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Maximizing the research output from a limited investment is often the major challenge for minor and underutilized crops. However, such crops may be tolerant to biotic and abiotic stresses and are adapted to local, marginal, and low-input environments. Their development through breeding will provide an important resource for future agricultural system resilience and diversification in the context of changing climates and the need to achieve food security. The African Orphan Crops Consortium recognizes the values of genomic resources in facilitating the improvement of such crops. Prior to beginning genome sequencing there is a need for an assessment of line varietal purity and to estimate any residual heterozygosity. Here we present an example from bambara groundnut ( Vigna subterranea (L.) Verdc.), an underutilized drought tolerant African legume. Two released varieties from Zimbabwe, identified as potential genotypes for whole genome sequencing (WGS), were genotyped with 20 species-specific SSR markers. The results indicate that the cultivars are actually a mix of related inbred genotypes, and the analysis allowed a strategy of single plant selection to be used to generate non-heterogeneous DNA for WGS. The markers also confirmed very low levels of heterozygosity within individual plants. The application of a pre-screen using co-dominant microsatellite markers is expected to substantially improve the genome assembly, compared to a cultivar bulking approach that could have been adopted. [ABSTRACT FROM AUTHOR]

Genetic diversity amongst genotypes of several Napier grass collections was analyzed and compared with the diversity in a set of open pollinated progeny plants. A total of 114,881 SNP and 46,293 SilicoDArT genome-wide markers were generated on 574 Napier grass genotypes. Of these, 86% of the SNP and 66% of the SilicoDArT markers were mapped onto the fourteen chromosomes of the Napier grass genome. For genetic diversity analysis, a subset of highly polymorphic and informative SNP markers was filtered using genomic position information, a maximum of 10% missing values, a minimum minor allele frequency of 5%, and a maximum linkage-disequilibrium value of 0.5. Extensive genetic variation, with an average Nei's genetic distance value of 0.23, was identified in the material. The genotypes clustered into three major and eleven sub-clusters with high levels of genetic variation contained both within (54%) and between (46%) clusters. However, we found that there was low to moderate genetic differentiation among the collections and that some overlap and redundancy occurred between collections. The progeny plants were genetically diverse and divergent from the germplasm collections, with an average FST value of 0.08. We also reported QTL regions associated with forage biomass yield based on field phenotype data measured on a subset of the Napier grass collections. The findings of this study offer useful information for Napier grass breeding strategies, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections. [ABSTRACT FROM AUTHOR]

Genetic diversity amongst genotypes of several Napier grass collections was analyzed and compared with the diversity in a set of open pollinated progeny plants. A total of 114,881 SNP and 46,293 SilicoDArT genome-wide markers were generated on 574 Napier grass genotypes. Of these, 86% of the SNP and 66% of the SilicoDArT markers were mapped onto the fourteen chromosomes of the Napier grass genome. For genetic diversity analysis, a subset of highly polymorphic and informative SNP markers was filtered using genomic position information, a maximum of 10% missing values, a minimum minor allele frequency of 5%, and a maximum linkage-disequilibrium value of 0.5. Extensive genetic variation, with an average Nei's genetic distance value of 0.23, was identified in the material. The genotypes clustered into three major and eleven sub-clusters with high levels of genetic variation contained both within (54%) and between (46%) clusters. However, we found that there was low to moderate genetic differentiation among the collections and that some overlap and redundancy occurred between collections. The progeny plants were genetically diverse and divergent from the germplasm collections, with an average FST value of 0.08. We also reported QTL regions associated with forage biomass yield based on field phenotype data measured on a subset of the Napier grass collections. The findings of this study offer useful information for Napier grass breeding strategies, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections. [ABSTRACT FROM AUTHOR]

