Cereals are rich sources of nutrients for both humans and animals. African cereals, particularly millets, have got high amounts of vitamins, calcium, iron, potassium, magnesium and zinc [21]. The straws and crop residues of cereals are also the main sources of livestock feed for farmers in developing countries. Crops such as finger and pearl millets were recently shown to have an anti-proliferative property, and might have a potential in the prevention of cancer initiation [22]. This anti-proliferative property is associated with the presence and content of phenolic extracts.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is dominantly cultivated as a food crop in the semi-arid areas of Asia and Africa due to its extreme tolerance to moisture deficit [10]. It is annually cultivated on about 16 million ha in Africa alone [23]. Finger millet (Eleusine coracana Gaertn.) is one of the important food crops in the semi-arid regions of Asia and Africa due to its adaptation to unfavorable climatic and soil conditions especially drought [2,8]. The seeds of finger millet contain valuable amino acids especially methionine [5], which is lacking in the diets of hundreds of millions of the poor who live on starchy staples such as cassava. Finger millet is also a popular food among diabetic patients because of its low glycemic index and slow digestion [24]. Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop mainly grown in the Horn of Africa, and its annual cultivation in Ethiopia alone accounts for over 2.8 million ha of land [25]. The crop is tolerant towards abiotic stresses, especially to poorly drained soils where other crops such as maize and wheat do not withstand [11]. In addition, tef is considered a healthy food since the seeds do not contain gluten [12,26], the cause for celiac disease. Fonio (acha) [Digitaria exilis (Kippist) Stapf. and D. iburua Stapf] is widely cultivated for human food in the semi-arid regions of West Africa. Fonio is not only drought-tolerant but also a very fast-maturing crop [5,8]. The seeds of fonio are nutritious, especially in methionine and cysteine, the two amino acids essential for human health, but deficient in major cereals such as wheat, rice and maize [27]. African rice (Oryza glaberrima Steudel) is mostly cultivated in West Africa especially in drought-prone areas and on impoverished soils [5,9]. Due to its early maturing property, African rice is the source of food during food shortage particularly just before other crops are harvested.

Legumes are the major source of protein for consumers. Due to their ability to fix atmospheric nitrogen and convert it to the available form for plants, legumes contribute towards improving the soil. Bambara groundnut [Vigna subterranean (L.) Verdc.] is grown for human consumption and is the third most important grain legume in Africa after cowpea and groundnut [28]. The seeds of bambara groundnut are known as a complete food because they contain adequate quantities of protein (19%), carbohydrate (63%), and fat (6.5%) [3]. Cowpea [Vigna unguiculata (L.) Walp.] is grown on about 10 million hectares of land in the world, mainly in Africa. The crop is tolerant towards drought and heat, and it also performs better than many other crops on sandy soils with low levels of organic matter and phosphorus [29]. Since cowpea has got a quick growth bringing about rapid ground cover, it is a useful crop in controlling erosion [30]. Grass pea (Lathyrus sativus L.) is grown for human and livestock consumption in Asia, Africa and Europe. In Africa, it is cultivated in Egypt, Ethiopia, Morocco and Algeria [13]. The plant is extremely tolerant towards drought and is considered as an insurance crop since it produces reliable yields when all other crops fail. Like other grain legumes, grass pea is a source of protein particularly for resource-poor farmers and consumers.

There are many indigenous or locally important vegetables in Africa. Among these, the following have benefits in some agronomic and/or nutritional traits: amaranthus (Amaranthus caudatus L.) matures fast and is nutritious [3]; dika [Irvingia gabonensis (Aubry-Lecomte ex O’Rorke) Baill] is rich in oil [3]; okra [Abelmoschus esculentus (L.) Moench] is fast maturing and nutritious [14]; and the Ethiopian mustard (Brassica carinata A. Braun), which is used both as a leafy vegetable and an oil crop, is tolerant towards drought and insect pests [15].

Among locally grown oil crops, the oil from noug [Guizotia abyssinica (L.f.) Cass.] and sesame (Sesamum indicum L) are used for human consumption while the one from vernonia [Vernonia galamensis (Cass.) Less.] is used in industry.

Among the root crops grown in Africa, cassava, yam, sweet potato and enset are the source of food for a large number of populations. Cassava (manioc; Manihot esculenta Crantz) is staple food for about 600 million people worldwide and for more than 200 million people in Sub-Saharan Africa [31]. In Africa, although it was cultivated on 64% of the global area in 2010, it accounted for only 53% of the total world production (Figure 1) [32]. This shows that the productivity of cassava is lower in Africa than in other parts of the world. Cassava is tolerant towards drought, and also performs better than other crops on soils with poor nutrients. Yam (Dioscorea sp) represents at least two species of the genus Dioscorea. In 2010, it was grown on about 4.8 million hectares of land worldwide, and of this 95% was in Africa [32]. The edible part of yam is similar to that of sweet potato [Ipomoea batatas (L.) Lam.], although they are not taxonomically related. Enset [Ensete ventricosum (Welw.) Cheeseman] is commonly known as ‘false banana’ for its close resemblance to the domesticated banana plant. Unlike banana where the fruit is consumed, in enset the pseudo-stem and the underground corm are the edible parts. Enset is the major food for over 10 million people in the densely populated regions of Ethiopia. It is considered as an extremely drought-tolerant crop that adapts to different soil types [19].

