Genetic Improvement of Minor Crop Legumes: Prospects of De Novo Domestication

Abstract

Minor crop species and their wild relatives are resilient to multiple environmental stressors and are a great potential resource for promoting global food and nutritional security. However, since many of these species are deficient in a few or several desirable domestication traits which reduce their agronomic value, further work on their trait improvement is required in order to fully exploit their food benefits. Thus, to some extent, a minor crop may be regarded as semi-domesticated species based on the extent to which it is deficient in a number of agronomically significant domestication traits. Quite recently, research has revealed prospects of creating new crops out of wild plant species via de novo domestication. Minor crops deficient in desirable domestication traits as well as their wild relatives can possibly be subjected to such a systematic process of redomestication and de novo domestication in order to increase their food, nutritional, or raw material utilization value. This review discusses the feasibility of employing CRISPR/Cas-mediated genome editing techniques for the genetic enhancement of minor legumes and de novo domestication of their wild relatives.

1. Introduction

The yield productivity of many major crop species, including those in the grain legume category, is hampered by unpredictable environmental conditions. This phenomenon has triggered the need to generate new crop species with prospects as good complements or alternatives to the major food crops [1, 2]. The new crops are not only expected to be endowed with better adaptation potential against one or multiple environmental threats, but also, they must exhibit preferred agronomic and nutritional composition attributes to satisfy growers, breeders, and consumers’ claims. Efforts have therefore been made over the past few years in the collection of crop wild relatives in order to exploit their essential alleles for genetic improvement of elite crop species. Minor crop species or neglected and underutilized crop species (NUCs) and their wild relatives are nutritionally important, just as the known crop wild relatives/progenitors of major crops [1, 3, 4]. Consequently, minor species have in recent times gained research recognition for their potential value for agricultural sustainability and for safeguarding against food insecurity [3, 5, 6]. These crops, which are members of the family of Leguminosae or Fabaceae have been considered as one of the most valuable species with numerous prospects for food in many parts of the world. As Leguminous species, these crops contain food nutrients that are essential for building a healthy human body [7, 8]. Also, they form a key component of many processed food products and animal feeds [9]. Legume species have over the years played significant roles in cropping systems for soil nutrient improvement, weed control, reclamation of wastelands and consequently contributed towards promoting ecological sustainability [1, 5]. Of the more than 20,000 plants species classified as legumes and distributed across some 800 genera [9, 10, 11] only a smaller number are fully explored and utilized for food, feed, and other agricultural and human required purposes [12].

Currently, genetic enhancement by de novo domestication of minor crops and their wild relatives using a genome editing system has been confirmed as a useful approach to explore and expand food crop resources for agricultural, food, and nutritional sustainability [13, 14, 15]. The technique offers prospects for developing new crops for today and future usage. However, scientific exposition in terms of the possibility of conducting de novo domestication schemes to convert semi-domesticated minor crops and their wild relatives to fully domesticated crop species is less reported. Now following advances in molecular biological technology, which provides powerful tools for genetic study, it has become more convenient to apply genomics to the study of minor crops which further paves the way for conducting de novo domestication experiments [16, 17]. Therefore, the current review discusses the feasibility of applying de novo domestication for the creation of new crop species from minor legumes and their wild relatives. Some suggested requirements for conducting a successful de novo domestication of a named minor legume which is also applicable in other non-leguminous minor crop species have been provided.

2. The need to explore minor legumes as alternative crop species

While there is much commitment to guarantee adequate food production, availability, and supply to people of all areas across the globe, agricultural productivity is still being confronted with several human-induced and exogenous environmental conditions (Figure 1) [1]. This forms an integral component of the reasons for the uncertainties in any attempts to safeguard against human food and nutritional insecurity [18, 19]. The current human population statistics reveal a predicted burgeoning trend across all continents and that from the present estimated 7.5 billion people, the global population is predicted to hit 8.5 billion by 2030, 9.7 billion by 2050, and beyond 11 billion by 2100 [20, 21, 22]. This phenomenon calls for increased agricultural productivity or increased food crop yields through the application of advanced agricultural technology and enhanced diversity of plant resources [6, 19]. Conversely, in many parts of the global agricultural productivity is low and this has partly been attributed to factors including low adoption of improved technology exacerbated by fluctuations in climatic conditions [18, 23, 24]. Rising urbanization with accompanying suite of developmental projects as well as indiscriminate exploitation of natural resources in some parts of the world is deteriorating and claiming vast areas of arable lands [15, 22, 23, 25, 26]. There is also increasing depletion and wilting of water bodies in some parts of the world [23]. The reality is that these factors in concomitant with human selectivity behavior for specific foods and food products will increasingly impose a great burden on food production, food quality, and supply systems in both the present and the future [25]. In addition, the major food crops feeding the world today are also a few with some of them cultivated outside of their historically originated and domesticated environments where they are probably better adapted to thrive well [6, 22, 27, 28]. Even those which are still being produced in their centers of origin, edaphic conditions, and altered climatic variables have become major limitations to their maximum growth and development resulting in a dwindling yield output [29].