Background: The Sodom apple (Calotropis gigantea), a member of the Asclepiadaceae family, is a large evergreen shrub native to continental Asia and northern Africa. As an important medicinal shrub and a fiber resource plant, there is an urgent need for developing molecular markers to facilitate breeding and genetic improvement of varieties. Results: In this study, using the Illumina high throughput sequencing technique we obtained about 45 million paired end sequencing reads, De novo assembled and generated a total of 133,634 transcripts with a mean of 1837.47 bp in length. Based on protein homology searches against available databases, a total of 21,851 unigenes were functionally annotated. In particular, many transcripts that encode for putative proteins involved in fiber and secondary metabolite biosynthesis were identified and analyzed. Key fiber genes identified were validated experimentally through Real-Time PCR technique. Various transcription factors involved in regulating plant response to abiotic stress were also identified. In addition, based on the unigene sequences assembled, 11,623 microsatellites loci were detected, which provide very useful resources for developing microsatellite molecular markers. Conclusion: This study is the first report on transcriptome information in the Calotropis species and provides rich gene transcript resources for conducting further studies on understanding the molecular basis of fiber and secondary metabolite biosynthesis, serving the genetic improvement and resource utilization in Calotropis plants. [ABSTRACT FROM AUTHOR]

Canarium tramdenum occurs naturally in subtropical and tropical regions of Indochina and China. The wood is used for making high quality furniture and the fruit and leaves are used in traditional medicine. However, a lack of information on genetic diversity and population structure has handicapped the genetic conservation and domestication of this high-value species. This study evaluated genetic variation within and among four C. tramdenum populations. Sixty individuals were collected from four natural populations in Vietnam in the provinces of Ninhbinh, Bacgiang, Nghean, and Backan. Genetic diversity and genetic structure were determined using 20 ISSR markers. A total of 192 DNA fragments with sizes ranging from 110 bp to 3,000 bp were detected, of which 154 segments (80.2%) were polymorphic and 38 segments (19.8%) were monomorphic. The ISSR data indicated a moderate degree of genetic diversity for the species (h = 0.252). The four populations were separated into three genetic clusters with low levels of genetic distance between them. AMOVA result showed that most (78%) of the genetic variation was within the populations. The moderate to high genetic diversity of C. tramdenum and the low genetic differentiation among populations suggested that all existing natural populations in the particular regions needed to be preserved to protect the genetic diversity of this species. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: The increasing occurrence of native and non‐native pests and diseases of trees in Africa is impacting rural livelihoods, economic development, and biodiversity across the continent. Here we provide an updated and comprehensive overview of insect pests and pathogens targeting natural and planted forests in Africa, and raise awareness of this growing emergency. Data availability and limited biosecurity of some countries are limiting the ability to tackle this invasion. An improved knowledge of taxonomy, distribution, and damage caused by these organisms will be crucial for developing continent‐wide strategies to manage this emergency and enhance country‐level intervention capacity. Summary: An increasing multitude of insect pests and pathogens is targeting indigenous trees of natural forests, agroforestry systems, and exotic trees in planted forests in Africa. This is raising major concerns for a continent already challenged by adaptations to climate change, as it threatens a vital resource for food security of rural communities, economic growth, and ecosystem conservation. The accidental introduction through trade of non‐native species in particular is accelerating, and it adds to the damage to tree‐based landscapes by native pests and diseases. Old‐time and new invaders heavily impact planted forests of exotic eucalypts, pines, and acacias, and are spreading quickly across African regions. But many non‐native pathogens are recently found affecting important indigenous trees. We describe the threat to African trees by providing an overview of highly relevant insect pests and diseases of indigenous and exotic trees in Africa, and discuss implications for management and future research. The implementation of an integrated and globally coordinated approach based on improved biosecurity, biological control, and tree resistance would contribute to mitigate the potentially devastating impact of these invasions on African natural resources. [ABSTRACT FROM AUTHOR]

