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Baobab (Adansonia digitata L., Malvaceae) seed oil contains Fatty Acids (FAs) with commercial and cosmeceutical value. The influence of provenance and geographical region on FAs profile and content of seed oil from baobab wild populations in sub-Saharan Africa (SSA) was assessed in this study. The FA profiles were determined as fatty acid methyl esters (FAME) by Gas Chromatography (GC). Generally, the seed oil contained 17–22% saturated fatty acids (SFA), 32–38% monounsaturated fatty acids (MUFA) and 22–26% polyunsaturated fatty acids (PUFA). Palmitic acid (C16:0) was the most abundant SFA, while oleic (C18:1) and linoleic acid (C18:2, LA) were the dominant MUFA and PUFA, respectively. There existed significant (p

The African Orphan Crops Consortium (AOCC) successfully initiated the ambitious genome sequencing project of 101 African orphan crops/trees with 6 genomes sequenced, 6 near completion, and 20 currently in progress. Addressing stunting, malnutrition, and hidden hunger through nutritious, economic, and resilient agri-food system is one of the major agricultural challenges of this century. As sub-Saharan Africa harbors a large portion of the severely malnourished population, the African Orphan Crops Consortium (AOCC) was established in 2011 with an aim to reduce stunting and malnutrition by providing nutritional security through improving locally adapted nutritious, but neglected, under-researched or orphan African food crops. Foods from these indigenous or naturalized crops and trees are rich in minerals, vitamins, and antioxidant, and are an integral part of the dietary portfolio and cultural, social, and economic milieu of African farmers. Through stakeholder consultations supported by the African Union, 101 African orphan and under-researched crop species were prioritized to mainstream into African agri-food systems. The AOCC, through a network of international-regional-public-private partnerships and collaborations, is generating genomic resources of three types, i.e., reference genome sequence, transcriptome sequence, and re-sequencing 100 accessions/species, using next-generation sequencing (NGS) technology. Furthermore, the University of California Davis African Plant Breeding Academy under the AOCC banner is training 150 lead African scientists to breed high yielding, nutritious, and climate-resilient (biotic and abiotic stress tolerant) crop varieties that meet African farmer and consumer needs. To date, one or more forms of sequence data have been produced for 60 crops. Reference genome sequences for six species have already been published, 6 are almost near completion, and 19 are in progress.

The inherent ability of seeds (orthodox, intermediate, and recalcitrant seeds and vegetative propagules) to serve as carriers of pests and pathogens (hereafter referred to as pests) and the risk of transboundary spread along with the seed movement present a high-risk factor for international germplasm distribution activities. Quarantine and phytosanitary procedures have been established by many countries around the world to minimize seed-borne pest spread by screening export and import consignments of germplasm. The effectiveness of these time-consuming and cost-intensive procedures depends on the knowledge of pest distribution, availability of diagnostic tools for seed health testing, qualified operators, procedures for inspection, and seed phytosanitation. This review describes a unique multidisciplinary approach used by the CGIAR Germplasm Health Units (GHUs) in ensuring phytosanitary protection for the safe conservation and global movement of germplasm from the 11 CGIAR genebanks and breeding programs that acquire and distribute germplasm to and from all parts of the world for agricultural research and food security. We also present the challenges, lessons learned, and recommendations stemming from the experience of GHUs, which collaborate with the national quarantine systems to export and distribute about 100,000 germplasm samples annually to partners located in about 90 to 100 countries. Furthermore, we describe how GHUs adjust their procedures to stay in alignment with evolving phytosanitary regulations and pest risk scenarios. In conclusion, we state the benefits of globally coordinated phytosanitary networks for the prevention of the intercontinental spread of pests that are transmissible through plant propagation materials.

The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization&rsquo, s global system of conservation and use of PGRFA. They also play an important supportive role in realizing Target 2.5 of the Sustainable Development Goals. This paper analyzes CGIAR genebanks&rsquo, trends in acquiring and distributing PGRFA over the last 35 years, with a particular focus on the last decade. The paper highlights a number of factors influencing the Centers&rsquo, acquisition of new PGRFA to include in the international collections, including increased capacity to analyze gaps in those collections and precisely target new collecting missions, availability of financial resources, and the state of international and national access and benefit-sharing laws and phytosanitary regulations. Factors contributing to Centers&rsquo, distributions of PGRFA included the extent of accession-level information, users&rsquo, capacity to identify the materials they want, and policies. The genebanks&rsquo, rates of both acquisition and distribution increased over the last decade. The paper ends on a cautionary note concerning the potential of unresolved tensions regarding access and benefit sharing and digital genomic sequence information to undermine international cooperation to conserve and use PGRFA.

