strategies to preserve their effectiveness. In two greenhouses and over a 7-month growing period, we evaluated the resistance to M. incognita and the agronomic behaviour as rootstocks of nine pepper (Capsicum annuum) accessions – HDA330 (Me1 carrier), Serrano Criollo de Morelos, (Me3 carrier), Yolo Wonder (partially resistant) and another six accessions of unknown resistance originating from cultivars well adapted to the local growing conditions. The resistance conferred by the Me1 gene was more robust than that conferred by Me3. Resistance to M. incognita was found in four new accessions: P13, CTL, CT5, and P14. In P13, the level of resistance was similar to that of HDA330. The resistant accessions showed better agronomic behaviour than the susceptible accessions, which was most noticeable towards the final of the growing period. Some accessions constitute a potential resource for use in the genetic breeding of RKN-resistant rootstocks.

Medicinal plants are the vital source of numerous structurally diverse pharmacologically active metabolites collectively called as secondary metabolites finding extensive applications in traditional systems of medicine and in pharmaceutical industries. Several distinctive and complex pathways operate in an interactive manner via metabolic networks that are responsible for the accumulation of such highly specialized metabolites. Secondary metabolites are believed to play a wide spectrum of physiological and functional roles in plants, many of which being investigated and supported by the experimental studies. Biosynthetic pathway related studies on various aspects in these medicinal plants have been found very tedious owing to several issues in plants such as considerably lower metabolite concentrations in native tissues, existence at different locations, and highly complex multi-step pathways, etc. Pathway elucidation and gene/enzyme discovery for studying metabolic pathway evolution and subsequent engineering could be better achieved by mining various pathway databases and reconstruction of metabolic networks available at different omics databases. Though medicinal plants have a limited range of genomic sequences available, however recently, next generation sequencing is being widely used to generate a comprehensive transcriptomic resource for these plants. It is anticipated that databases and resources generated from these studies are likely to play a key role towards the study and exploitation of metabolites from medicinal plants in near future. In this review, we have discussed next generation sequencing approaches, which were used for the generation of transcriptomic resources for several medicinally important plants. The relevance of transcriptomic approaches in curation of the pathways linked with the synthesis of major secondary metabolites along with their precursors of pharmaceutical importance in medicinal plants is also comprehensively analysed.

Genetic diversity of 30 common vetch (Vicia sativa L.) lines and cultivars obtained from various resources or collected from natural flora of Turkey was evaluated by using 55 sequence-related amplified polymorphism (SRAP) and five inter-simple sequence repeat (ISSR) primer sets, and their nuclear DNA contents were determined by flow cytometer. A total of 188 polymorphic loci were detected, with an average of 3.62 loci per primer. The percentage of polymorphic loci was 82.1%. The polymorphism information content values ranged from 0.12 to 0.96, with an average of 0.63. The genetic distance coefficients were in the range of 0.112–0.627. Cluster analysis revealed that the 27 lines and three cultivars could be divided into two main groups. No polyploidy was detected within any vetch lines tested while significant (P< 0.0001) nuclear DNA content differences were determined. The present study revealed that fast and accurate fingerprinting analysis could be done using SRAP and ISSR markers, which indicated existing significant variation among common vetch lines and cultivars.

Iron (Fe) and zinc (Zn) contents in hexaploid wheat are very low and are further reduced because of the removal of micronutrient-rich bran of wheat grains during milling and processing. Therefore, hexaploid wheat, its wild species and wheat–Aegilops kotschyi substitution lines were evaluated to identify the genome(s) carrying gene(s) for high Fe and Zn concentrations in bran and endosperm fractions of grains. It is reflected from the results that Triticum monococcum (acc. W463) may serve as a promising donor for biofortification of Fe, and Aegilops speltoides (acc. 3804) may serve as a promising donor for biofortification of Zn in the endosperm of cultivated wheat. Further, among the three wheat–Ae. kotschyi substitution lines, the higher concentration of Fe and Zn in endosperm fraction was observed in BC2F4 63-2-13-1. The work on precise transfer of useful gene(s) from 7Uk chromosome of this line is in progress to reduce linkage drag.

This paper aims to propose an international list of descriptors for Butia odorata (jelly palm), using scientific documentation methods and farmers' knowledge to allow the germplasm characterization for conservation and sustainable use. It is an attempt to promote the development of new approaches to documenting crop genetic resources using a blend of these two sources of knowledge, frequently perceived as conflicting. This long-lived and useful palm is a neglected and subutilized species, and its genetic diversity and associated knowledge are under severe erosion. A list of 11 morphological descriptors is proposed based on observations, literature review and discussions with farmers who know and use the plant. These descriptors were used to characterize 303 adult jelly palms conserved in situ. Descriptive results are presented. Only five morphological characteristics were reported by farmers as important to discriminate individual plants, indicating that farmers have simpler and more rapid ways to differentiate diversity than do the scientists based on their uses. Standard list of descriptors developed by ex situ conservationists are widely used by breeders, but they rarely reach out to farmers and other user groups, a fact that limits the full use of germplasm collections around the world. Conversely, farmer-based descriptors, which are the expression of deep knowledge of diversity and its deployment by traditional communities, are rarely considered by breeders, mainly because they are not available. In this paper, we support the idea that a blend of these two methods – in a standard format – is highly strategic to promote an effective in situ conservation-through-use approach.