Baobab ( Adansonia digitata L.) is an indigenous fruit tree associated with the Savannah drylands of sub-Saharan Africa. Local communities mainly utilize the leaves, pulp, and seeds of baobab as a source of food and for income generation. The present study was conducted to determine the nutritive attributes of baobab fruit pulp and seeds across provenances in east, west, and southern Africa and to determine whether the nutrient content varied with the provenance of origin. Pulp and seed proximate composition and mineral element concentration were determined using the AOAC 1984 methods and inductively coupled plasma atomic emission spectroscopy ( ICP- AES), respectively. The results showed that there exist significant variation ( p < .05) in pulp moisture, protein, fiber, ash, and elemental content among provenances. The highest mean pulp crude fiber (8.68 g 100 g−1 dw) was recorded in Kenya. At country level, Malawi had the highest mean pulp potassium (22.2 mg g−1), calcium (4,300 mg kg−1), magnesium (2,300 mg kg−1), sodium (1,000 mg kg−1), and phosphorus (1,100 mg kg−1) levels. Kenya had the highest mean pulp iron (57.4 μg g−1) and manganese (27.2 μg g−1) content, while Mali had the lowest iron (13.1 μg g−1) and manganese (8.6 μg g−1). At country level, the mean seed calcium content was highest (3,200 mg kg−1) in Malawi and lowest (2,000 mg kg−1) in Kenya. The highest mean iron content of 63.7 μg g−1 was recorded in seeds from Kenya, while the lowest (25.8 μg g−1) was in Mali. Baobab seed mineral and proximate content varied significantly ( p < .001) among the selected countries. Overall, baobab fruit pulp and seeds contain significant amounts of nutritionally essential minerals and proximate components but the amounts varied significantly among the selected countries. This variation offers opportunities for selecting provenances to concentrate on during germplasm collection for conservation and domestication of baobab. [ABSTRACT FROM AUTHOR]

Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional breeding programs in order to efficiently optimize productivity. [ABSTRACT FROM AUTHOR]

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. [ABSTRACT FROM AUTHOR]

The pumpkin is a rich source of nutrients and has medicinal properties. However, owing to the perception that it is a traditional food and majority of the Kenyan populace being unaware of its high nutritional value it still remains unexploited. The main aim and objective of this work was to determine the composition of fatty acids and vitamin E in seed oils ofpumpkins (Cucurbita spp) collected from selected regions in Kenya. The pumpkin samples were graded on the basis of colour, nine varieties were identified. The seeds were removed from the fruits and dried under shade and grounded into fine flour prior to analysis. Data analysis was done using Genstat statistical package. The oil yields were obtained by solvent extraction and analysed for fatty acids by Gas Chromatography (GC). The oil yields of the seeds were found to be ranging between 31.9 to 39.44%. Both saturated and unsaturated fatty acids were identified in all the seed oils with the latter being the predominant with linoleic acid ranging between 43.4% to 58.29% and oleic acid ranging between 20.27% to 40.51%. Vitamin E ranged between 9.42 and 122.65 ¡g/g. There was significant decrease in percentage saturated FA, increase in percentage unsaturated FA with increase in vitamins E concentration in all the seed oils. The seed oils have many FA such as oleic acid, and a-linoleic acids which are of biological and industrial significance to humans thus could be potentially exploited domestic use. [ABSTRACT FROM AUTHOR]

Background and Aims Afromontane forest ecosystems share a high similarity of plant and animal biodiversity, although they occur mainly on isolated mountain massifs throughout the continent. This resemblance has long provoked questions on former wider distribution of Afromontane forests. In this study Prunus africana (one of the character trees of Afromontane forests) is used as a model for understanding the biogeography of this vegetation zone. Methods Thirty natural populations from nine African countries covering a large part of Afromontane regions were analysed using six nuclear microsatellites. Standard population genetic analysis as well as Bayesian and maximum likelihood models were used to infer genetic diversity, population differentiation, barriers to gene flow, and recent and all migration among populations. Key Results Prunus africana exhibits strong divergence among five main Afromontane regions: West Africa, East Africa west of the Eastern Rift Valley (ERV), East Africa east of the ERV, southern Africa and Madagascar. The strongest divergence was evident between Madagascar and continental Africa. Populations from West Africa showed high similarity with East African populations west of the ERV, whereas populations east of the ERV are closely related to populations of southern Africa, respectively. Conclusions The observed patterns indicate divergent population history across the continent most likely associated to Pleistocene changes in climatic conditions. The high genetic similarity between populations of West Africa with population of East Africa west of the ERV is in agreement with faunistic and floristic patterns and provides further evidence for a historical migration route. Contrasting estimates of recent and historical gene flow indicate a shift of the main barrier to gene flow from the Lake Victoria basin to the ERV, highlighting the dynamic environmental and evolutionary history of the region. [ABSTRACT FROM AUTHOR]