Figure 1.

Why there is a need for alternative crop species.

In the midst of the above global worries [18, 20, 22, 23, 24, 26] food production must not only increase but also worldwide availability and supply must be guaranteed. So, there is increasing interest to discover new opportunities and means required to increase the human food resources base. The cultivation, utilization, breeding, and preservation of leguminous crop species are well discussed, and they represent one of the food resources extensively consumed across the globe [30, 31]. Therefore, it is imperative to explore and exploit these new crop species as an alternative or supplement food resources endowed with economically valuable traits such as resiliency to environmental threats and adaptation to different production conditions. In this way, minor crop legumes will thrive well in their niches and consequently attain their maximum growth, development, and consequently, improved yield output [32].

3. Legumes and minor legumes: an overview

Generally, grain legume species are angiosperms and members of the family of Fabaceae with a characteristic high protein composition in their grains. They are specifically grown or harvested for human consumption needs mainly as food, unlike forage or pasture legumes which are used for animal feed. Legume species are regarded either as major or minor by virtue of the extent of their consumption utilization, economic value, as well as research and breeding commitment, received. The major legume crops are known for their full domestication, a high and broad range of consumption, extensive cultivation, efficient utilization in research and genetic improvement as well as their popularly exchanged status across wider geographical regions. These features make major legumes distinct from minor ones.

Minor legumes constitute one of the most attractive categories of legume species identified and though spread across the world, and existing as both cool-season and warm-season legumes [33], they are predominantly endemic to tropical regions [3, 24, 31]. The significance of these species has in recent times been well expounded. They are a source of food security crops for rural farmers during lean cropping seasons and also possess valuable traits which can be exploited for modern crop breeding programs. They are endowed with agriculturally significant attributes such as resiliency to multiple biotic and abiotic conditions, thus making them essentially significant for incorporation into cropping and food systems [31, 34, 35]. However, most of these species may be vulnerable to extermination under unprotected agro-biodiversity fields with the few surviving not being fully exploited in terms of their incorporation into crop production and breeding programs. As a result of the increasing global demand for grain legumes and their products, there is now extensive research commitment by various governments and institutions to expand crop germplasm resource base including minor crops and their wild relatives, and consequently improve upon their economically significant traits.

4. Minor legumes as food and nutritional security crops

Leaders and diverse communities across the world endorse the fundamental rights of all persons irrespective of the location to have adequate food and thus stay out of persistent hunger or food deprivation [36, 37]. However, over 800 million people especially in less privileged locations of the world still require a great effort in order to meet their food requirements [38, 39]. Malnutrition is still a worry in various parts of the world and one out of every nine people across the globe suffers from persistent hunger [40]. This phenomenon appears to raise major concerns globally, especially by policymakers and international communities such as the United Nations and FAO who are tasked with specific roles of promoting adequate food supply to all persons [36, 37]. Across the globe now, matters of food insecurity have become a concern, and strategic modalities to assuage a likely worsening occurrence are extensively been discussed [41, 42, 43]. To help tone down food and nutritional insecurity, there must be an increasing effort to search and utilize alternative opportunities especially by promoting diversity within crop species [6, 24, 44]. Therefore, advancing sustainable agricultural productivity has become one of the keys focuses to realize this goal. Grain legumes are noted for their potential in the maintenance of food and nutritional security since they contain numerous nutritional requirements and most of these species are resilient against diverse environmental conditions responsible for general crop yield reduction [5, 45, 46]. At present, there is enough evidence that minor crop species could help in addressing these challenges especially in less developed economies and arid regions which are more vulnerable to food shortages [18, 24]. To bridge food and nutritional requirement gaps, it is estimated that some additional boost of 70% of food must significantly be produced within this period up to 2050 during which the world’s human population is predicted to grow from 7.5 to 9.7 billion [47, 48]. It is obvious that many developing countries with burgeoning population growth rates but fewer agricultural technology applications will be most seriously hit. Given this occurrence, minor crop species which are more endemic in these regions have become one of the best alternative approaches to help avoid food insecurity [3, 24].

