Evaluation of the genetic diversity of Malawian pigeonpea using simple sequence repeats markers

Abstract

Pigeonpea (Cajanus cajan (L.) Millsp.) is a drought tolerant legume of the Fabaceae family in the order Fabales and the only cultivated species in the genus Cajanus. It is mainly cultivated in the semi-arid tropics of Asia and Oceania, Africa and America. In Malawi, one of the top producers of pigeonpea in Africa, it is grown by small scale farmers as a source of food and income and for soil improvement in intercropping systems. However, varietal contamination due to natural outcrossing causes significant yield losses for farmers. In this study, 48 polymorphic SSR markers were used to assess diversity in all pigeonpea varieties cultivated in Malawi with the aim of developing a genetic fingerprint to distinguish the released varieties. SSR alleles were separated by capillary electrophoresis on an ABI 3700 automated sequencer and allele sizes determined using GeneMapper 4.0 software. Allelic data was analysed with PowerMarker. A total of 212 alleles were revealed averaging 5.58 alleles per marker with a maximum number of 14 alleles produced by CCttc019 (Marker 40). Polymorphic information content (PIC) ranged from 0.03 to 0.89 with an average of 0.30. DARwin software was used to generate a neighbour-joining tree that displayed three major clusters with two sub clusters in Cluster I. The released varieties were scattered across all the clusters observed, indicating that they generally represent the genetic diversity available in Malawi, although it was observed that there is substantial variation that can still be exploited through further breeding. Screening of the allelic data associated with five popular pigeonpea varieties for which a DNA fingerprint was to be developed, revealed 6 markers – CCB1 (Marker 1), CCB7 (Marker 2), Ccac035 (Marker 7), CCttc003 (Marker 15), Ccac026 (Marker 37) and CCttc019 (Marker 40)– which gave unique allelic profiles for each of the five varieties. With further tests needed for its robustness, this genetic fingerprint can be used for seed certification to ensure only genetically pure seeds are delivered to Malawi farmers.