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The number of people suffering from chronic undernourishment in sub-Saharan Africa has increased. The potential of the cowpea to be the crop of the future to address food and nutrition insecurity is evident in sub-Saharan Africa. This study was carried out to identify early maturity and drought tolerant genotypes with potential for higher yields for smallholder farmers in South Sudan. One hundred and six cowpea accessions were sourced from different backgrounds. Their genetic diversity was assessed using both agro-morphological traits and molecular approaches. Nine discriminatory clusters yielded cophenetic correlation coefficient values of 0.76. Results of molecular study revealed existence of a genetic divergence among the assembled cowpea panel creating an opportunity for population development through introgression of new alleles. The SNP markers used in this study could be utilized to analyse and group collections in the future. Forty-nine accessions selected from 106 genotypes were screened under well-watered and drought stressed conditions for identification of parental lines for population improvement using a 7×7 alpha lattice design. Five cowpea accessions from South Sudan and three from Burkina Faso, Niger and Nigeria were identified and selected for crosses. Hybridisation was carried out using hand emasculation and pollination. The North Carolina II mating design generated 15 F1 populations. The F1s were then backcrossed to the local parent to develop BC1F1. The 15 BC1F1 populations with their parents as checks were evaluated using an alpha lattice design to advance promising genotypes to the next round of backcrossing cycles. The resultant F2 offspring arranged in a split-plot design were evaluated to determine the genetics of early maturity and drought tolerance under well-watered and drought-stressed conditions using rainout shelters. At backcross three, (BC3F1), the population was selfed twice before running multi-location trials in Legon (5°38'N, 0°10'E), Fumesua (6°41′N, 1°28′W), and Nyankpala (9°24′N, 0°59′W), Ghana. The study included a total population of 9000 plants, with 3000 plants per experiment. The trials were laid out in a 5×5 alpha lattice design with three replications and two watering regimes. The plot size was 1.2 m2, the distance between plants was 20 cm and 60 cm between rows. Data were collected on agronomic traits and subjected to analysis of variance and path analysis. Stability analysis identified best performers for earliness, drought tolerance, and seed yield stability. Additive main effects, multiplicative interaction (AMMI) stability analysis, and GGE biplot analysis ranked genotypes based on their performance in relation to environment, whereas Eberhart and Russell (1966) and Finlay and Wricke’s (1963) stability approaches gave holistic information about those genotypes with outstanding seed yield stability. The genotype by environment analysis confirmed that environment accounted for 63.8% of the variability in the experiments, genotype accounted only for 10.8%, and the interaction between genotype and environment accounted for 24.4% of the variation. Ten genotypes, A1B−D, A1B−I, A1B−M, BA−D, BA−M, BA−I, L1B−D, TA− M, TA−D, and TA−M that mature in 60 days or less after planting were identified. Four genotypes, BC−M, L1B−I, TA−M, and A1B−M, were found to combine drought tolerance with stable yield potential. Two genotypes, A1B−M and TA−M, demonstrated both early maturity and drought tolerance. Five recommendations were drowned from this study for future research.