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This study was conducted in Nigeria to: (i) assess farmer and consumer perceptions and preferences on grain quality traits in cowpea (ii) assess the variability of grain nutritional values (protein, iron and zinc content) of cowpea accessions from Africa and other parts of the world; (iii) determine the inheritance of iron and zinc content in cowpea grains and (iv) determine the relationship between zinc concentration and yield components. Farmers preferred cowpea variety that combines high yield with rough texture, white or brown colour. Consumers‘grain quality preferences were consistent with those of farmers, except for women who prioritized cooking time and oil consumption. Farmers pointed out inadequate improved cowpea seed at planting time and lack of resistant varieties to pod sucking and pod boring insects as the major constraints to cowpea production in the areas. Significant genetic variations were observed in: zinc content (1.01 to 329.15mg/kg); iron content (10.01 to 386.3 mg/kg); protein content (1.72 to 29.93 %) and other physicochemical properties of grain. Many of these variations can be generated by conventional breeding method to attend the nutritional needs in developing countries. In addition, three accessions: TVu-13088, TVu-13495 and TVu-9725 that gather the largest number of desirable nutritional attributes were identified which can be nominated for anti-nutritional testing and recommendation for infant diets formulation and general use. For nutrient specific, five accessions each were identified for protein content, zinc content and iron content were also identified. Genetic diversity of 169 cowpea accession using 119 SNP markers clustered the accessions into two main group on a genetic distances (0.00 to 0.212) with small genetic differentiation (0.26 to 0.45) between African and USA cowpea accessions indicates that the entire genetic diversity in the African germplasm might already have spread over cowpea- growing regions in the world as a whole, though not completely within any single region. The total PIC values ranged from 0.2366 (7344_500 SNP) markers to 0.427 in two SNP markers (4749_1972 and 14929_258). Negative correlation exists between Iron content and fat (r= -0.18, p < 0.007), iron content and carbohydrate (r= -0.18, p < 0.007) but iron content was positively correlated with protein (r= 0.26, p < 0.001) content. Fat content was negatively correlated with Ash content (r= -0.13, p < 0.05) and protein content (r= -0.85, p<0.001). Ash content correlated positively with protein (r=0.14, p<0.05) and negatively with carbohydrate (r=-0.23, p<0.001). Protein was negatively correlated with carbohydrate (r= -0.29, p < 0.01). Zinc concentration showed weak negative significant (P < 0.05) correlation with number of number of pod per plants. No significant correlation was observed between zinc concentration and grain weight. Similarly negative correlation was observed between zinc content and number of pod per plant implying an increase in zinc content may lead to decrease in pod yield. Generation mean analysis of the six basic generations showed significant (P < 0.001). The significant variation of generation mean performance with transgressive segregants among the progenies and two fold increases in mean zinc concentration of F2 population over the high zinc content parent (82.54 mg/kg > 37.70 mg/kg), implies that cowpea can be enhance with essential micronutrients using conventional approach. Additive [a] and additive by dominance [ad] model explain inheritance of iron and zinc content in cowpea grain. Maternal effect was observed in iron content inheritance indicating non suitability to make selection in early generation of selfing. Seed weight is predominantly under complementary gene action in this study, suggesting the possibility of considerable amount of heterosis for seed weight, while plant height is under the control of complementary gene action.