5. Genomics and genome sequencing of legume resources

In recent times, following the emergence of next-generation sequencing technology many cultivated crop species have had their genomes sequenced [19, 49]. With the increasing number of molecular databases and computational analyses tools, genome information of such species has been stored making these crops now more amenable to crop improvement by molecular and genomic techniques [49, 50]. The molecular databases have particularly paved the way for mapping and identifying causal mutations, candidate genes, or QTLs associated with diverse traits of domesticated legumes [51, 52, 53]. Therefore, in modern crop improvement systems, the application of genomics as a complement to conventional breeding schemes has become a common practice [54]. Through genomic-based techniques, traits that are deficient in the major legume cultivars can now be introduced from other plant species. A few years ago, research about minor crop species was very much focused on their collection, morphological characterization as well as other information required for their documentation such as degree of consumption, production, nutritional value, market value, medicinal value, and, ethnobotanical descriptions [39]. Now it has become more convenient to apply genomics to minor crops and develop databases for storing and making available detailed information about their genome sequences [55, 56, 57]. Thus, there are some minor crop species that have now entered a genomic epoch (Figure 2) with research efforts ongoing to convert several of these species into genomic resource-rich crops [3, 31, 56, 97]. In this way, the beneficial traits or gene constituents of these species can fully be exploited and incorporated into the basket of major legume crops feeding the world today. Additionally, there are minor crops that have desirable traits and are good model species for research. Thus, vital information such as minor crop legume evolution dynamics can easily be delineated and promote effective breeding [49].

Figure 2.

Some genomic-rich legume species [58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96].

Besides, the application of functional gene cloning and marker-assisted selection in crop breeding has gained momentum and is currently being extended from sole application in major crop species to minor crop species. Following the release of the genome sequences of some minor legume crops, further molecular genetics and genomic studies have been conducted to delineate causal mutations, genes, and QTLs underlying specific traits [49]. Whole-genome resequencing, genome-wide association studies, whole-genome organization analysis of genes of interest, and genomic selection techniques have been employed to study domesticated traits in some minor legume crops [16, 17, 98, 99, 100, 101, 102, 103, 104, 105]. The increasing understanding of the genomics of major-minor crop legume species is accelerating the process of their genetic enhancement and paving the way for the domestication of their wild relatives by de novo approaches [106, 107]. Intuitively, a minor crop with available reference genome sequence information will easily be amenable to the genetic enhancement and de novo domestication of its wild relative than the one without a reference genome sequence. With the presence of a reference genome sequence, variations in phenotypic and genotypic attributes of the model and target minor crop species are easily compared, discerned and the requisite information elucidated. The genome sequences of many plant species including cultivated crops, and model plants, are currently available [4] and such known genomic information can be translated to other closely related species [105].

6. Crop domestication

Since the time of Vavilov’s concept on the origin of domestication of cultivated crops [108] the topic of crop domestication and evolution of agriculture has received in-depth research interest [15] with much enthusiasm from diverse disciplines including genetics, history, archeology, paleobotany, and anthropology [109, 110]. Generally, hunting of wild animals and gathering of crop species for human sustenance was a stage in the history of early humans that preceded the Neolithic revolution age [111]. The Neolithic revolution marked the era of major agricultural innovations and inventions. Perhaps one of the foremost events which occurred during this period of human existence was the shift from hunting and gathering to the culture of sedentary living. It was during this period that crop domestication commenced. The domestication events generally proceeded as a gradual trait transformation process where plant species were unconsciously made adapted for agriculture and hence the two events, domestication and agriculture can be postulated to have occurred concurrently. The Neolithic era form of domestication involved the selection of specific plant species by virtue of human desired traits and over a longer period of continuous selection, the selected species were attuned to human cultivation and management practices. The Neolithic humans selected plant species endowed with preferred phenotypic attributes or traits such as better yield, taste, storability, increased seed size, less dormancy, and adaptability to management tools [112, 113, 114] thus leaving the rest (the largest chunk) as wild in their natural settings. This phenomenon differentiated crops domesticated from their wild relatives and progenitor species. As a result of few plant species selected for cultivation, the domesticated ones were positioned to have a narrowed biological diversity relative to their wild relatives and progenitors [115, 116, 117]. Over a longer period of continuous cultivation, genetic and genome alterations possibly occurred, and sometimes created new genotypic and phenotypic variants [118]. Therefore, genes of the domesticated crops became fixed and linked to specific plant phenotypes or traits [119, 120]. These selected genes are called domesticated genes and their underlying traits are domesticated traits [118]. Intuitively, the selection of a given plant species as a domesticated crop based on its phenotype also meant an indirect selection of certain mutations and genes which remained unknown until plant breeding began. A further crop genome alteration in the post-domestication period can largely be attributed to the emergence of classical plant breeding [15].

