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bioRxiv · 10.64898/2025.12.19.695351

Genetic Linkage Studies in F2 Cowpea (Vigna Unguiculata (L.) Walp) Mapping Populations Using Qualitative Morphological and SNP Markers

MENSAH, H. K.·Nortey, R. A. K.·Asante, I. K.·Oppong-Adjei, F.
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Abstract

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 and 17 morphological markers. The segregation ratios were analyzed revealed that five traits (growth habit, growth pattern, leaf shape, plant hairiness and pod hairiness) segregated significantly according to 3:1 mendelian classical ratio for inheritance whilst the remaining 13 showed 9:7 ratios. Genetic linkage mapping was performed by using the software QTLiCIMapping version 4.2. All the markers used were polymorphic. Eleven linkage groups were detected which spanned a total map length of 93.8217 cM at a LOD score of 4. Variation in marker distribution on all the 11 linkage groups was observed. Fourteen markers were distributed on Chromosome 1. In all cases, segregation distortion was observed for all the markers in each of the linkage groups. Segregation distortion in Chromosome 1, Chromosome 5, Chromosome 8 and Chromosome 11 were highly skewed to the wild parental type. This work provides one of the few integrated morphological-SNP linkage maps for cowpea and highlights genomic regions associated with non-Mendelian inheritance. These findings supply foundational genetic information for QTL discovery, marker-assisted selection, and breeding strategies aimed at improving yield, nutrition, and climate resilience in cowpea. Author SummaryIn this study, we set out to understand how important physical traits in cowpea are passed from one generation to the next, and to build a simple genetic map that can guide future crop improvement. Cowpea is a major source of food and nutrition for millions of people, especially in Africa, yet progress in improving the crop has been slowed by limited genetic information. By crossing a cultivated cowpea variety with its wild relative, we examined how traits such as growth form, leaf shape, pod appearance, and seed characteristics segregate in their offspring. We also combined these observations with DNA markers to create a genetic map showing how these traits and markers are arranged along the chromosomes. Our results show that some traits follow the classic patterns of inheritance, while others are influenced by interactions between pairs of genes. We also discovered regions of the genome where inheritance was skewed toward one parent, offering clues about underlying biological processes. By providing one of the few combined morphological and DNA maps for cowpea, our work creates a foundation that breeders and researchers can use to develop improved, desired, and climate-resilient cowpea varieties.

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MENSAH, H. K., Nortey, R. A. K., Asante, I. K., Oppong-Adjei, F.. 2025-12-22. Genetic Linkage Studies in F2 Cowpea (Vigna Unguiculata (L.) Walp) Mapping Populations Using Qualitative Morphological and SNP Markers. https://doi.org/10.64898/2025.12.19.695351

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