Development of structured populations and breeding lines for trait analysis and improved varieties in Bambara Groundnut (Vigna subterranea L. Verdc)

Underutilised crop species have the potential to contribute significantly to increased crop diversity and to improved food and nutrition security worldwide. Bambara groundnut [Vigna subterranea (L.) Verdc.] is an underutilised, protein-rich and self-pollinating legume, which can withstand high temperatures and drought stress, and mainly grown in semi-arid Africa. The crop is still largely grown as landraces (a mixture of genotypes) and has limited established structured populations and breeding lines due to a lack of genetic improvement activities and commercial interests. Twelve genotypes of bambara groundnut collected from East, West and Southern Africa and Southeast Asia were used to evaluate the variation in phenotypic traits and the correlation between the observed variation and the landraces’ geographical origins in randomised complete block design (RCBD). All phenotypic traits in the twelve genotypes were significantly influenced (p < 0.01) by genotypes. Principal component analysis (PCA) showed that PC1 accounted for 97.33% of the 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. The variation observed within the twelve genotypes of bambara groundnut provides a breeding resource pool for use in controlled crossing to develop ideotypes with desirable phenotypic traits, i.e., high harvest index, 100-seed weight, early days to flowering or short life cycle. Two F2 bi-parental segregating populations of bambara groundnut derived from different geographical origins, IITA-686 (Tanzania, East Africa) × Tiga Nicuru (Mali, West Africa) and S19-3 (Namibia, Southern Africa) × DodR (Tanzania, East Africa) were developed to obtain structured populations and breeding lines for genetic analysis and trait dissection. 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 the two F2 bi-parental segregating populations and the negative relationship between morphological traits and yield-related traits provide resources for development of structured populations and selection of breeding lines for bambara groundnut breeding programme. Assessment of segregating populations for their ability to withstand drought stress conditions is one of the best approaches to develop breeding lines and drought-tolerant varieties. The genotype S19-3 exhibits short life cycle and is considered as drought resistant landrace while DodR is reported to have comparatively high 100-seed weight and yield. A total of 114 individual lines derived from S19-3 × DodR were advanced into F3 and F4 segregating populations and examined in a rainout shelter to identify superior lines under drought stress. Drought stress significantly reduced (p < 0.05) shoot dry weight, seed weight per plant, harvest index, shelling percentage, chlorophyll content index and quantum yield PSII photochemistry (FV/FM) in the F3 and F4 segregating populations of bambara groundnut. Stomatal conductance, photosynthesis rate, transpiration rate and intracellular CO2 were significantly reduced (p < 0.05) while leaf water use efficiency was significantly increased (p < 0.05) towards the end of the drought stress period in the F4 segregating population. Individual lines with higher chlorophyll content index, quantum yield PSII photochemistry (FV/FM), relative water content, stomatal conductance, leaf water use efficiency, seeds weight per plant and harvest index were identified. These individuals could be selected as superior lines for genetic analysis and variety development for drought adaption. In order to dissect the complexity of drought resistance, the inheritance of yield-related and morphological traits and to use genomic tools for yield enhancement of bambara groundnut under drought-stressed conditions, a genetic linkage map covering 1,040.92 cM across 11 linkage groups was constructed using 228 DArTseq markers in the F2 segregating population derived from S19-3 × DodR. Significant QTLs for shoot dry weight were mapped on LG10 accounting for 15.5% of the phenotypic variation explanation (PVE) under well-watered conditions and a putative QTL for the same trait mapped on LG10 with reduced PVE (10.10%) under drought-stressed conditions in the F3 segregating population. Significant QTLs associated with number of seeds per plant, number of double-seeded pod per plant, seed weight per plant and pod weight per plant were mapped on LG4 (nearest marker: 4181663 and 4175954) with overlapping confidence intervals and explaining 21.9%, 21.8%, 23.5% and 19.9% of the PVE, respectively, under well-watered conditions in the F4 population, which could be considered as major QTL involved in the control of these traits. Fourteen QTL loci that were found to be consensus QTLs for yield-related, morphological and physiological traits across LG1A, LG2, LG3, LG4, LG5, LG7A, LG7B, LG10 and LG11. This study provides a pipeline for the development of breeding resources, including structured populations and breeding lines, for genetic analysis, trait dissection and potentially development of new improved varieties. The study also provides fundamental knowledge of QTLs associated with yield components, morphological and physiological traits under well-watered and drought-stressed conditions in bambara groundnut, which is also essential for yield improvement of bambara groundnut in response to drought stress