Joel KA, Runo S, Muchugi A. 2018. Genetic diversity and virulence study of Striga hermonthica from Kenya and Uganda on selected sorghum varieties. Nusantara Bioscience 10: 111-120. Parasitic weeds pose a severe problem in agricultural production, causing massive crop losses in many regions of the world and especially Africa. One example to be considered the most significant biological constraint to food production in sub-Saharan Africa (SSA) is Striga hermonthica, the most widespread among the Striga species in the semi-arid tropical African zones. The wide geographical distribution set conditions for genetically structured populations. The genetic variations among the weed populations allow for the quick breakdown of resistance in crops hence making control of the weed difficult. Efficient and effective control of S. hermonthica demands knowledge on inherent genetic variability within local and regional races of the weed. However, the genetic diversity and virulence of S. hermonthica ecotypes in Kenya and Uganda on selected sorghum varieties remain unknown. This study aimed at evaluating the genetic diversity among seven S. hermonthica populations from locations in Kenya and Uganda using 5 primer sets of Expressed Sequence Tags-Simple Sequence Repeats (EST-SSR). The genetic diversity was moderate as shown by the Nei’s genetic distance values. AMOVA measured low genetic differentiation among the populations. This study also investigated twelve sorghum varieties for their response to S. hermonthica infection. The result demonstrated that the varieties resistance responses to S. hermonthica varied widely. The phenotype of resistant interaction was characterized by the inability of the weeds haustoria to penetrate the sorghums root endodermis due to severe necrosis and in rare cases the parasites radicle growing away from the host root. The resistant sorghum varieties were the Asareca W2, Asareca AG3, N13 and the Wild-type which had low mean number of S. hermonthica plantlets growing on their roots, while the most susceptible varieties were Sap 027, Epurpur which had the highest mean number of S. hermonthica plantlets growing on their roots. There was a highly significant difference in the means of the number of Striga growing on the roots of sorghum varieties, Striga dry biomass and S. hermonthica length between the susceptible and resistant ones. This knowledge holds unique potentiality since resistant sorghum germplasm tested will be sourced and targeted to the seven specific geographical areas where virulence of the particular S. hermonthica populations was characterized.

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

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.

BackgroundThe African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops.ResultsWe assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome.ConclusionsThe genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

Warburgia ugandensis Sprague (Canellaceae) occurs in East and Central Africa and is an important multipurpose tree species. Over-exploitation of natural forests for medicinal purposes and clearance for farming threaten the species survival. Cultivation of the tree species would ensure sustainable medicinal source and its conservation. However, on-farm genetic diversity of the species is currently unknown. The genetic diversity of the on-farm W. ugandensis populations and their proximate natural populations were analyzed using the amplified fragment length polymorphism (AFLP). Four primer combinations produced a total of 223 polymorphic bands. Both the natural and on-farm populations had high genetic diversity ranging from H = 0.2892 to H = 0.1278. Principal co-ordinates analysis and dendrogram separated the ten populations into two major groups corresponding to Kenyan and Tanzanian populations, respectively. Ugandan populations were shared between the two major groups; this is probably because Uganda is believed to be the centre of diversity for W. ugandensis. Close genetic relationships between the on-farm and their proximate natural population were revealed. Analysis of molecular variance (AMOVA) revealed that a total of 54% AFLP variation resided within populations with 46% reside among populations. The high genetic diversity of W. ugandensis on-farm populations could be useful in germplasm collection and conservation strategies. Key words: Warburgia ugandensis, amplified fragment length polymorphism (AFLP), domestication, genetic diversity, on-farm, natural.

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.

Dacryodes edulis is a multipurpose tree integrated in the cropping system of Central African region still dominated by subsistence agriculture. Some populations grown are wild which can provide information on the domestication process, and could also represent a potential source of gene flow. Leaves samples for DNA extraction were collected from wild forms in Mbakwa supe region and from cultivated forms in Yaounde and Santchou region. Six microsatellites DNA markers were employed in genotyping to analyze population structure and gene flow. Amplification rate was high and genotyping revealed high level of genetic variation. The overall polymorphic level at the six loci was also high with average expected heterozygosity of 0.53; polymorphism of 0.46; mean allelic diversity of 0.5 and mean allele number of 8.33. There were no clear differences with only 1% variation among the three populations and 6% variation among individuals within populations. In contrast, the rate of heterozygosis was high in all the three populations. Both the number of migrant per generation (Nm=20) and the Wright’s F-statistics (FST=0.012) suggest that there was substantial gene flow among the populations. These findings indicate that D. edulis possess a great potential of pollen dispersal and dominant cross-pollination within populations. Most of the loci with private alleles (45%) were found in wild individuals which could be a source of pollen for crossing their cultivated relatives. Key words: Dacryodes edulis, domestication, genetic diversity and structure.