Banana and plantain (Musa spp.) are among the major fruit crops grown in Africa. In the year 2010, about 13 million tons of banana and 27 million tons of plantain were produced in the continent [32]. According to Fungo [33], banana, especially the orange pulped type with high carotenoid and iron content, could reduce Iron Deficiency Anemia (IDA) by over 50% and also Vitamin A Deficiency (VAD) in East Africa, where both IDA and VAD affect a large number of people. Plantain is the staple food in central Africa, and it is mostly considered more as a vegetable than as a fruit since the fruit is used for cooking. In general, both banana and plantain are considered as a healthy food, and they are also rich in essential nutrients for humans.

Food security is defined as the state in which people at all times have physical, social and economic access to sufficient food that meets their dietary needs for a healthy and active life [34]. Due to the high population increase in Africa, the demand for food is increasing over time. Figure 2 shows the total production and import of cereal crops from the early 1990s to late 2010 for Ethiopia and Malawi. Despite some years of crop failures due to drought, crop production was significantly increasing year to year (Figure 2A) [32]. However, the import of grains was also in an increasing trend, especially for Ethiopia (Figure 2B) [35]. This high demand for grain might be due to the huge population growth in the country. During the same period, the population of Ethiopia increased by 53%, i.e., from 53 million in 1993 to 81 million in 2009 (Figure 2C) [36]. In order to achieve agricultural sustainability, the increase in food production should be at least proportional to the rate of population growth. It is, however, expected that with the current level of crop productivity, it might be difficult to feed the population in the developing world, especially in Africa, where the population is growing at an alarming rate. According to Tilman et al. [37], the demand for global food is rising rapidly with about 100%–110% increase in crop demand expected from 2005 to 2050. In general, there is big gap between increase in population and crop production.

The major achievement of the Green Revolution in the 1960s and 70s was the development and introduction of semi-dwarf varieties of wheat and rice along with optimum levels of input. These broadly adapted semi-dwarf cultivars responded to fertilizer application and led to a tremendous increase in productivity. According to the International Food Policy Research Institute [38], the Green Revolution represented the successful adaptation and transfer of scientific revolution in agriculture. However, this agricultural revolution, which boosted crop production in Asia and Latin America, did not occur in Africa. This is mainly due to the fact that the Green Revolution was implemented on rice and wheat, but not on African crops such as sorghum and millets [39,40].

As indicated above, most understudied or orphan crops perform better under adverse climatic and soil conditions than the exotic crops. In addition, orphan crops are compatible with the agro-ecology and socio-economic conditions of the continent. However, when these crops were replaced by other crops new to the locality, some problems were reported. The best example is from a study made in northwestern Ethiopia where the incidence of malaria increased when exotic crops, specifically maize, substituted large areas previously occupied by indigenous crops such as tef [41,42,43]. Tef is the staple food crop for about 50 million people in Ethiopia. Malaria is a major health problem in the world, particularly in Africa. In 2010, it caused an estimated 655,000 deaths mostly among Africans [44]. The pollen from maize facilitates optimum conditions for the anopheles mosquitoes, which carry Plasmodium parasites that cause malaria. Larvae of the mosquito had a survival rate of 93 percent when it fed on maize pollen, as opposed to a survival rate of only about 13 percent when it fed on other possible food sources. As a result, the cumulative incidence of malaria in high maize cultivation areas was 9.5 times higher than in areas with less maize [41]. This shows that the introduction of new crops to the local community might bring some adverse effects on the health of the population.

African crops, despite their huge importance, have generally received little attention by the global scientific community. Due to a lack of genetic improvement, these crops produce inferior yields in terms of both quality and quantity. For instance, the seed yields of tef and millets are extremely low. The main cause for poor productivity of tef is its susceptibility to lodging [45]. Tef plants possess tall and tender stems, which are susceptible to lodging by wind and rain, and, therefore, lodging (the permanent displacement of the stem from the up-right position) inflicts significant loss in production. Some of the negative features associated with African rice (Oryza glaberrima Steud.), unlike Asian rice (O. sativa L.), are rapid shattering of the seeds, difficulty of milling the grain, and lower seed yield [9].

Poor crop productivity in Africa is also due to the use of inefficient agricultural practices starting from land preparation, sowing, weeding, harvesting and finally to threshing. Post-harvest losses also account for over 10% yield losses in Africa [46]. In addition, sub-optimal use of inputs such as fertilizers, herbicides and pesticides are also responsible for the low productivity of crops in the continent [47,48].

Root and tuber crops such as cassava and enset produce high yields, however; the products are largely starchy materials that are deficient in other essential nutrients, particularly protein. Recent studies showed that children in Kenya and Nigeria who consumed cassava as a staple food were at greater risk of inadequate dietary protein [49], zinc, iron, and vitamin A [50] intake than those children who consume less cassava in their staple diet. Although these crops are staple food crops for a large number of Africans, supplementation with other nutrients, especially proteins and vitamins, is required.

