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Pigeonpea (Cajanus cajan [L,] Millspaugh) is an important source of grain protein for low-income countries such as Malawi. Knowledge of the genetic diversity in pigeonpea is essential for an effective breeding program. The study objective was to assess the genetic diversity among diverse pigeonpea accessions to select complementary and unique genotypes for breeding. Eighty-one pigeonpea accessions were evaluated in six environments in Malawi using a 9 × 9 alpha-lattice design with two replications. The cross-tabulation analysis revealed a significant genotype variation on plant growth, flower, and seed traits. The combined analysis of variance identified genotypes MWPLR 14, ICEAP 01170, ICEAP 871091, and ICEAP 01285 as early maturing varieties, while Kachangu, MWPLR 16, TZA 5582, No. 40, and MWPLR 14 were identified as high-yielding genotypes. The correlation analysis revealed a significant positive correlation between grain yield and a hundred seed weight (HSWT) (r = 0.50, p < 0.01), suggesting the usefulness of this trait for selection. The nonlinear principal component analysis identified grain yield (GDY), days to 50% flowering (DTF), days to 75% maturity (DTM), number of pods per plant (NPP), number of racemes per plant (NRP), 100 seed weight (HSWT), leaf hairiness (LH), and number of seeds per pod (NSP) as the most discriminated traits among the test genotypes. The cluster analysis using morphological traits delineated the accessions into three clusters. The selected high-yielding and early-maturing genotypes may be recommended as parental lines for breeding and grain yield improvement in Malawi or similar agro-ecologies.

Knowledge of genetic interrelationships and grouping among pigeonpea germplasm collections is fundamental to selecting breeding parents with unique genetic constitutions. The objectives of this study were to assess the genetic diversity and genetic grouping present among 81 pigeonpea genotypes collected from Malawi, Tanzania and Kenya using 4122 single nucleotide polymorphism (SNP) markers and complementary morphological traits. The SNP markers and phenotypic traits revealed significant genetic variation among the assessed genotypes. The test genotypes were resolved into three distinct clusters based on both marker systems. The mean gene diversity and the polymorphic information content (PIC) were 0.14 and 0.11, suggesting moderate genetic differentiation among the genotypes. The analysis of molecular variance revealed that differences among populations accounted for only 2.7% of the variation, while within the population (among individuals) accounted for 97.3% of the variation. The results based on the DArT SNP genotyping complemented the phenotypic data and led to the selection of unique pigeonpea genotypes for effective breeding programs in Malawi and related agroecologies. This suggested that unique breeding populations could be created by identifying and selecting divergent individuals as parental lines. There is a need to create a new genetic variation or introgress genes from genetically unrelated parents to increase the genetic base of the current pigeonpea breeding populations.

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