The process of domestication also led to today’s concept of genetic bottlenecks, and domestication syndrome, the suite of traits that confers a distinguishing characteristic on domesticated crops relative to their progenitors [111]. Domestication syndrome serves as an important cursor to facilitate discovering, mining and utilizing unexploited, underutilized, and neglected genes in crop wild relatives and minor crops [121, 122]. Generally, the combined effects of domestication and plant breeding are the result of altered crop phenotypic and genotypic architecture. Insight into crop domestication syndrome is particularly a prerequisite for effective and efficient minor crop domestication in this era of genomics and genome editing in crop breeding [123].

6.1 Crop redomestication for genetic enhancement of minor legumes

The major global agricultural challenges have already been mentioned previously in this work, and now there are uncertainties with regard to meeting the food and raw material needs of the ever-burgeoning human population. To tackle this occurrence with forethought, there is a need to take expedient actions that can facilitate expanding the human food resources base. This condition has been necessitated based on the established reality that only a negligible number out of the earth’s endowed thousands of known plant species have been fully domesticated and currently been used as human food, animal feed, and raw material resources [124]. These major crops are losing their conferred natural adaptation potential such that their products will require human manipulation, especially where these crops are to be cultivated outside their original environmental niches [15]. The numerous species left in the wild as crop wild relatives and progenitors possess a wider genetic diversity and offer an ideal opportunity to be exploited for crop genetic enhancement. Now, as a result of the adoption of the major crop species many crops which are endowed with value for food have been less utilized or neglected though they have received some amount of domestication (semi-domesticated). These categories of crop species especially, legumes harbor essential alleles which can be exploited for improving upon the traits of cultivated ones. There is now an idea to revisit minor species and crop wild relatives which have either received some amount of domestication or none at all for their incorporation into major food crop resources. These semi-domesticated species including minor crops which are deficient in one or more desirable domestication traits can then be redomesticated using modern molecular breeding techniques. For minor crop species, their collection and further usage for experimental studies are being conducted along with their wild relatives.

By and large, plant breeding has become the surest way to adapt or develop new crops for major cultivation in unfamiliar environments. The utilization of alleles from crop wild relatives and progenitors for the genetic enhancement of domesticated or semi-domesticated traits of crop species is generally referred to as redomestication. This holds immense prospects to attune cultivated species to the prevailing environmental stresses. Another way, the traditional approach to achieve redomestication of lost or neglected crop species is perhaps, to encourage their extensive cultivation in their inhabiting niches. Crop redomestication is an opportunity to circumvent agricultural challenges arising from climate change, reduce crop diversity, and consequently help promote agricultural sustainability. Genome editing has become the most convenient and fastest technique for achieving precise and targeted genome modification in crops and can be used for genetic enhancement or redomestication of economically useful domesticated minor legumes.

6.2 De novo domestication

Extensive effort in crop varietal development with the intent to raise crop yield productivity must be carried out along with exploration of new opportunities. As a way to enhance increased crop productivity, the application of biological science, technology, and innovations have been advanced to facilitate efforts in discovering new and suitable alternative techniques for raising food crop productivity and quality [125]. Among others, exploiting the benefits of crop germplasm resources is suggested and currently, there is extensive work in progress towards identifying, characterizing and utilizing new genes and QTLs of crop wild relatives and progenitors for crop improvement projects. As a way of incorporating alternative strategies, the concept of crop domestication has been revisited in order to domesticate new crops for increasing the human food resource base [106]. A major goal of domesticating new crops is to attune them to thrive well under human management and manipulative control [126]. So, those plant species which to date are not very much amenable to human cultivation and management environment but possess valuable properties for food, feed, and raw materials can be subjected to a new form of domestication. Domesticating new crop species will increase crop diversity and resiliency of agriculture for crop improvement [15]. However, the Neolithic era form of crop domestication takes many years or generations to select for desired crop species with conferred modified phenotypic characteristics (acquisition of domestication traits and thus be an adaptation for cultivation) [117]. Based on the current genome engineering techniques combined with OMICs technology there is now a possibility to domesticate new crops on a fast-track approach [117, 127].