Genetic diversity identified in the Capsicum genepool has been utilized extensively to improve pepper disease resistance, fruit quality and varied yield attributes. Little attention has been dedicated to evaluating the breadth of potential diversity within Capsicum for fresh-cut attributes and genetic enhancement of fresh-cut fruit quality. We evaluated fresh-cut attributes in pepper accessions with diverse fruit phenotype selected from available cultivars and the USDA, ARS Capsicum genebank. Subjective assessment of product quality and objective measurement of package atmospheric composition, tissue juice leakage and membrane electrolyte leakage after 7, 10 and 14 d of storage identified significant differences for fresh-cut attributes among as well as within sweet bell, large elongate, jalapeno and serrano germplasm. Sweet bell and large elongate fruited accessions generally exhibited increasing electrolyte leakage over days of storage, whereas jalapeno and serrano accessions maintained stable electrolyte leakage levels. Jalapeno and serrano fruit classes were typified by faster decline in package headspace O2 and accumulation in CO2 partial pressures in comparison to sweet bell and large elongated fruit classes. Regression analysis demonstrated a relationship between overall visual quality and electrolyte leakage after 14 d of storage for sweet bell and large elongated fruit classes. The results demonstrate extensive variation in Capsicum germplasm to improve pepper for fresh-cut applications and facilitate research to better understand physiological and heritable determinants of fresh-cut product quality.

Musa L. was previously separated into five sections (Eumusa, Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on basic chromosome numbers and morphological characters. However, several molecular analyses currently support restructuring of Musa species into two sections, Musa and Callimusa. The application of simple sequence repeat molecular marker analysis to Musa phylogeny provided valuable, supplemental information about the classification of, and relationships between, Musa species and subspecies. Totally, 28 accessions of Musa acuminata Colla subspecies and varieties and 25 accessions of other Musa species were evaluated; 12 primers produced 91 polymorphic bands, polymorphic information content ranged from 0.4473 to 0.8394 (average = 0.7226), indicating that the primers showed a high level of polymorphism. Our results generally agreed with previous phylogenetic analyses based on molecular data. One clade comprised species of sections Australimusa and Callimusa (X= 10/9); most species of sections Eumusa and Rhodochlamys (X= 11) formed the other clade. The relationships between most species were as expected; however, some species did not conform to findings of previous studies. A wide range of variability was observed in the M. acuminata complex. M. acuminata var. chinensis and M. acuminata subsp. 522 showed the most distant relationships to other subspecies: Musa laterita, Musa ornata and Musa velutina clustered with M. acuminata var. chinensis, suggesting that they may constitute a secondary gene pool for the improvement of cultivated bananas. Molecular data indicated that Musa tongbiguanensis Chen You & Yao-Ting Wu, which was observed and described by our research group in Yunnan, China, was a distinct, new species.

Mucuna pruriens (L.) DC is a tropical legume cover crop with promising nutritional and agronomic potentials. It is also a key source of 3,4 dihydroxy-L-phenylalanine (L-Dopa) – a precursor of dopamine used in the treatment of Parkinson's disease. However, lack of well-characterized germplasm plus poor accessibility to genomic resources has hindered its breeding programs. Furthermore, the cause and effect of various biotic and abiotic stresses impacting yield is also little studied. Systematic collection and evaluation of Indian germplasm by our group revealed presence of a diverse gene pool in India that can support a variety of breeding needs. The stability of L-Dopa trait across environments examined through Genotype and environment (G × E) interaction studies, as well as feasibility check on barcoding and phylogenetic analyses based on karyotype and conserved nuclear and chloroplast genes showed promising outcome. Germplasm screening for select biotic abiotic stresses identified resilient genotypes. Advances in use of DNA markers for diversity analysis, linkage map development, tagging of genes/quantitative trait loci for qualitative and quantitative traits, and progress in genomics are presented.