Abstract: Prunus africana – an evergreen tree found in Afromontane forests – is used in traditional medicine to cure benign prostate hyperplasia. Different bioactive constituents derived from bark extracts from 20 tree populations sampled throughout the species’ natural range in Africa were studied by means of GC–MSD. The average concentration [mg/kgw/w] in increasing order was: lauric acid (18), myristic acid (22), n-docosanol (25), ferulic acid (49), β-sitostenone (198), β-sitosterol (490), and ursolic acid (743). The concentrations of many bark constituents were significantly correlated and concentration of n-docosanol was highly significantly correlated with all other analytes. Estimates of variance components revealed the highest variation among populations for ursolic acid (66%) and the lowest for β-sitosterol (20%). In general, environmental parameters recorded (temperature, precipitation, altitude) for the samples sites were not correlated with the concentration of most constituents; however, concentration of ferulic acid was significantly correlated with annual precipitation. Because the concentration of compounds in bark extracts may be affected by tree size, the diameter of sampled plants at 1.3m tree height (as proxy of age) was recorded. The only relationship with tree diameter was a negative correlation with ursolic acid. Under the assumption that genetically less variable populations have less variable concentrations of bark compounds, correlations between variation parameters of the concentration and the respective genetic composition based on chloroplast and nuclear DNA markers were assessed. Only variation of β-sitosterol concentration was significantly correlated with haplotypic diversity. The fixation index (FIS ) was positively correlated with the variation in concentration of ferulic acid. Principal Components Analysis (PCA) indicated a weak geographic pattern. Mantel tests, however, revealed associations between the geographic patterns of bioactive constituents and the phylogenetic relationship among the populations sampled. This suggests an independent evolution of bark metabolism within different phylogeographical lineages, and the molecular phylogeographic pattern is partly reflected in the variation in concentration of bark constituents. The results have important implications for the design of strategies for the sustainable use and conservation of this important African tree species. [Copyright &y& Elsevier]

• The genetic variations of the wild and cultivated castor bean were demonstrated. • Chloroplast genomes are conserved with potential DNA barcoding regions. • Several non-synonymous mutations in conserved protein domains were identified. • Cultivars could be derived from multiple wild progenitors. The high usage of castor oil in industrial applications and bio-diesel production has led to an increase in castor bean (Ricinus communis L.) cultivation in many countries. Wild species present a source of genetic variation for germplasm improvement, often important because of their adaptation to a wide range of habitats and stresses. Chloroplast genomes are widely used in population genetics and evolutionary studies. Herein, we carried out plastome genome sequencing of 20 wild and cultivated castor bean accessions to examine plastome structural variations (PSVs). Further, single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels), were identified and plastome sequences used to infer phylogenetic relationships. All the chloroplast genomes were quadripartite, with a length between 162,673 bp and 163,210 bp, with 112 genes (78 protein coding genes; PCGs, 30 tRNAs, and four rRNAs). The chloroplast genomes where conserved in terms of structure and content, with no significant PSVs detected except for a slight inverted repeat (IR) contraction in one accession. A total of 162 SNPs and 92 InDels were uncovered across the plastomes, with an average SNP and InDel density of 0.99 and 0.56 per kb respectively. Some of the non-synonymous mutations caused amino acid changes in functional domains. Intergenic spacers trnE-UUC-trnT-GGU and AccD-psaI were identified as potential barcoding regions. The phylogenetic analyses and neighbor-joining network supported three distinct lineages in castor bean. Genetic diversity was greater in one clade than the other, with implications for identifying adaptive germplasm in the wild. These results demonstrate the genetic variations and phylogenetic relationships between the wild and cultivated lineages and add insights into the origin of cultivation and spread of castor bean. [ABSTRACT FROM AUTHOR]

Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism. [ABSTRACT FROM AUTHOR]

Background The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution. Results Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea, and M. oleifera, we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes. Conclusions These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs. [ABSTRACT FROM AUTHOR]