Minor crop legumes, though are promising genetic resources required for advancing effective crop breeding, their utilization has been limited by virtue of certain undesirable traits associated with them. Therefore, minor crop species are also regarded as semi-domesticated species, lacking vital domestication traits [128]. Genome editing as a breeding tool is of immense prospects in the quest to increase crop productivity, in particular the interest in breeding minor crops. Many important traits associated with crop wild relatives and minor crop species can now be exploited to enhance crop productivity [129]. However, these traits are controlled by polygenic inheritance patterns. The polygenic genes of these categories of species are somewhat difficult to be manipulated for incorporation into cultivated crop genetic backgrounds [13]. Consequently, in order to take full advantage of their beneficial traits, a genome editing approach can be used to edit target loci in minor crops and their wild relative species in order to confer on them desired domestication traits [127]. This form of domestication is recommended and it is commonly referred to as “de novo crop domestication”. By definition, de novo domestication is an innovative strategy proposed for breeding new crop species where domestication genes are introduced into non-domesticated and semi-domesticated plants [15]. In this approach, crop wild relatives or semi-wild plants, or non-domesticated species are made to acquire desirable domestication traits [106, 130] while their inherent desired phenotypes such as resilience to biotic and abiotic conditions are maintained [54, 128]. The possibility to successfully perform de novo domestication of crop wild relatives has been ascertained based on recent successful experimental studies reported [14, 118, 126, 128]. These achievements provide a solid prospect for addressing a number of conditions that are constraints in general crop production such as reduction in crop diversity. For instance, considering that most crop wild relatives are endowed with special adaptation potential to numerous environmental stresses [131], de novo domestication offers a possibility to expand agricultural production to land areas that perhaps are considered unproductive and marginal lands for crop cultivation. The technique presents a unique opportunity and prospects to incorporate several crop species into the list of crops feeding the current global population. Still, in addition to their inherent desired properties such as climate resilience, the new crops are anticipated to be conferred with beneficial domestication traits and therefore produce breeders, processors, and consumers’ desired traits. Among others, such beneficial traits will include improved performance of agronomic traits, increased edible yields, and improved quality attributes. Perhaps, what is more, intriguing about de novo domestication to the crop breeder is that the new crop domesticates will potentially address the current declining nature of crop diversity [3].

6.3 Genome editing as a tool for de novo crop domestication

Generally, crop species are endowed with a plethora of phenotypic traits which play major roles in determining the overall yield productivity. Nonetheless, some species may have certain inherent characteristics which rather place a limitation on their growth, development, and yield productivity. In crop breeding, desirable traits are maintained in the host or transferred to other species for the genetic improvement of their traits via isolated genes. Though more often, many undesirable characteristics may be associated with undomesticated, semi-domesticated, or wild/weedy forms of plant species, these species are endowed with key genes which are worth exploiting for achieving specific breeding goals. In crop improvement, various genes underlying desirable traits of wild relatives have been introgressed into the genetic backgrounds of elite cultivars [132]. Both conventional and molecular approaches are amenable for accomplishing this goal. Conversely, genes can also be isolated and transferred from domesticated crop species into that of wild-type plant species genomic backgrounds. The resulting newly created crop species is made to acquire an ideal domestication trait. Though both conventional and molecular techniques are applicable, the conventional approaches are less speedy, and sometimes unintended and undesirable traits or genes are incorporated [133]. In this instance, molecular techniques are found more versatile.

In recent times, creating new crop species from wild crop relatives on a fast-track approach has been possible through genome sequencing technology which has made available to the public, information on the genome sequences of several crop species [24]. The availability of genome sequences has further enabled the identification of genes and QTLs of several domestication genes and their underlying traits. Stacking domesticated genes in the genetic backgrounds of targeted crop wild relatives holds a possibility to develop new crop species/varieties by de novo [13]. The emergence of genome editing technology has added much impetus to crop improvement programs [118, 134, 135] where many genes can be targeted simultaneously to confer multiple traits on undomesticated or semi-domesticated species (Figure 3). Genome editing is considered the most cogent way to create new crop species from wild relatives in the process of de novo domestication [24, 136] especially traits that are monogenically inherited [118].

Figure 3.

The process of de novo domestication of minor crops and their wild relatives.

6.4 CRISPR-Cas-mediated approach to de novo domestication

Extensive effort in crop varietal development with the intent to raise crop yield productivity must be carried out along with exploration of new opportunities. As a way to enhance increased crop productivity, the application of biological science, technology, and innovations have been advanced to facilitate efforts in discovering new and suitable alternative techniques for raising food crop productivity and quality [125]. Among others, exploiting the benefits of crop germplasm resources is suggested and currently, there is extensive work in progress towards identifying, characterizing and utilizing new genes and QTLs of crop wild relatives and progenitors for crop improvement projects. As a way of incorporating alternative strategies, the concept of crop domestication has been revisited in order to domesticate new crops for increasing the human food resource base [106]. A major goal of domesticating new crops is to attune them to thrive well under human management and manipulative control [126]. So, those plant species which to date are not very much amenable to human cultivation and management environment but possess valuable properties for food, feed, and raw materials can be subjected to a new form of domestication. Domesticating new crop species will increase crop diversity and resiliency of agriculture for crop improvement [15]. However, the Neolithic era form of crop domestication takes many years or generations to select for desired crop species with conferred modified phenotypic characteristics (acquisition of domestication traits and thus be an adaptation for cultivation) [117]. Based on the current genome engineering techniques combined with OMICs technology there is now a possibility to domesticate new crops on a fast track approach [117, 127].