Periwinkle [Catharanthus roseus (L) G. Don] has become one of the very extensively investigated medicinal plants after the discovery of two powerful anti-cancer alkaloids, vinblastine and vincristine, in its leaves more than 50 years ago. These alkaloidal drugs are still in clinical use. Also, periwinkle is still the only source of these alkaloids and their precursors, catharanthine and vindoline. Low concentrations of these alkaloids in the plant and, therefore, high costs of their extraction have led to tremendous efforts towards understanding their biosynthesis and exploration of alternate ways of their production such as, chemical synthesis, cell, tissue and hairy root cultures, and metabolic engineering of heterologous organisms. Literature on this plant is quite voluminous, with an average of about 80 publications per year during last three decades (1985–2015). Nearly 60% of these publications are on physiology, biochemistry, cell and tissue culture, phytochemistry, metabolic and genetic engineering aspects. In spite of these efforts, an economically viable alternative to field-grown periwinkle plants as a source of these alkaloids has not yet been found. Biosynthesis of C. roseus alkaloids is a complex process involving many genes, enzymes, regulators, inter- and intra-cellular transporters, cell types, organelles and tissues and its current understanding is still considered to be incomplete to produce C. roseus alkaloids through metabolic engineering/synthetic biology. Till such time, breeding periwinkle varieties with higher concentrations of anti-cancer alkaloids for cultivation can be an alternate approach to meet the demand for these alkaloids and reduce their costs. While literature on cell and tissue culture, phytochemistry, metabolic and genetic engineering aspects of periwinkle has been reviewed periodically, crop production and plant breeding aspects have received little attention. In this paper, an attempt has been made to bring together published information on genetics and breeding of periwinkle as a medicinal plant. Some probable constraints which may have hindered taking up periwinkle breeding are identified. Initially, quite a few attempts have been made at genetic improvement of periwinkle through induced polyploidy, and subsequently through induced mutagenesis. Mutations, both natural and induced, provide a valuable resource for use in breeding and in functional and reverse genomics research. It is only during last 6–7 years, genetic diversity has been assessed using molecular markers and very recently molecular markers have been identified for marker-assisted selection for alkaloid yield.

Sweet sorghum is highly coveted to contribute and take up food and energy challenges. A collection of 84 West Africa landraces mostly from Senegal and four control cultivars were screened to identify relevant accessions and trait combination for multi-purpose (sugar/grain/biomass). The implication of photoperiod sensitivity was particularly addressed. A total of 20 traits related to phenology, morphology, grain and sugar production were assessed in two sowing dates (July and August) at CNRA Bambey in Senegal. Late sowing resulted in shortened vegetative phase and a significant decrease in traits related to plant size, stem sugar, biomass and grain productions. Broad-sense heritability was moderate to high for most of the phenology, morphology, grain and sugar-related traits, suggesting their interest for breeding. All the traits related to plant size were positively correlated with plant sugar production except plant height. A cluster analysis identified three groups contrasting in their ability to combine sugar, grain or fodder production based on 18 traits measured for the early sowing. Clusters I and III were suitable for one purpose: grain and sugar, respectively. Cluster II was the most suitable for multi-purpose, showing the best trade-off among grain, sugar and vegetative biomass production. The best accessions for stem sugar yield belonged to durra, caudatum and their intermediate types. The relationship between internode size and sweetness should be further studied, in particular exploring their relationship with internode tissue anatomy. Further studies are also needed to evaluate the role that stay-green can play in sugar yield maintenance under post-flowering drought.

Understanding the genetic composition and population structure of plant species at a molecular level is essential for the development of adequate strategies aimed at enhancing the conservation and use of their genetic resources. In addition, such knowledge can help to plan ahead for a scenario under which wild and cultivated species come into contact with their genetically modified (GM) counterpart(s). Using ten simple sequence repeat markers, we genotyped 409 samples pertaining to the species in the Manihot genus known to occur in Colombia, i.e. cassava (Manihot esculenta) and its wild relatives Manihot brachyloba, Manihot carthaginensis and Manihot tristis. High genetic variation was observed in all the species (HE= 0.212–0.603), with cassava showing highest diversity. Most of the genetic variation was found within species populations. Our results suggest that outcrossing events among populations occur much more frequently in M. tristis and M. esculenta, and particularly so in the latter, where the exchange of varieties among local farmers plays a key role in maintaining and introducing new genetic diversity. The occurrence of gene flow within and among populations of Manihot species in Colombia becomes relevant in a biosafety context, where gene flow from GM cassava, if introduced to the country, might have detrimental effects on the structure and dynamics of populations of wild species. The baseline information on the genetic diversity and structure of the four Colombian species that we have presented here provides a first and indispensable step towards the development of targeted interventions necessary to preserve their genetic resources.

We analysed the natural variation of drought response in 11 Tunisian populations of Medicago truncatula sampled from environments that varied in soil composition, salinity and water availability. Plants were cultivated in a greenhouse under well-irrigated and water-deficit treatments (50% of field capacity), and a number of traits associated with drought response were measured. Variance analysis indicated that the variation of phenotypic traits was explained by the effects of population, line, treatment, and population × treatment and line × treatment interactions, with treatment being the one with the greatest effect. A large degree of phenotypic variation for most traits in the two water treatments was found within populations. Most of the measured characters showed higher broad-sense heritabilities (H2) in well-irrigated treatment than in water-deficit treatment. Furthermore, the largest population differentiation (QST) for most of the measured traits was observed under drought stress. Most of the correlations between measured traits under both treatments were positive. Four groups of lines differing in drought tolerance were identified, with 45 susceptible, 14 moderately susceptible, 31 tolerant and 23 most tolerant lines. The tolerant group experienced lowest reductions in the length of plagiotropic axes, length of stems, number of internodes and number of leaves. The large phenotypic variation of M. truncatula in response to drought stress can be used to identify genes and alleles important for the complex trait of drought tolerance.