QTL Identification for Morphological and Phytochemical Traits in 45 F2 Cowpea (Vigna Unguiculata (L.) Walp) Mapping Populations

The research was conducted to study genetic linkage in 45 F2 cowpea mapping populations derived from a cross between two inbred lines Golinga (cultivated variety) and a Wild relative. The data used for the study were based on 13 polymorphic SNPs markers, 47 morphological and 23 phytochemical traits (18 amino acids and 5 polyphenols). The morphological variables involved 17 qualitative and 30 quantitative variables of cowpea vegetative and yield and yield-related traits whereas the phytochemical traits involved. Genetic linkage mapping and QTL mapping were performed by using the software QTLiCIMapping version 4.2. All the 17 qualitative markers were polymorphic. Eleven linkage groups were detected at a LOD score of 4. Fourteen markers were distributed on chromosome 1. A total of 79 QTLs were identified which were distributed over four linkage groups. Contributions of the QTLs to percentage phenotypic variation ranged from 0.00% to 27.62% (quercetin). Multiple QTLs located at the same location were identified on chromosomes 1 and 4 indicating potential pleiotropy. QTLs identified for seed related traits were mapped to the same region on chromosome 4. QTLs for the vegetative traits namely, number of branches, number of leaves and branch length were mapped on the same region on chromosome 4. The identification of moderate- to large-effect QTLs on chromosome 4, especially qSDWG4.1, offers promising targets for seed weight improvement in cowpea. A total of 42 QTLs were detected for amino acids, most of which were located on chromosome 1, with additional loci on chromosomes 4, 7, and 9. Nine QTLs were identified for phenolic acids. Two QTLs for the flavonoids rutin and quercetin were mapped to a shared region on chromosome 4. This study provided an integrated QTL framework for morphological, reproductive, amino acid, and phenolic traits in cowpea, revealing major genomic regions on chromosomes 1 and 4 that controlled both domesticated-related and nutritional traits. The results offer foundational genomic resources for future fine mapping, candidate gene discovery, and nutritional improvement in cowpea breeding programs. Author SummaryCowpea is an important food and nutritional security crop, yet many traits that influence its yield, seed quality, and nutrient composition remain poorly understood. In this study, we examined an F2 population produced by crossing a cultivated cowpea variety ( Golinga) with a wild relative to explore genetic factors that control key agronomic and nutritional traits. We measured vegetative, phenological and yield and yield-related traits, 18 amino acids, and five phenolic compounds, and used morphological and SNP markers to identify genomic regions associated with their variation. We detected 79 QTLs across four chromosomes. Many important seed and reproductive traits were controlled by QTLs on chromosome 4, while chromosome 1 carried major clusters of QTLs for amino acids and phenolic acids. These results reveal genomic "hotspots" that influence both domestication-related traits and nutritional quality. By identifying the genetic regions associated with these traits, our work provides valuable tools for breeding programs aimed at improving cowpea productivity and enhancing seed nutritional composition. The findings also contribute to a deeper understanding of how wild relatives can introduce beneficial variation into cultivated cowpea.