Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for minor and underutilised crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata). From these comparisons we identify conserved synteny blocks corresponding to the Linkage Groups (LGs) in bambara groundnut genetic maps and evaluate the potential to identify genes in conserved syntenic locations in a sequenced genome that underlie a QTL position in the underutilised crop genome. Two individual intraspecific linkage maps consisting of DArTseq markers were constructed in two bambara groundnut (2n = 2x = 22) segregating populations: 1) The genetic map of Population IA was derived from F2 lines (n = 263; IITA686 x Ankpa4) and covered 1,395.2 cM across 11 linkage groups; 2) The genetic map of Population TD was derived from F3 lines (n = 71; Tiga Nicuru x DipC) and covered 1,376.7 cM across 11 linkage groups. A total of 96 DArTseq markers from an initial pool of 142 pre-selected common markers were used. These were not only polymorphic in both populations but also each marker could be located using the unique sequence tag (at selected stringency) onto the common bean, adzuki bean and mung bean genomes, thus allowing the sequenced genomes to be used as an initial ‘pseudo’ physical map for bambara groundnut. A good correspondence was observed at the macro synteny level, particularly to the common bean genome. A test using the QTL location of an agronomic trait in one of the bambara groundnut maps allowed the corresponding flanking positions to be identified in common bean, mung bean and adzuki bean, demonstrating the possibility of identifying potential candidate genes underlying traits of interest through the conserved syntenic physical location of QTL in the well annotated genomes of closely related species. The approach of adding pre-selected common markers in both populations before genetic map construction has provided a translational framework for potential identification of candidate genes underlying a QTL of trait of interest in bambara groundnut by linking the positions of known genetic effects within the underutilised species to the physical maps of other well-annotated legume species, without the need for an existing whole genome sequence of the study species. Identifying the conserved synteny between underutilised species without complete genome sequences and the genomes of major crops and model species with genetic and trait data is an important step in the translation of resources and information from major crop and model species into the minor crop species. Such minor crops will be required to play an important role in future agriculture under the effects of climate change.

The ability to grow crops under low-water conditions is a significant advantage in relation to global food security. Bambara groundnut is an underutilised crop grown by subsistence farmers in Africa and is known to survive in regions of water deficit. This study focuses on the analysis of the transcriptomic changes in two bambara groundnut landraces in response to dehydration stress. A cross-species hybridisation approach based on the Soybean Affymetrix GeneChip array has been employed. The differential gene expression analysis of a water-limited treatment, however, showed that the two landraces responded with almost completely different sets of genes. Hence, both landraces with very similar genotypes (as assessed by the hybridisation of genomic DNA onto the Soybean Affymetrix GeneChip) showed contrasting transcriptional behaviour in response to dehydration stress. In addition, both genotypes showed a high expression of dehydration-associated genes, even under water-sufficient conditions. Several gene regulators were identified as potentially important. Some are already known, such as WRKY40, but others may also be considered, namely PRR7, ATAUX2-11, CONSTANS-like 1, MYB60, AGL-83, and a Zinc-finger protein. These data provide a basis for drought trait research in the bambara groundnut, which will facilitate functional genomics studies. An analysis of this dataset has identified that both genotypes appear to be in a dehydration-ready state, even in the absence of dehydration stress, and may have adapted in different ways to achieve drought resistance. This will help in understanding the mechanisms underlying the ability of crops to produce viable yields under drought conditions. In addition, cross-species hybridisation to the soybean microarray has been shown to be informative for investigating the bambara groundnut transcriptome.

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip. A total of 753 markers grouped at an LOD (Logarithm of odds) of three, with 527 markers mapped into linkage groups. From this initial map, a spaced expression marker-based genetic map consisting of 13 linkage groups containing 218 GEMs, spanning 982.7 cM (centimorgan) of the bambara groundnut genome, was developed. Of the QTL detected, 46% were detected in both control and drought treatment populations, suggesting that they are the result of intrinsic trait differences between the parental lines used to construct the cross, with 31% detected in only one of the conditions. The present GEM map in bambara groundnut provides one technically feasible route for the translation of information and resources from major and model plant species to underutilised and resource-poor crops.

Underutilised species such as bambara groundnut (Vigna subterranea (L.) Verdc.) have the potential to contribute significantly to meeting food and nutritional needs worldwide. We evaluated phenotypic traits in twelve bambara groundnut genotypes from East, West and Southern Africa and Southeast Asia and two F₂ bi-parental segregating populations derived from IITA-686 ×Tiga Nicuru and S19-3 ×DodR to determine phenotypic trait variation and their potential contribution to the development of improved crop varieties. All phenotypic traits in twelve genotypes were significantly influenced (p < 0.01) by genotypes. Principal component analysis (PCA) showed that PC1 accounted for 97.33% variation and was associated with four genotypes collected from East and Southern Africa. PC2 accounted for 2.48% of the variation and was associated with five genotypes collected from East, West and Southern Africa. Transgressive segregation for a number of traits was observed in the two F₂ bi-parental populations, as some individual lines in the segregating populations showed trait values greater or less than their parents. The variability between twelve genotypes and the two F₂ bi-parental segregating populations and the negative relationship between plant architectural traits and yield related traits provide resources for development of structured populations and breeding lines for bambara groundnut breeding programme.

Characterizing the morphological variability in root system architecture (RSA) during the sensitive pre-flowering growth stage is important for crop performance. To assess this variation, eight bambara groundnut single genotypes derived from landraces of contrasting geographic origin were selected for root system architecture and rooting distribution studies. Plants were grown in a polyvinyl chloride (PVC) column system under controlled water and nutrient availability in a rainout shelter. Days to 50% plant emergence was characterized during the first two weeks after sowing, while taproot length (TRL), root length (RL), root length density (RLD), branching number (BN), branching density (BD) and intensity (BI), surface area (SA), root volume (RV), root diameter (RDia), root dry weight (RDW), shoot dry weight (SDW), and shoot height (SH) were determined at the end of the experiment, i.e., 35 days after emergence. Genotypes S19-3 and DipC1 sourced from drier regions of sub-Saharan Africa generally had longer taproots and greater root length distribution in deeper (60 to 90 cm) soil depths. In contrast, bambara groundnut genotypes from wetter regions (i.e., Gresik, Lunt, and IITA-686) in Southeast Asia and West Africa exhibited relatively shallow and highly branched root growth closer to the soil surface. Genotypes at the pre-flowering growth stage showed differential root foraging patterns and branching habits with two extremes, i.e., deep-cheap rooting in the genotypes sourced from dry regions and a shallow-costly rooting system in genotypes adapted to higher rainfall areas with shallow soils. We propose specific bambara groundnut genotype as donors in root trait driven breeding programs to improve water capture and use efficiency.