Wild relatives play an important role in the genetic improvement of cultivated crops. Cajanus scarabaeoides (L.) Thouars is one of the important wild species, which possess several desirable traits. Investigations on 67 accessions of C. scarabaeoides and 3 cultivated varieties for total soluble seed protein profiles using Sodium Dodecyl Sulphate-Poly Acryl amide Gel Electrophoresis resolved the protein bands ranged from 4–11. Based on the presence or absence of bands, similarity values were calculated and dendrogram was constructed using Unweighted Pair Group Method with Arithmetic Mean analysis. The dendrogram formed two main clusters. The first main cluster consisted of three cultivated varieties and 55 accessions of C. scarabaeoides and the second main cluster comprised of remaining 12 accessions of C. scarabaeoides. Similarity percentage ranged from 38.5 to 100. ICP15728 is the lone genotype which is distinctly different from remaining genotypes formed separate sub-cluster in the second main cluster with 38.5% similarity. Thirty eight accessions of C. scarabaeoides were screened against Fusarium wilt under glass house conditions. Of the 38 accessions screened seven accessions (ICP12707, ICP15689, ICP15692, ICP15732, ICP15744, ICP15748 and ICP15754) showed resistance to Fusarium wilt. Therefore, these accessions could be utilized in breeding programmes to increase the levels of resistance to Fusarium wilt in the pigeonpea cultivars, after further testing.
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