Some widely cultivated crops produce a variety of toxic substances that affect human health. The roots of cassava contain poisonous compounds called cyanogenic glycosides (CG), which liberate cyanide [18]. Konzo is a paralytic disease associated with consumption of insufficiently processed cassava. The pods and seeds of the hyacinth bean [Lablab purpureus (L.) Sweet] are poisonous due to high concentrations of cyanogenic glycosides, and they can only be eaten after prolonged boiling [2]. The seeds of the African yam bean [Sphenostylis stenocarpa (Hochst. ex A.Rich.) Harms] contain anti-nutritional factors such as cyanogenic glycosides and trypsin inhibitors. Cooking is required to reduce the toxins to safe levels, although prolonged cooking also decreases the level of nutrients in the seed [2]. The seeds of the grass pea contain a neuron-toxic substance called ODAP [β-N-Oxalyl-L-α, β-diaminopropanoic acid] [51]. ODAP is the cause of the disease known as neuro-lathyrism, a neuro-degenerative disease that causes paralysis of the lower body. Serious neuro-lathyrism epidemics have been reported during famines when grass pea was the only food source [52].

Since most fertile lands are used to grow crops other than African indigenous crops, the productivity of the African native crops under the less fertile and moisture-deficit soils is extremely low. In addition, crop productivity is affected by a variety of abiotic and biotic stresses. Major abiotic stresses are drought, soil salinity and soil acidity. There is some evidence that, in recent decades, agricultural land has been lost to desertification, salinization, soil erosion and other consequences of unsustainable land use [40]. From the total global arable area, a third is affected by salinity and 40% by acidity [53]. Biotic factors such as diseases, insects and weeds also reduce crop production tremendously. Their adverse effects on crop productivity are more obvious in the tropical regions due to their presence in high density and diversity.

There is some evidence that the current changes in climate affect crop productivity in Africa. According to Müller et al. [54], climate change poses a significant threat to the present African production systems, infrastructures, and markets. The yield of rice declines by 10% for every 1 °C increase in temperature during the growing season [55]. The study by Funk et al. [56] using in situ station data and satellite observations indicated that the rainfall decreased by about 15% in the main growing-season in food-insecure countries in Eastern and Southern Africa. The authors predicted that due to the warming in the central Indian Ocean, the continental rainfall in Africa will decrease, and this will create a drought, which, as a consequence, will increase the number of undernourished people by 50% by 2030. Fauchereau et al. [57] indicated that due to the long-term variability and changes of rainfall in Southern Africa, droughts have become more intense and widespread. The probable changes in precipitation were also estimated for Southern and East Africa based on global climate models [58,59]. While a delay in the onset of the rainy season is the cause for the shortening of the rainy season in almost the entire region of Southern Africa [58], in East Africa, a wetter climate with more intense wet seasons and less severe droughts is expected [59]. The prediction in West Africa also indicates a decrease in rainfall and an increase in temperature in the Sahel coastline [60]. According to Sarr [60], the most drastic effect of climate change on agriculture will be from the late onset and early cessation of rainfall, and reduction of the length of the growing period.

Crop domestication is the earliest improvement method in which humans selected for valuable traits such as non-shattering of grains, big grain or useable part size and loss of seed dormancy. The current important cereal crops including maize, rice and wheat were domesticated around 7000 to 10,000 years ago [61]. Advances made in understanding some domestication traits or genes were reported for these crops [61]. Methods applied in crop domestication and perceptions regarding the timing and spatial patterning of crop domestication have recently been reviewed by Gross and Olsen [62].

Selection is an ancient breeding method that is still implemented on a large-scale to improve crop plants. The technique relies mainly on the selection of plants according to their phenotype and performance. Diverse types of selection techniques have been developed for a variety of crops depending on the pollination behavior and other factors. For example, mass selection is applied to a certain level in self-fertilizing plants and is an effective method for improving landraces, especially for transferring highly heritable traits [63]. Mass selection refers to the technique whereby individual plants are selected based on their phenotypic performance, and bulk seeds from selection are used to produce the next generation.

Artificial hybridization or introgression refers to crossing closely related species in order to create genetic variation, which can be utilized for improving traits of choice. According to Baenzinger et al. [64] the success in hybridization depends mainly on the selection of parents. Hybridization can be broadly grouped into intra-specific (crossing within the species) or inter-specific (crossing between different species). Successes in intra-specific crosses resulted in semi-dwarf cultivars of wheat and rice, which boosted the productivity of both crops during and after the Green Revolution [65]. Intra-specific hybridization also increases phenotypic properties including important agronomic traits especially in cross-pollinated crops such as maize. This phenotypic superiority over the parents, which is exhibited only in the first generation of the cross, is known as heterosis or hybrid vigor. Although farmers need to buy F₁ seeds at every planting, the use of hybrid crop outweighs the use of open-pollinated crops. Genes responsible for these robust effects on yield or architecture of the plants are studied using diverse genomics tools [66].

The crosses between individuals from either different species or different genera (also known as wide crosses) are useful in transferring valuable traits from wild species to crop plants. The major breakthrough from the inter-specific crossing was the development of an artificial cereal called Triticale. Triticale is a cross between wheat and rye, and it proved to be tolerant towards abiotic stresses such as soil acidity [67]. According to Sharma [68], successful wide hybrids with wheat were obtained when species with lower chromosome numbers were used as female parents.

Mutation breeding relies on the implementation of either physical or chemical agents in order to create variability in the population of interest. While mutagens such as EMS (ethyl methane sulfonate) mainly create a point mutation in which a single nucleotide is altered, fast neutron removes pieces of DNA, which could be detected using a Deleteagene technique [69]. Mutations created by these mutagens were the base to develop and release more than 2000 crop varieties in the last seventy years [70]. Most mutation breeding programs aimed at altering traits such as plant height and disease resistance in well-adapted plant varieties of rice, barley and wheat.

