Genetic diversity analysis using phenotypic and SSR markers with trait association and multivariate analysis in cowpea (Vigna unguiculata (L.) Walp.) genotypes

The low productivity of cowpea is primarily attributed to inadequate utilisation of genetic diversity for the improvement of local cultivars. The present study was conducted to assess genetic diversity utilising 17 yield and biochemical traits along with simple sequence repeat (SSR) markers. Fifty cowpea genotypes were assessed during summer 2024 at Chaudhary Charan Singh Haryana Agricultural University (CCSHAU), India. Genotypes were planted with three replications in a randomised block design. Significant genetic variability was observed in the studied traits. The minimal differences between phenotypic and genotypic coefficients of variation (CV) indicated that the observed variation primarily stemmed from the genetic component. Most traits showed high heritability, with varying levels of genetic advance. Trait association revealed a positive interrelationship among yield-contributing traits, suggesting their utility for selection for cowpea yield improvement. Cluster I possessed better-performing genotypes for yield traits. Principal component analysis emphasised that pods per cluster (PCL), pods per plant (PPL) and clusters per plant (CPL) were the major contributing traits in principal component 1 (PC1). Out of 64 SSR markers screened, 40 showed successful amplification and 18 were highly polymorphic and used for diversity analysis, with an average of 2.94 alleles per marker. PIC values varied from 0.11 to 0.78. Highly informative markers (Vm 39, Vm 31, Vm 27, CP 1) were valuable for diversity assessment. Overall, the genotypes PGCP-89, PGCP-70, PGCP-90, KVCP 17-15, GC 2202 and GC 2105 were found to be superior for yield and contributing traits. These genotypes can be useful for further breeding and hybridisation for cowpea improvement; however, they require multi-environment validation.