Minor crop legumes, though are promising genetic resources required for advancing effective crop breeding, their utilization has been limited by virtue of certain undesirable traits associated with them. Therefore, minor crop species are also regarded as semi-domesticated species, lacking vital domestication traits [128]. Genome editing as a breeding tool is of immense prospects in the quest to increase crop productivity, in particular the interest in breeding minor crops. Many important traits associated with crop wild relatives and minor crop species can now be exploited to enhance crop productivity [129]. However, these traits are controlled by polygenic inheritance patterns. The Polygenic genes of these categories of species are somewhat difficult to be manipulated for incorporation into cultivated crop genetic backgrounds [13]. Consequently, in order to take full advantage of their beneficial traits, a genome editing approach can be used to edit target loci in minor crops and their wild relative species in order to confer on them desired domestication traits [127]. This form of domestication is recommended and it is commonly referred to as “de novo crop domestication”. By definition, de novo domestication is an innovative strategy proposed for breeding new crop species where domestication genes are introduced into non-domesticated and semi-domesticated plants [15]. In this approach, crop wild relatives or semi-wild plants, or non-domesticated species are made to acquire desirable domestication traits [106, 130] while their inherent desired phenotypes such as resilience to biotic and abiotic conditions are maintained [54, 128]. The possibility to successfully perform de novo domestication of crop wild relatives has been ascertained based on recent successful experimental studies reported [14, 118, 126, 128]. These achievements provide a solid prospect for addressing a number of conditions that are constraints in general crop production such as reduction in crop diversity. For instance, considering that most crop wild relatives are endowed with special adaptation potential to numerous environmental stresses [131], de novo domestication offers a possibility to expand agricultural production to land areas that perhaps are considered unproductive and marginal lands for crop cultivation. The technique presents a unique opportunity and prospects to incorporate several crop species into the list of crops feeding the current global population. Still, in addition to their inherent desired properties such as climate resilience, the new crops are anticipated to be conferred with beneficial domestication traits and therefore produce breeders, processors, and consumers’ desired traits. Among others, such beneficial traits will include improved performance of agronomic traits, increased edible yields, and improved quality attributes. Perhaps, what is more, intriguing about de novo domestication to the crop breeder is that the new crop domesticates will potentially address the current declining nature of crop diversity [3].

7. Requirements for a successful de novo domestication experiment

7.1 Orthologous genes for de novo crop domestication

Functional conservation of gene orthologs within and across species facilitates the improvement of traits associated with undomesticated species and hence the development of new crops out of minor species [49]. Many previous reports on orthologous gene analysis are available in diverse crop species including legumes [137]. In a situation where a minor legume has no available reference genome sequence, ortholog genes of a related species or a relevant model species such as genes identified in Arabidopsis thaliana can be used. This idea is based on the premise that two or more crop species that share close characteristics for their phenotypes will likely share the same underlying genes and thus the same mechanism of genetic architecture for the traits in question. If this condition is justified, then the genes implicated for the occurrence of similar phenotypes in different crops or species are orthologous and will likely share sequence similarities and often many similar functional roles [6]. Many functional gene orthologs and their significant roles in phenotypic variations in diverse crops have been previously reported [138, 139, 140, 141]. For instance, several gene orthologs of A. thaliana are known in other domesticated crops for which reason knowledge about orthologous genes of domesticated species or a model species can be transferred for genetic enhancement and domestication of minor crops and their wild relatives. An orthologous gene with high sequence affinity to the phenotype common among different domesticated crop species is an indicator of its potential and significance to be mined and utilized for minor crop improvement [6, 49]. Domestication gene orthologs that are functionally characterized can be targeted for CRISPR-Cas9/sgRNA-mediated gene knock-out, knock-in, activation, or inactivation in minor legumes, thereby generating new species conferred with domestication phenotypes. Silencing a gene reduces the gene’s molecular function and, in this case, a genome sequence of the target minor legume is required in order to identify gene orthologs associated with domestication traits in a related or model species [106]. The success of mutating target genes to create new phenotypes in-ground cherry was based on knowledge about orthologous genes via the study of domesticated tomatoes [128]. Details of the possibility of employing gene orthology for domesticating new crops (de novo domestication) or improvement of minor crops which have already undergone some degree of domestication are explicitly explained in previous review work by Dawson et al. [6].