Fertilizer trees, the nitrogen-fixing legumes, such as gliricidia (Gliricidia sepium) and tephrosia (Tephrosia spp.) have been used to improve soil fertility for higher crop yields in nitrogen deficient soils. Many studies have focused on how these fertilizer trees improve maize yield, but there has been a dearth of information on the effect of fertilizer tree species on cotton growth and yield. A study was undertaken for two cropping seasons (2012/13 and 2013/14) with the objective of assessing IRM 81 cotton growth and yield responses to tephrosia and/or gliricidia biomass with or without inorganic fertilizer application. Boll opening significantly varied (P

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.

Mating system of a species is critically important both genetically and ecologically in developing plans for breeding and gene conservation. This study was conducted to assess twenty provenances of Sclerocarya birrea (A. Rich.) Hochst. planted in Malawi. The trial was assessed for mating system and sex ratio at eighteen years of age. The results revealed that the mating system in S. birrea occurred from selfing, insect, and wind-mediated pollination. There were no significant (P>0.05) differences on seed germination percentage among the three mating systems. The germination percentages were 47%, 44%, and 43% for insect, wind, and self-pollinations, respectively. This implies that the seeds were viable in all the three mating systems. Production of viable seed from selfed flowers ruled out the possibility of apomixes in S. birrea. Most frequent flower visitors were the orders Hymenoptera and Lepidoptera with peak visitation period being from 7:00 to 11:30 hours in the morning and then 15:30 to 18:00 hours in the afternoon (+2 GMT) when temperatures were cooler. There were significant (P

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.

Forest and woodland landscape restoration is a key undertaking of renewed interest for forestry and conservation practitioners, but is hampered by the lack of information on the distributions of tree species and of patterns of intra-specific genetic variation. Through the first meta-analysis of its type, we here tested the utility of a high-resolution potential natural vegetation (PNV) map for eastern Africa (vegetationmap4africa) for supporting restoration activities by comparison with 20 molecular marker genetic datasets, identified through literature review and other sources, for ten indigenous tree species. Our analysis indicated that site suitability and stability values from PNV-based ecological niche modelling involving current and past climate scenarios were positively related to population genetic diversity values revealed by molecular markers, supporting the value of PNV maps for the practical planning of restoration activities accounting for anthropogenic climate change. Furthermore, population pairwise genetic divergence was strongly positively correlated with population pairwise geographic distances for most datasets, indicating generalizable sampling implications for tree genetic resource conservation in the region. Population pairwise genetic divergence was however not well explained by sampling across PNV and wider physiognomic types, possibly due to molecular markers’ adaptive neutrality and high rates of recombination in trees, among other factors. Patterns of neutral molecular marker variation are thus no substitute for trials of adaptive variation for confirming or refuting the utility of vegetation boundaries in defining tree planting zones. We discuss the importance of results for eastern Africa and more widely.

Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.

We evaluated the genetic diversity of the African poplar (Populus ilicifolia) populations found in Kenya compared with reference samples of five poplar species from North America and one species introduced in Kenya from India (KEFRI-Kenya). Amplified fragment length polymorphism (AFLP) was used with the objective of providing important information for breeding and in situ/ex situ conservation of this species. Samples collected from three locations along the species’ natural range (Athi, Ewaso Nyiro, and Tana rivers) were compared with four samples of locally planted Populus deltoides stand introduced from India and ten reference samples from North America. Six AFLP primer combinations produced 521 clear bands for analysis. The percentage polymorphic loci were lowest in Tana (20.4 %) and highest in Athi (40.6 %). The average heterozygosity across the studied populations was between 0.07 and 0.3. AMOVA revealed more genetic variation partitioning within population (87 %; P

Tea is the most popular non-alcoholic beverage worldwide and is one of the most important tree cash crops in East Africa. However, no comprehensive study has been carried out on the genetic structure and diversity of tea germplasm for this region to date. In the present study, 193 tea accessions held at the ex situ Germplasm Bank of the Tea Research Institute (TRI), Kenya, were analysed using genetic data from 23 polymorphic simple sequence repeat (SSR) loci. A total of 266 alleles were detected with the number of alleles per locus ranging from 4 to 19 with an average of 7.88. Genetic clustering by STRUCTURE was used to correct misidentified accessions based on morphological characters. After reassignment of the tea accessions, Camellia assamica exhibited the lowest genetic diversity (Hs = 0.648) despite being the most widely cultivated tea type in the East African region. C. assamica subsp. lasiocalyx showed the highest genetic diversity (Hs = 0.76), which supported its origin by hybridization among tea types. Tea cultivars cultivated across the region exhibited lower genetic diversity (Hs = 0.661) compared to material held at the ex situ Germplasm Bank of TRI. Tea accessions clustered in the neighbour-joining tree on the basis of geographical origin, pedigree and leaf pigmentation, indicating their common origin. Our results indicated further that East African tea germplasm has a complex breeding history with a majority of the hybrids being F2 generation and backcross plants. C. assamica contributed significantly more genetic materials in the tea breeding programmes in East Africa. This study highlights the importance of ex situ germplasm banks to conserve the highest genetic diversity, which is an important resource for future tea crop improvements in East Africa.