Plant tissue culture is the aseptic in vitro culture of cells, tissues, organs, and their components under defined physical and chemical conditions [71]. Developing an efficient regeneration system requires optimization for various types of explants and media components. Hormones and growth regulators play a key role in determining the conversion of somatic cells to embryogenic tissues [72]. The tissue culture techniques have been successfully implemented in diverse types of plants including cereals [73,74], legumes [75], vegetables [76,77], oil plants [78], fruits [79], trees [80], and forestry [81]. Tissue culture also enables to rescue and utilize desirable properties of endangered plant species [79,82]. Among diverse tissue culture techniques, the doubled haploids are becoming a popular method in crop improvement [83]. Uma and colleagues [79] developed an efficient regeneration method for wild banana, Pisang Jajee (AA), in which zygotic embryos were excised and cultured on 6-benzyl adenine (BA) and indole acetic acid (IAA) containing media followed by callus or plantlet formation. While fully matured embryos of wild banana regenerated directly into plantlets without producing callus, immature embryos required a medium supplemented with plant growth regulators (PGRs) for successful regeneration [79].

Successful embryo rescues were reported for diverse crop plants crossed with wild relatives. By applying the rescue technique developed for the inter-specific cross between cassava and Manihot esculenta ssp flabellifolia, almost 100% of the plantlets transplanted were established [84]. This shows that by applying appropriate tissue culture technique, cassava breeding could be enhanced. Although inter-specific crosses between chickpea (Cicer arietinum L.) and its wild relatives were not successful due to post-zygotic barriers, which result in abortion of the immature embryo, appropriate rescue time overcomes the problem. In this particular case, rescuing applied at the early globular stage of embryogenesis for chickpea × C. bijugum crosses and at the heart-shaped or torpedo stages for chickpea × C. pinnatifidum was found to be optimum [85]. The presence of strong reproductive barriers between sorghum (Sorghum bicolor) and its wild relative S. macrospermum negatively affects the formation of a zygote, but a viable hybrid was developed using embryo rescue [86].

Marker-assisted selection (MAS) is the utilization of molecular markers located near genes, which can be traced, to breed for traits that are difficult to observe. Tester and Langridge [87] indicated the benefits of applying new technologies and molecular markers in crop improvement. These molecular markers are utilized to effectively assemble favorable alleles in phenotypic selection [88]. According to Collard and Mackill [89] the following factors should be considered before selecting the type of marker to apply: reliability, quantity and quality of DNA required; technical procedure for marker assay; level of polymorphism; and cost. The most common markers in use are SSRs (Simple Sequence Repeats, or microsatellites), SNPs (Single Nucleotide Polymorphisms) and INDELs (Insertions and Deletions). SSRs refer to a repeat of two to six nucleotides in the DNA sequences, and they are highly polymorphic and abundant in the genomes of organisms. SNP is a type of polymorphism, in which a considerable amount of differences in a single nucleotide is present among genotypes. INDELs refer to small sequences, which are either inserted in one genome or deleted from another genome. Commonly applied marker-assisted techniques are briefly described below.

AFLP (Amplified Fragment Length Polymorphisms): This is a genetic mapping method for detecting DNA polymorphism following restriction enzyme digestion of DNA and selective amplification of the resulting DNA fragments. The technique has been widely implemented in diverse crops especially in creating genetic maps for new species, determining relatedness among cultivars, establishing linkage groups in crosses, and studying genetic diversity and molecular phylogeny [90].

Association Mapping: This is a method of mapping quantitative trait loci (QTLs), and it involves the correlation of phenotypes to genotypes in unrelated individuals and is relatively more rapid and cost-effective than the traditional linkage mapping [43]. However, the major drawbacks of association mapping are the need for a large number of plants for screening, and the need for specific and accurate high-throughput phenotyping [91]. So far, the technique has been successfully implemented in identifying plant resistance to insects [91], wheat resistance to stripe rust [92], wheat resistance to Fusarium head blight [93], and dwarfing genes in sorghum [94].

QTL Pyramiding: This has also been implemented in several crops in order to come closer to the target trait. It enabled the breeders to dissect genes responsible for stripe rust of barley [95], crown rot of wheat [96], and blast resistance in rice [97]. In the latter case, the Jin 23B rice cultivar with extreme susceptibility to blast was introgressed to either one or more lines with blast resistance. According to the results, the level of resistance to blast improved by increasing the number of resistance genes, indicating the presence of a strong dosage effect on the resistance to blast [97].

GBS (Genotyping-by-sequencing): This is a recently discovered marker-related technique considered to be simple, extremely specific and highly reproducible in high diversity species [98]. Since the technique uses restriction enzymes to construct the library by using methylation-sensitive restriction enzymes, repetitive regions of genomes can be avoided and lower copy regions are targeted, which ultimately increases the efficiency [98].

RAD Tags: SSR and SNP markers could also be discovered in plants using a recently developed RAD (Restriction-site Associated DNA) tag method, which also involves high-throughput sequencing using the Illumina platform. The technique enabled the discovery of a large number of DNA markers in eggplant (Solanum melongena L.) in which about 10,000 SNPs, 1000 indels, and 2000 SSRs were obtained [99]. RAD tags were also used to identify three quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in perennial ryegrass (Lolium perenne L.) from crosses between a susceptible and a resistant plant [100].