7.2 A prior knowledge of domestication traits and gene loci

By applying the techniques of genome editing, many domestication syndrome traits can be integrated into minor legumes [128, 142]. Therefore, the conversion of undomesticated, semi-domesticated, wild relatives or minor crop species to full beneficial domestication crop species implies the incorporation of the desired gene from a model species or editing of targeted domestication genes or gene loci [13]. Here, the expression of the modified gene or genes will intuitively confer domestication traits on the intended minor crop species. Consequently, prior knowledge about domestication traits and their controlling gene loci (domestication genes) (Figure 3) in the major legume crops is a prerequisite for accomplishing de novo crop domestication [6, 31, 143]. Besides, the current scientific research using molecular approaches has equipped us with a deeper insight into several of the mutations which occurred during the era of domestication, the affected gene loci, as well as implicated biological pathways. The type and nature of the mutations have also been well elucidated in many cultivars. The emergence of genomic technology and bioinformatics has further made it easier to isolate these genes for further analysis and utilization in crop breeding [55, 144]. Now, based on the understanding of the causal mutations association with plant phenotypes as well as the genes involved, it has become much more convenient to edit targeted genomic loci by the process of genome editing technology. Consequently, when de novo domestication is mentioned, genome editing becomes the focus as it represents the most vigorous molecular-based technique applied in the development of new crops out of the wild and minor species [118]. A clear understanding of domestication traits and their associated genes which are needed for effective and efficient genome editing is obligatorily [6, 111].

7.3 Well established efficient transformation protocol

One of the most important conditions required to achieve a successful goal in de novo domestication of a named minor legume is an experimentally established efficient genetic transformation protocol for the target species [50, 106, 145]. During transformation, especially via plant tissue culture system, a number of factors influence both success and efficiency and must be well established for the target species. This includes selection and optimization of vector construct, Vector constructs and delivery, transgene expression, selection of appropriate explants, and an assessment of overall transformation efficiency [13, 146, 147]. Since this knowledge may not be readily available for many minor crop species, research commitment in optimizing ideal transformation protocol will be practically essential to facilitate de novo domestication of undomesticated and semi-domesticated plant species [13, 135, 148, 149]. Whether or not the transformation system involves Agrobacterium tumefaciens- or A. rhizogene-mediated system or by particle bombardment approach, prior knowledge of an experimentally proven protocol is highly ideal to facilitate accomplishing a speedy and desirable result (Figure 3).

7.4 Genome sequencing information of the target minor crop legume

To have an available genome sequence of an organism is a fundamentally significant requirement for conducting molecular-based analysis including the identification and isolation of desirable genes for trait improvement programs [132]. The availability of genome sequence information of a target species offers a great opportunity to conduct a successful and resourceful experiment in the breeding of minor species. So far there has been much impetus in sequencing the genomes of some minor legume species. Similarly, interest and commitment to advance genome sequencing projects of several other species have also been reported [150]. For instance, the African Orphan Crops Consortium seeks to embark on genome sequencing projects by targeting over 100 minor plant species including minor legumes [49]. At present, the complete or drafted genome sequences of a number of minor legumes have been released [20, 22, 62, 151]. This facilitates the mapping of quantitative trait loci (QTLs), functional gene isolation, marker-assisted selection as well as genome engineering [152]. Among others, the economic value for nutrition and general food security, raw material, and desirable agronomic traits will likely form part of the major considerations in selecting a minor crop for whole genome sequencing or genome assembly [22]. For minor legumes in which there are readily available reference genome sequences, further genome resequencing experiments have already been conducted to identify target genes [17, 33, 99, 86, 153, 154]. Such available information makes these crops more amenable for genome engineering experiments to improve upon specific traits and for conducting de novo domestication of their wild relatives.

7.5 Available reference genome sequence of related species

Knowledge gained by studying domestication events in model crops can be translated into the breeding of related crop wild species as well as minor crops and their wild relatives. This process requires detailed knowledge of the genome features of the model and target plant. That is when a minor legume targeted for de novo domestication has no available reference genome sequence but is closely related to a model species at the level of family, genera, or species, knowledge about the model species becomes easier and more applicable for manipulating the minor crop genome by editing targeted genes [155]. Knowledge about genes and genomic features underlying domesticated crop phenotypes are a rich resource for identifying their orthologous genes which must be targeted for de novo domestication of minor legume, their wild relatives, or minor crop species as a whole). In this case, ortholog forms of genes known to be associated with the domestication traits become the target to generate de novo genome-edited minor crop (Figure 3). For instance, in their experiment, Lemmon et al. [128] studied the wild relative of tomato (Physalis pruinosa) which belongs to the Solanaceae family as the cultivated tomato with many conspicuous phenotypes of P. pruinosa akin to the S. pinpinellifolium. Here, mutating ortholog genes of domesticated tomatoes in the wild relative as possible. The success reports of previous works in de novo domestication experiments involving crop wild relatives were in part due to background knowledge about their model species and domestication traits. Therefore, genome editing technology holds immense prospects for creating new crops out of minor crop species.

