African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops.

MAIN CONCLUSION: 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 role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition.

Especially in low-income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low-input conditions. The evolving space for these crops in production systems presents particular genetic improvement requirements that extensive gene pools are able to accommodate. Particular needs for genetic development identified in part with plant breeders relate to three areas of fundamental importance for addressing food production and human demographic trends and associated challenges, namely: facilitating integration into production systems; improving the processability of crop products; and reducing farm labour requirements. Here, we relate diverse involved target genes and crop development techniques. These techniques include transgressive methods that involve defining exemplar crop models for effective new and orphan crop improvement pathways. Research on new and orphan crops not only supports the genetic improvement of these crops, but they serve as important models for understanding crop evolutionary processes more broadly, guiding further major crop evolution. The bridging position of orphan crops between new and major crops provides unique opportunities for investigating genetic approaches for de novo domestications and major crop 'rewildings'.

Nutrient composition of selected indigenous fruits from sub-Saharan Africa.

Indigenous fruits constitute an important part of human diets in many sub-Saharan African countries, particularly in rural areas and during droughts. In order to promote and expand the utilisation of these fruits, knowledge on their nutritional composition is essential. This review presents the results of a literature research of the nutritional composition of ten selected indigenous fruits from sub-Saharan Africa. Species were selected based on their current importance as well as their future potential for nutrition, processing and cash income generation. Compositional data were compiled and mean values of components per species were calculated. Most papers were compiled for Adansonia digitata (26) and Dacryodes edulis (16), followed by Tamarindus indica (ten), Balanites aegyptiaca (nine), Sclerocarya birrea (nine), Ziziphus mauritiana (nine), Vitex doniana (seven) and Irvingia gabonensis (five), and least for Uapaca kirkiana (three) and Syzygium guineense (three). Fruits were found to be mainly analysed for macronutrients and minerals. Vitamins, apart from vitamin C, were rarely reported. Substantial compositional differences were found among as well as within the different fruit species. The results of this study emphasise the need to generate more high-quality data on a wider spectrum of components of the selected indigenous fruits in sub-Saharan Africa.

GlobalUsefulNativeTrees, a database documenting 14,014 tree species, supports synergies between biodiversity recovery and local livelihoods in landscape restoration.

Tree planting has the potential to improve the livelihoods of millions of people as well as to support environmental services such as biodiversity conservation. Planting however needs to be executed wisely if benefits are to be achieved. We have developed the GlobalUsefulNativeTrees (GlobUNT) database to directly support the principles advocated by the 'golden rules for reforestation', including planting tree mixtures that maximize the benefits to local livelihoods and the diversity of native trees. Developed primarily by combining data from GlobalTreeSearch with the World Checklist of Useful Plant Species (WCUPS), GlobUNT includes 14,014 tree species that can be filtered for ten major use categories, across 242 countries and territories. The 14,014 species represent roughly a quarter of the tree species from GlobalTreeSearch and a third of the plant species from WCUPS. GlobUNT includes over 8000 species used as materials (9261 species; 68.4% of the total in WCUPS for that use category) or medicines (8283; 31.1%), over 2000 species with environmental uses (3317; 36.9%), used as human food (3310; 47.0%) or fuel (2162; 85.5%), over 1000 species used as gene sources (1552; 29.8%), animal food (1494; 33.7%), social uses (1396; 53.8%) or poisons (1109; 36.8%), and 712 species (68.4%) as insect food.

'Systems approach' plant breeding illustrated by trees.

The linkage in new and creative ways of existing plant breeding methods responsive to different global trends and values provides a 'systems approach' to address a broad set of global production challenges more effectively. Here, we illustrate such an approach through its application to trees, chosen because of their extensive diversity in features, uses, users, production contexts, and domestication pathways. We coin the resulting strategy 'tree diversity breeding' and consider it with reference to trends and values related to participation, environment, biotechnology, and markets as examples. Features of the approach for trees are applicable to plant breeding more widely, as we seek to address complex problems through strategic biodiversity use.

Transforming food systems with trees and forests.

The global food system is failing to deliver sufficient and nutritious food to all, while damaging the earth and unsustainably drawing down its resources. We argue that trees and forests are essential to solving these challenges. We outline the current contributions of trees and forests to the global food system and present recommendations to leverage these contributions as part of the efforts to reshape food systems to better support healthy diets and environmental sustainability. Trees and forests provide nutrient-rich foods, incomes for food security, ecosystem services for food production, and add resilience to food systems. At the same time, trees and forests protect biodiversity and mitigate climate change through carbon sequestration. We recommend four approaches to realise the full potential of trees and forests to contribute to healthy and sustainable food systems: scaling up current tree-based food production, reorientating some agricultural investments towards nutrient-dense food production, repurposing production incentives from support of calorie-rich but nutrient-poor foods to support nutrient-dense foods, and integrate nutrition objectives into forest conservation and restoration programmes. Trees and forests have important roles to play in the transformation of our food systems, but more needs to be done to ensure that these roles are realised.

Chromosome evolution and the genetic basis of agronomically important traits in greater yam.

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

State of ex situ conservation of landrace groups of 25 major crops.

Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation.

Genomic Resources to Guide Improvement of the Shea Tree.

A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.

Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis).

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.

Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome.

BACKGROUND: The 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. RESULTS: We 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. CONCLUSIONS: The 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.

The draft genomes of five agriculturally important African orphan crops.

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.

Nutritional variation in baobab (Adansonia digitata L.) fruit pulp and seeds based on Africa geographical regions.

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.

tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

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.

Trypanosoma brucei: composition, organisation, plasticity, and differential transcription of NlaIII repeat elements in drug-resistant and sensitive isolates.

A Trypanosoma brucei brucei DNA repeat sequence termed NlaIII repeat (NR) was originally isolated from a multidrug-resistant field isolate CP547 [Jamnadass, R., 1995. Identification and characterisation of an extrachromosomal element from a multidrug-resistant isolate of T. brucei brucei, Ph.D. thesis, Brunel University, UK]. Subsequently studied in a laboratory strain (Tb427) [Alsford, N.S., Navarro, M., Jamnadass, H.R., Dunbar, H., Ackroyd, M., Murphy, N.B., Gull, K., Ersfeld,K., 2003. The identification of circular extrachromosomal DNA in the nuclear genome of T. brucei. Molecular Microbiology 47, 277-288], NRs were exclusively episomal. Here we show that NR sequences in CP547 are present on linear chromosomes as well as on episomal circular elements. Sequence analysis shows that NRs are composed of three classes of sub-repeat arranged in a specific order. Heterogeneity in size and sequence of an episomal 6.6kbp element was shown in successive passages of the original CP547 isolate and derived clones in mice. Its copy number was unstable and was affected by selective pressure with the trypanocide diminazene aceturate. Some of the extrachromosomal elements appear to be composed of RNA-DNA hybrids. NR sequences were transcribed in a developmentally regulated manner but transcripts did not contain the spliced-leader sequence found on all trypanosome mRNAs.