GWAS (Genome Wide Association Studies): This is a method of scanning the whole genome of the organism in order to analyze genetic differences, particularly SNPs, between genotypes of interest. The major benefit of GWAS is that it provides higher resolution mapping that is mostly at the gene level [48]. The technique was recently applied in Chinese maize inbred lines to identify candidate genes that affect plant height [101]. GWAS has also successfully identified multiple loci for aluminum resistance in wheat (Triticum aestivum L.) germplasm [102].

CGA is based on the hypothesis that genes with a known function in other species (i.e., functional genes) or genes that are in close proximity to loci controlling the trait (positional genes) could control a similar function or trait in a target crop of interest [103]. Hence, research on understudied crops of Africa could benefit from this approach based on already known genes and knowledge in other well-studied crops.

TILLING (Targeting Induced Local lesions IN Genomes): This is a non-transgenic and a reverse genetics method, which uses traditional mutagenesis followed by high-throughput screening in order to identify single base pair changes in a target gene [104,105]. Some of the benefits of TILLING are: (i) It produces a spectrum of allelic mutations that are useful for genetic analysis; (ii) mutations difficult to know by forward genetics could be revealed since it can focus on a particular gene of interest; and (iii) it is a non-transgenic method, hence the product is readily accepted by all sectors of society. TILLING has been successfully implemented in maize [106], wheat [107,108], rice [109,110], barley [111,112], sorghum [113], and orphan crops such as tef [114].

Eco-TILLING: This is the modified form of TILLING, and in this case polymorphisms are detected in a natural population without the use of mutagenesis [115]. In general, TILLING and Eco-TILLING are useful in rapidly detectable point mutations in populations irrespective of genome size, reproductive system and generation time.

Transgenic technology is proved to improve the productivity of crops. The technique enables molecular biologists to transfer a single or multiple gene(s) of interest to the plant of choice. As a result, plants, which are tolerant towards a multitude of environmental stresses or those with improved nutritional qualities, are obtained [116]. Due to the high adoption rate of the technology, the global area under transgenic crops has increased tremendously from just 1.7 million ha in 1996 to about 160 million ha in 2011 [35].

RNAi (RNA Interference): This technique is more and more widely applied in plant biotechnology, both as a useful tool for discovering or validating gene functions and as a quick way of engineering specific reductions in the expression of chosen genes [117]. The technique relies on the suppression of some biological activities in plants thereby resulting in plants with expected phenotypes [118]. Hence, RNAi has an enormous application in crop improvement. The application of RNAi in improving the nutritional value of plants, especially metabolomics, has recently been reviewed [119]. RNAi had also enabled the development of plants resistant to nematodes, herbivorous insects, parasitic weeds and fungi [120,121].

Marker-free Transgenics: Although transgenic technology has shown significant impact in increasing crop productivity, its expansion to other crops and geographical regions is restricted due to extensive regulatory procedures and negative public perception [87]. Some of the recent investigations on transgenics dealt with solving the major concerns affecting the acceptance by the public. Among the concerns, the presence of antibiotic- or herbicide-resistance markers and non-plant promoters are the major ones. Hence, it would be desirable to remove these markers or foreign genes in order to increase the acceptance of transgenic products. Mentewab and Stewart [122] enabled the substitution of antibiotic resistance markers with those without any adverse effects. Bhatnagar et al. [123] also recently developed a transgenic peanut without any selectable marker by using marker-free binary vectors harboring either the phytoene synthase gene from maize or the chitinase gene from rice inserted into the plant, and that can be identified by PCR. Advances in increasing the efficiency of gene targeting as demonstrated by Shukla et al. [124] and Townsend et al. [125] using zinc-finger proteins will also promote specific or targeted gene transfer and avoid unwanted or unnecessary pieces of DNA movement to the crop of interest.

Cisgenesis: This refers to a method recently developed by the group at Wageningen University, in which plant-specific promoters are used to drive the gene of interest instead of foreign promoters from bacteria or other organisms [126]. According to the inventors, materials developed through cisgenesis should be exempted from a stringent regulations set for genetically modified organisms [127].

Intragenesis: This is a technique, in which genetically modified plants are created that contain elements only from within the sexual compatibility group, as it excludes unknown or foreign DNA [128]. It is also claimed that as the technique mimics traditional plant breeding, that the products from intra-genics are as safe as those from traditional breeding [128,129].

TALEN (Transcription Activator-like Effector Nuclease): In this method, targeted expression of a gene of interest is made using sequence-specific nuclease [130]. The method was recently implemented in developing disease-resistant rice [131].

Due to their high capacity sequencing, next generation sequencing (NGS) platforms such as 454, Illumina and Solid, provide large amounts of sequence information, which have direct application in other crop improvement techniques. Some improvement techniques, which rely on genome and transcriptome sequencing, are TILLING and Eco-TILLING, SSRs and SNPs, and markers linked to genes and QTLs [132].

RNASeq: This was used to obtain the reference transcriptome for sugar beet (Beta vulgaris sp. vulgaris) and to investigate global transcriptional responses to vernalization and GA treatment [133]. The expression profiles due to vernalization and GA treatment suggest that RAV1-like AP2/B3 domain protein is involved in vernalization and efflux transporters in the GA response [133].

MutMap: This is a recently discovered method, which successfully identified the unique genomic position harboring mutations in semi-dwarfism in rice [134]. The technique was applied to an EMS (ethyl methane sulfonate) mutagenized population. MutMap is based on whole-genome re-sequencing of pooled DNA from a segregating population of plants that show a useful phenotype [134]. Selected mutant lines are first introgressed to the original non-mutagenized line and then self-pollinated in order to obtain F₂ progenies for SNPs discovery.

