International Research Journal of Plant Science (ISSN: 2141-5447) Vol. 2(5) pp. 119-128, May, 2011 Available online http://www.interesjournals.org/IRJPS Copyright © 2011 International Research Journals Full length Research Paper Phylogenetic relationships of Crotalaria species based on seed protein polymorphism revealed by SDS-PAGE L. Joelri Michael Raj 1* , S.John Britto 1 , S.Prabhu 1 , and S.R.Senthilkumar 2 . 1 The Rapinat Herbarium and Center for Molecular Systematics, St. Joseph’s College, Tiruchirappalli – 620 002, South India. 2 Department of Plant Biology and Plant Biotechnology, St. Joseph’s College, Tiruchirappalli – 620 002, South India. Accepted 13 May 2011 Seed protein profile of 12 accessions belonging to 9 species of genus Crotalaria were investigated through SDS-PAGE. Intra and inter specific relationship was estimated using Nei and lei’s genetic distances. A dendrogram based on UPGMA revealed the inter relationship of species within Crotalaria. Most species had distinctly different protein patterns but close association was found between C.pallida and C.laburnifolia. The Morphological variation observed between the two specimens of C. grahamiana collected from two different geographical regions showed good variations in their protein profiles also, that are enough to give it the rank of sub species of C. grahamiana. PCA had grouped C.verrucosa and C.beddomeana together where both are specifically characterized by the presence of well developed stipules indicating it as a phylogenetically important character. The present study provides useful markers for the identification of the taxa, their relationship and the delimitation of their taxonomic status both at interspecific and intraspecific levels.The phylogenetic tree obtained by DAMBE predicts sequence of evolution within the genus. Keywords: Crotalaria; Seed proteins; SDS-PAGE; UPGMA; PCA; Phylogenetic tree. INTRODUCTION Crotalaria is a species complex genus and is considered to be the third largest genus of Papilionoideae, with around 600 species distributed throughout the tropics and subtropics (Polhill 1982). They are used as a source of fibers, silage and green manure which are its agronomic traits (Cook and White, 1996; Ramos et al., 2001; Sakala et al., 2006). Crotalaria species can be used as forage for horses and cattle owing to the large amounts of water soluble gums and proteins in their seeds(Purseglove, 1981; Pandey and Srinivatsva, 1990). Their ability to fix nitrogen enables these plants to be used for enhancing soil fertility (Samba et al., 2002). Moreover these leguminous plants develop a high resistance to main species of root knot nematodes which cause severe *Corresponding author Email: joelriraj@gmail.com damage to crops (Antonio and Neumaier, 1986). Crotalaria species are used as food plants for larvae of Lepidoptera species (Eisner et al., 2000). The toxic alkaloids produced by some members of this genus are known to be incorporated by these larvae and used to secure their defense from predators (Bernays et al., 2003). Alkaloid monocrotaline, a pyrrolizidine alkaloid is the main toxic principle of genus Crotalaria which is used to induce experimental pulmonary hypertension in laboratory animals (Werchan et al., 1989). Thus there arises a great need to unravel the phylogenetic relationship of such an agronomic ethnomedicinal and horticulturally important genus. Moreover morphological markers used in the past are insufficient for their correct and proper identification. Sodium Dodecyl Sulphate PolyAcrylamide Gel Electrophoresis (SDS-PAGE) technology is widely used to study plant taxonomy,