8. Conclusion and future perspectives

Certainly, the current food crops were domesticated thousands of years ago by the early humans during the period historically termed as the Neolithic era. Following crop domestication, are the various strategies of crop genetic improvement including phenotypic selection, hybridization, mutagenesis, biotechnology, and the most recent tool, genome editing. However, in the past, the application of crop improvement techniques focused mainly on trait enhancement of major crop species resulting in research neglect of minor crop species. This phenomenon caused a majority of crop species to be tagged as minor, orphan, or neglected and under-utilized species. The minor crop species are huge in number and widely spread across the globe. Following the rapid growth rate of the human population, climate change, the continuous reduction of arable lands, and food and nutritional security concerns, there is a need to look back to minor crops and their wild relatives. The recognition of minor crops is based largely on their numerous economic values including adaptation to biotic and abiotic conditions, medicinal endowment, presence of desirable alleles, and potential as model species. Of the 2000 legume species known, only a few including soybean, peanut, have been fully explored and utilized for food, feed, and other agricultural purposes. Efforts have been made in the collection of legume crop wild relatives in order to exploit essential alleles that they harbor for the purpose of genetic improvement of crop species. Legume species play significant roles in the cropping systems for soil nutrient improvement, weed control, and reclamation of wastelands for arable crop production. Minor legumes are specifically important in the quest to meet the protein requirements of all people, especially in parts of the globe where vegetable proteins have become the key source of human protein requirements in diets. To increase the diverse utilization value of minor crops such as for food, feed for livestock, and their potential for soil nutrient management, there is the need for further trait improvement or genetic enhancement of their traits. Current research findings have underscored the prospects in creating new crops out of minor crop species which are deficient in economically desired agronomic traits. One of the recent approaches in the genetic enhancement of minor crop species is de novo crop domestication. While de novo crop domestication approaches are diverse, genetic engineering (or transgenesis) and genome editing are the most rapid ways to generate new crop species. However, over the years, the production and consumption of transgenic crops have always been debated about and hence do not have full acceptance by the general republic. The emergence of genome editing as a molecular breeding tool presents a solution to the limitations associated with transgenic crop production. For instance, using genome editing tools, a loss-of-function mutation occurring within a domesticated gene could potentially confer a desired domesticated phenotype on the target species (redomestication). Similarly, mutations occurring in non-domesticated genes can give rise to new individuals conferred with domesticated traits (de novo domestication). The multiplex editing potential of the CRISPR-Cas system has been used to achieve simultaneous editing of multiple loci and thus create new edited individuals endowed with a range of complex traits. De novo domestication has previously been successfully applied in genetic modification to increase the trait values of tomato and rice. Considering that minor grain legumes are important food and nutritional security commodities in many parts of the world, and thus the need to increase their food value, the de novo domestication technique holds huge prospects in the genetic enhancement of these underutilized legumes and their wild relatives. The different mechanisms of CRISPR-Cas applications can be employed for genetic enhancement or de novo domestication in minor legume species and their wild relatives to generate new alternative crops. The current challenges that need to be addressed include a boost of public confidence in research findings and the need for openness in the application of modern molecular technology. De novo domestication offers prospects for developing new crops for today and the future in a relatively smart fashion and thus, safeguards food security and agricultural sustainability. While over the years many research efforts have been seen in promoting the utilization of minor crop legume species, there is yet more work to be done in areas including (1) documentation and conservation of minor crop species in gene banks, (2) comprehensive characterization of minor crop species at both phenotypic and molecular levels, (3) collaborative research among domestic and international researchers and institution in identifying and promoting the utility value of minor crops and their wild relatives, (4) research partnership in a multidisciplinary and inter-institutional approach aimed at converting many minor crop species into genome-rich resources and (5) training to increase research expertise in genetic enhancement and domestication of minor crop species and their wild relatives. Overall, it must be reemphasized that genome sequencing of minor crop species is fundamentally requisite in the quest to develop alternative crops since the identification of target gene loci and QTLs are central to achieving successful genome editing experiments and consequently de novo crop domestication. However, it must be noted that de novo domestication via genome editing system may not necessarily be a universal approach to extract the full benefits preserved in minor crop legumes and their wild relatives, instead regional or sub-regional specific approaches should be considered paramount.