The primary goals of many crop-breeding programs are to improve the productivity of crops, especially the edible and/or economically important parts. Since yield is affected by multiple traits, breeding programs focus mainly on improving individual traits known as yield components or yield-related traits such as panicle yield, number of tillers, seed weight, and others.

Due to the presence of extreme climatic and soil conditions, which adversely affect crop productivity, many breeding programs are geared towards developing crops, which are resistant to some of these environmental calamities. Breeding for effective use of water (EUW) is considered the best strategy towards mitigating the effects of moisture scarcity and to develop drought-tolerant crops [165]. Several tools have also been developed to create crops tolerance towards or resistance against a variety of weeds, diseases and insect pests.

Among traits that contributed to higher crop productivity in the last century, those, which alter the architecture of the plant, rank first. Architectural changes include alterations in branching pattern and reduction in plant height. Semi-dwarf wheat and rice varieties developed during the Green Revolution elevated the productivity of these crops tremendously. Plants with an erect leaf phenotype or narrow leaf angle were also efficient in capturing light, which also contributes towards increasing productivity.

Traits, which improve the nutritional level of food crops, are also important, as edible parts of some staple crops such as cassava are deficient in protein, fat, and vitamins. In addition, traits related to consumer preference (e.g., cooking and eating quality, color of grain, etc.) are also useful to incorporate in the breeding program.

The Forum for Agricultural Research in Africa (FARA) website offers information about organizations, projects and experts in the agricultural research system in Africa [166]. The search tool gives options to obtain information on the thematic groups such as plant production, animal production, socioeconomics, farming systems, and others for each country's or regional organizations. Information about organizations and projects present in each African country is also available. According to the website, the total number of national institutes in the continent are 867, while countries with over 50 institutes are only South Africa (71), Uganda (57), Kenya (54), and Egypt (53) [167].

The CGIAR is a global network of 15 international research centers with a strategy to tackle the major global problems in agricultural development. In their research and development programs, the CGIAR centers give particular emphasis to Africa. The recently revised CGIAR programs focus on improving: i) yields and profits of crops, fish, and livestock; (ii) sustainability and environmental integrity, and adaptation to and mitigation of climate change; (iii) productivity, profitability, sustainability, and resilience of entire farming systems; (iv) policies and markets; and v) nutrition and diets [204]. According to Renkow and Byerlee [205], the contributions of CGIAR to crop genetic improvement, pest management, natural resources management, and policy research gave strongly positive impacts relative to the investment, while crop genetic improvement research resulted in the most profound positive impacts.

Improved cultivars of NERICA were developed in early 2000 by the Africa Rice Center (ex-WARDA: West Africa Rice Development Association) through crossing the high yielding Asian rice (Oryza sativa L.) with the locally adapted African rice (O. glaberrima Steud.). Some of the desirable properties of NERICA rice are high grain yield, high protein content, early-maturity, resistance to diseases and insects, and good taste. On-farm studies in Uganda indicated that a higher yield of NERICA was obtained by farmers who had rice-growing experience than by those who had no previous experience [209]. This suggests the need for improving the training and extension along the promotion of NERICA. A three-year study in Western Kenya using four NERICA and one local variety showed that NERICA 1 gave superior yield over the other varieties [210]. The adoption study with 600 rice farmers in Gambia indicated that significantly higher seed yield and income were obtained by NERICA adopters than by the non-adopters [211]. Another study involving 1500 farmers in Côte d’Ivoire showed that, although the potential adoption rate for NERICA was 27% in the year 2000, the actual adoption was only 4%, indicating a potential for high adoption through successful NERICA dissemination [212].

Although tef is a staple food for about 50 million people in Ethiopia alone, it suffers from low productivity. Over 30 improved tef varieties were released to the farming community in the last several decades, however; the recently released Quncho variety received a nation-wide popularity. Quncho was developed from the cross between improved varieties Magna (DZ-01-196), a variety with consumer-preferred white grain color but with low productivity, and Dukem (DZ-01-974), a high yielding variety but with low market price due to the pale white grain color. Hence, a targeted cross was made between the two varieties with the objective of selecting lines combining the high yield of Dukem and the seed quality trait of Magna. Quncho was developed as a recombinant inbred line (RIL) through an F₂-derived single-seed descent method followed by a series of multi-environment yield tests in various major tef-growing regions of the country [213].

In order to speed up the supply of quality seeds of the Quncho to ultimate users, an intensified seed multiplication scheme was followed by involving research centers, seed enterprises, farmers, and private seed growers. Through the use of on-farm seed production, efforts were made towards exploitation of the indigenous knowledge in tef seed production and maintenance [214]. An effective innovative approach was adopted in the demonstration, popularization and dissemination of the Quncho tef technology. The major features of this approach were; (i) dissemination of technology as a package; (ii) use of large farmers’ fields for on-farm demonstrations and scaling-up of the technology; (iii) coordinated multi-stakeholders’ partnership extension approach; (iv) distribution of improved seed on ‘revolving seed loan’ basis; (v) provision of regular training on the technologies for farmers, development agents and extension personnel; (vi) regular follow-up and supervision of the scaling-up activities by a team of researchers and extension agents; and (vii) provision of inputs and marketing options through farmers’ cooperatives and cooperatives’ unions. Due to the implementation of the above extension system, over 31,000 tef-producing farmers’ households with an area of more than 10,000 ha directly participated in the scaling-up activities of Quncho. This activity was carried out by the collaborating research centers and the National Crop Technology Scaling-up Program and enabled the distribution of about 306 tons of seeds, and the average yield obtained by the farmers ranged from 2.0 to 2.3 t ha⁻¹.

