The rate of annual yield increases for major staple crops must more than double relative to current levels in order to feed a predicted global population of 9 billion by 2050. Controlled hybridization and selective breeding have been used for centuries to adapt plant and animal species for human use. However, achieving higher, sustainable rates of improvement in yields in various species will require renewed genetic interventions and dramatic improvement of agricultural practices. Genomic prediction of breeding values has the potential to improve selection, reduce costs and provide a platform that unifies breeding approaches, biological discovery, and tools and methods. Here we compare and contrast some animal and plant breeding approaches to make a case for bringing the two together through the application of genomic selection. We propose a strategy for the use of genomic selection as a unifying approach to deliver innovative 'step changes' in the rate of genetic gain at scale.

This paper follows the transition from ethnobotany to a deeper scientific understanding of the food and medicinal properties of African agroforestry tree products as inputs into the start of domestication activities. It progresses on to the integration of these indigenous trees as new crops within diversified farming systems for multiple social, economic and environmental benefits. From its advent in the 1990s, the domestication of indigenous food and non-food tree species has become a global programme with a strong African focus. This review of progress in the third decade is restricted to progress in Africa, where multi-disciplinary research on over 59 species has been reported in 759 research papers in 318 science publications by scientists from over 833 research teams in 70 countries around the world (532 in Africa). The review spans 23 research topics presenting the recent research literature for tree species of high priority across the continent, as well as that in each of the four main ecological regions: the humid zone of West and Central Africa; the Sahel and North Africa; the East African highlands and drylands; and the woody savannas of Southern Africa. The main areas of growth have been the nutritional/medicinal value of non-timber forest products; the evaluation of the state of natural resources and their importance to local people; and the characterization of useful traits. However, the testing of putative cultivars; the implementation of participatory principles; the protection of traditional knowledge and intellectual property rights; and the selection of elite trees and ideotypes remain under-researched. To the probable detriment of the upscaling and impact in tropical agriculture, there has been, at the international level, a move away from decentralized, community-based tree domestication towards a laboratory-based, centralized approach. However, the rapid uptake of research by university departments and national agricultural research centres in Africa indicates a recognition of the importance of the indigenous crops for both the livelihoods of rural communities and the revitalization and enhanced outputs from agriculture in Africa, especially in West Africa. Thus, on a continental scale, there has been an uptake of research with policy relevance for the integration of indigenous trees in agroecosystems and their importance for the attainment of the UN Sustainable Development Goals. To progress this in the fourth decade, there will need to be a dedicated Centre in Africa to test and develop cultivars of indigenous crops. Finally, this review underpins a holistic approach to mitigating climate change, as well as other big global issues such as hunger, poverty and loss of wildlife habitat by reaping the benefits, or ‘profits’, from investment in the five forms of Capital, described as ‘land maxing’. However, policy and decision makers are not yet recognizing the potential for holistic and transformational adoption of these new indigenous food crop opportunities for African agriculture. Is ‘political will’ the missing sixth capital for sustainable development?

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.

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.