İnvestigation of DNA fingerprinting and population structure of cowpea plant gene resources by using SCoT markers

Genetic diversity assessment plays an important role in the development of crop breeding strategies by helping to identify desirable traits and select diverse germplasm. In this study, Start Codon Targeted Polymorphism (SCoT) markers were used to investigate genetic diversity within cowpea germplasm. The 14 highly polymorphic SCoT markers yielded 287 reproducible bands. Polymorphic bands exhibited a range of 12 to 24 per primer, with an average polymorphism rate of 86.74%. In particular, the number of effective alleles ranged from 1.351 to 1.767, while gene diversity ranged from 0.224 to 0.419. STRUCTURE analysis classified the accessions into two main populations (A and B) based on geographical origin, with an additional population not classified due to low membership coefficients. The Neighbour-Joining tree supported the findings of the STRUCTURE analysis and classified the germplasm into two groups (B1 and B2). More importantly, the clustering model revealed genetic similarities between material from West Africa, the Indian subcontinent and Turkey. The grouping of accessions from West Africa and the Indian subcontinent within the same population supports the idea that cowpea originated from these regions, as reported in previous studies. This research highlighted the significant genetic variability within cowpea germplasm, underlining the utility and effectiveness of the SCoT marker system. In particular, the Pakistan 1 x Turkey 2 accession pair exhibited the greatest genetic distance and demonstrated its potential as a valuable genetic resource for future breeding programmes