The Tef Improvement Project (TIP): This is based at the Institute of Plant Sciences in University of Bern, Switzerland, with the goal of boosting the productivity of tef by tackling major production constraints. Priority is given to developing semi-dwarf and lodging tolerant tef cultivar(s). Tef has a tall and tender stem that is susceptible to damage by wind and rain. As a consequence, the yield from the crop is severely reduced in terms of total yield and quality of both the grain and straw. The project applies the following strategies: (i) implementing TILLING on a population of about 6000 mutagenized families in order to identify mutations important for the traits of interest; (ii) phenotypic screening of the mutagenized population for traits such as drought tolerance; (iii) sequencing and analyzing the genome and transcriptome of tef; and iv) collaborating with the Ethiopian agricultural research system in the area of new variety development and training. Several semi-dwarf and lodging tolerant candidate lines obtained from the mutagenized population have been introgressed to high yielding tef cultivars and are currently being evaluated in the field in Ethiopia. The project also focuses on developing drought-tolerant tef lines, in which two drought-tolerant candidate lines are under field-testing in Ethiopia. Although products from TIP have not yet reached farmers, the performance of several lines at the on-station testing is encouraging.

About a decade ago, African countries agreed to allocate at least 10% of their national budgetary resources to agriculture and rural development policy implementation. However, among 24 countries, only six countries achieved the target by 2005 [215]. African governments also need to implement policies, which support agricultural development. These include conducive policies on land, marketing, and credits, which favor productivity. Commitment to invest in African research also comes from the private sector. Syngenta has recently announced to invest a total of $500 million over 10 years to transform African agriculture with shared knowledge, tools, technologies and services by focusing on seven countries, namely: Ethiopia, Ghana, Ivory Coast, Kenya, Mozambique, Nigeria and Tanzania [216].

The germplasms of many understudied crops have not been properly collected and utilized by researchers. Hence, collections of these germplasms need to be done from diverse agro-ecologies. In order to harness the genetic diversity among the landraces, the germplasm also need to be available to researchers from both developed and developing countries.

Among diverse types of tools developed for major crops of the world, those, which are efficient, cost-effective and easily applicable to the present conditions and institutions of each country should be selected and implemented. Some of the major tools currently applied in crop improvement (as shown in Figure 2) have already been discussed in earlier sections.

Ideotype breeding refers to theoretically defining the most efficient plant type for a particular crop and environment, and then breed towards this goal. The ideotype approach has been used in global rice breeding programs where ‘super’ hybrid cultivars with high yield potential were developed [217]. In this case, emphasis was given to obtain rice plants with large panicle size, reduced tillering capacity, and improved lodging resistance. Ideotype breeding was mostly done to determine the morphology or architecture of the plant, which include the height of the stem, branching pattern and the angle and size of leaf. Sarlikioti et al. [218] indicated that a new tomato ideotype with more spacious canopy architecture due to long internodes and long and narrow leaves led to a 10% increase in crop photosynthesis.

Berry et al. [219] indicated that the best ideotype of wheat plant would be one with the yield potential of 8 t ha⁻¹. Key parameters required to develop this type of wheat are shorter plant height, wider root plate, and appropriate stem strength especially at the bottom internode [219]. Breeding tools such as marker-assisted selection were efficient to create the ideotype of choice. For instance, a rice line with submergence tolerance and best cooking quality (also called ideotype 1, ID1) was developed using this method [220]. In addition to being tolerant to waterlogging and having jasmine-like cooking quality, ID1 lines exhibited a low-amylose content, a fragrance and a high alkali spreading value. According to Mi and colleagues [221], in order to efficiently utilize nitrogen, maize plants need to have the following three root ideotypes: (i) deeper roots with high activity that are able to uptake nitrate before it moves downward into deep soil; (ii) vigorous lateral root growth in order to increase N availability in the soil; and (iii) strong response of lateral root growth to localized nitrogen supply so as to utilize unevenly distributed nitrate, especially under limited N conditions.

Food security is becoming the major concern especially due to the high level of population growth. According to Parry and Hawkesford [222], integrated and sustainable crop production approaches should be urgently implemented in order to achieve the projected doubling of food production by 2050. Misselhorn et al. [223] also suggested strong interaction between diverse actors and sectors ranging from primary producers to retailers and consumers, and the use of frontier technologies in order to obtain global food security. Hence, due to the diversity in the agricultural conditions, the goals of breeding programs and the tools applied also vary.

Narrowing the yield gap is crucial to provide food for every citizen of the world. Based on the study in Yaqui Valley in Mexico, Ahrens et al. [224] indicated that the yield gap in wheat could be minimized by improving nitrogen use efficiency (NUE). According to them, split applications of N fertilizer significantly increased seed yield and profit, and reduced N pollution. Based on earlier studies, Lobell et al. [225] estimated the yield potential for several cereal crops in irrigated and rain-fed systems. Although up to 80% of the yield potential was achieved for irrigated wheat, rice, and maize, a maximum of only 50% of the yield potential was obtained for rain-fed conditions, indicating that large increases in crop production is expected from the latter system [225]. Studies on the yield potential and gap for several understudied crops such as cassava and tef showed that crop productivity could be increased several-fold for these orphan crops using improved genotype and/or management (Table 4). Since studies also indicated that agricultural production increased in Africa through optimum use of input such as fertilizers, herbicides and pesticides [47,48], this sector should also be given priority.

