Tag: orphan crops
African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops
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.
Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome
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. 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. 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.
Delivering Perennial New and Orphan Crops for Resilient and Nutritious Farming Systems
Supporting the diversification of African agricultural systems by the further integration of nutritious, perennial ‘new and orphan crops’ (NOC) is seen as an important means to address malnutrition in Africa. The approach may be of particular relevance in the context of climate change, with the diversification of food systems possibly supporting more resilient food provision in the face of more variable weather patterns. Here, we relate how perennial NOC can support dietary diversity at a subnational level within a seasonal context based on crop portfolios. We also explore the resilience of the production of perennial crops, based on year-on-year crop yield data for eastern and southern African countries provided by the Food and Agriculture Organization Corporate Statistical Database (FAOSTAT). These analyses support the role of perennial NOC in creating resilient food systems and indicate a potential for compensatory annual–perennial crop combinations, although further research is needed on this point. Making use of FAOSTAT country-level trend data, we also relate constraints and potential opportunities for perennial food crop production. We then explain how NOC are currently being promoted in the region, with specific reference to the work of the African Orphan Crops Consortium and its breeder-training programme. We discuss the challenges faced in delivering perennial NOC planting material to farmers, which are exacerbated by climate change, and the measures that are being taken to overhaul delivery systems.
The draft genomes of five agriculturally important African orphan crops
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. 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. 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.
Supporting human nutrition in Africa through the integration of new and orphan crops into food systems: placing the work of the African Orphan Crops Consortium in context
Better integrating currently under-researched nutrient-rich new and orphan crops (NOC) into food systems could play an important role in addressing poor human diets. Understanding the multiple interventions required to support effective integration is, however, not straightforward. Current research to support this objective has generally been inadequate, in large part because insufficient attention has been given to draw together the multiple disciplines needed to explore and reach solutions. A broad interdisciplinary research programme is needed to provide answers to the following questions: how do dietary diversity and crop diversity interrelate at national and local food system levels? What drives crop integration or exclusion in food systems over time? How can new technologies be embraced in combination with best existing practices to genetically improve, better manage and more effectively process crops? And what are the best approaches to bring about behavioural change among farmers, food processors, consumers and other stakeholders to introduce new practices and foods?
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’.
Breeders’ views on the production of new and orphan crops in Africa: a survey of constraints and opportunities
New and orphan crops, which in the past have received only limited research attention, have great potential to support healthy diets in Africa. However, limited systematic data are available on the constraints to production faced by these annual and perennial crops, and the possible opportunities for intervention to remove critical barriers. We report on the results of a survey of African plant breeders to begin identifying constraints to crop production, guide the direction of crop genetic improvement activities and identify appropriate agronomic management interventions. The survey was completed by 67 plant breeders affiliated with institutions in 18 African countries and focused on crops prioritized for genetic improvement by the African Orphan Crops Consortium (AOCC). Of the survey respondents, 38 worked on new or orphan crops on the AOCC crop list. In total, respondents provided specific data on 30 of these crops. We discuss the findings of the survey, which indicate that pest and disease attacks, and lack of access to – or availability of – high-quality planting material are important barriers to be addressed in enhancing production. Other insights from the survey include the differentiation of responses based on the part of the crop used for food, and breeders’ views on the future importance of these plants. These results and additional findings are elaborated along with opportunities for future research to delve deeper into production constraints and solutions for new and orphan crops.
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 greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility 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.
Determining appropriate interventions to mainstream nutritious orphan crops into African food systems
Nutritious ‘orphan’ crops could (re)diversify African food systems, but appropriate means to bring this about are required. A review of the literature on crop intervention options suggested success and failure factors in promotion, but indicated little about the relative importance of production-versus consumption-based measures and how these interact. An analysis of secondary crop production data indicated that addressing food policies could be valuable for orphan crop mainstreaming, but, as with literature review, did not provide clear guidance on the importance of different interventions. A survey of experts suggested that cross-disciplinary teams are important for developing mainstreaming strategies, but revealed no clear consensus on the importance of particular measures for specific orphan crops. We discuss the implications of these findings.