The main reason for poor productivity of African crops is related to little investment in research and development of these crops. African crops were not represented in the famous Green Revolution, which doubled or tripled productivity of major crops. According to Ejeta [39], in order to achieve a Green Revolution in Africa, locally appropriate technologies need to be developed in addition to human and institutional capacity building as well as forming conducive policies. Due to the large diversity in agricultural systems and crops cultivated in Africa, some institutions or individuals suggest “rainbow evolutions” that differ in nature and extent among the many systems from a single “Green Revolution” type that occurred in Asia [230]. According to Horlings and Marsden [231], the real green revolution will be realized in Africa by implementing an ecological modernization process, which includes social, cultural, spatial and political aspects. In this approach, also known as “agri-food eco-economy”, the collaboration of many stakeholders including farmers, consumers and those in the marketing is important [231].

Since abiotic stresses such as drought, salinity and heat as well as the changing of climate substantially affect the productivity of crops and food security, future research should also focus on developing resistance or tolerance against these environmental calamities. Ahuja et al. [232] enumerated some physiological and molecular mechanisms involved in plant stress adaptation especially on how genes, proteins and metabolites change after individual and multiple environmental stresses. In order to identify adaptation priorities, Lobell et al. [233] analyzed climate risks for crops in 12 food-insecure regions in Asia and Africa. According to them, due to extreme predictions for negative impact of climate change, priorities for adaptation should be given to sorghum (Sorghum bicolor L. Moench) in the Sahel region, and maize in Southern Africa [233].

Stakeholders involved in African agricultural research and development need to invest in agricultural innovation, as it contributes towards improving the production, marketing or distribution system. A study in Cameroon on plantain banana (Musa paradisiaca L.) indicated that both institutional and organizational innovations play key roles in increasing crop productivity and income in rural areas, and also in the production of human and social capital and the protection of forest resources [234].

Among agricultural innovations made in Africa, the Push-Pull system [235], which was developed by the International Centre of Insect Physiology and Ecology (ICIPE) in Kenya, is remarkable. The system is effective in protecting maize from dangerous stem borer and a parasitic weed called Striga. In this system, maize is intercropped with Desmodium whereas Napier grass is planted around the field. While Desmodium produces a smell that drives away stem borer adults and also a chemical that prevents Striga from attaching to maize roots, the Napier grass attracts stem borer adults towards it. The adult insects lay their eggs on the Napier grass and when the eggs hatch, the grass produces a sticky substance that kills the larvae or young stem borers. The system is also useful in reducing the amount of pesticide application [236]. The uptake and dissemination of the ‘Push-Pull’ technology was studied in Western Kenya using randomly selected 112 farmer teachers and 560 follower farmers who had adopted the technology [237]. In addition to improving the productivity of maize through controlling insect pests and parasitic weed, the Push-Pull technology also provides forage for the livestock, releases essential plant nutrients to the soil and reduces soil erosion [238]. In order to further investigate the adoption of the Push-Pull technology, a four-year on-farm study was made in 14 districts of Western Kenya involving twenty randomly selected farmers who had adopted the technology from each district [239]. According to the interviewed farmers, the ‘Push-Pull’ technology is outstanding in reducing stem borers and Striga infestation and in increasing soil fertility and maize grain yield. African agricultural researchers could also learn from innovations implemented in developing and successfully disseminating technologies of NERICA rice and Quncho tef (both technologies are described above).

African countries also need to focus on achieving sustainability in their agricultural research and development. A recent study showed that 40 projects from 20 African countries benefited over 10 million farmers and their families [240]. According to Pretty et al. [240], the outputs from sustainable intensification are two-fold: multiplicative (boosting yield per unit area) and additive (diversification through introducing new crops or other food items).

Success in agricultural development is not achieved without the adoption of improved technologies by a vast number of farmers. This calls for the establishment of a strong extension system, which links the research community to the farming community. The transfer of new technologies to farmers is facilitated if the studies are made towards solving the major constraints and also by involving farmers from an early stage of technology development as it enhances the ultimate acceptance of the technology. Since farmer-to-farmer extension is more efficient in expanding the new technologies than the formal system, involving farmers in seed production and distribution is important as it has been witnessed in the dissemination of Quncho technology (also indicated above) [214].

Establishing a genuine partnership with national, regional and international institutions is important for the success of any intended project. Nowadays, public-private partnership (PPP) is considered as an effective system to bring together the public and the private sectors towards enhancing agricultural sustainability in the developing world. Ferroni and Castle [241] presented several promising PPPs in which the Syngenta Foundation for Sustainable Agriculture has been actively involved over the last decade. These partnership projects in Africa include a lodging tolerant and semi-dwarf tef [242], rust-resistant wheat, and biofortification of sweet potato. Spielman et al. [243] also investigated 75 PPP projects carried out by the International Agricultural Research Centers considering three criteria: (i) the contribution towards reducing the cost of research; (ii) added value to research by facilitating innovation; and (iii) impact of research on smallholders and other marginalized groups in developing country agriculture.