656 In summary, the present study identified 5,692 unique candidate SFPs extending the marker repertoire with functional marker systems in pigeonpea. Allele-specific sequencing of a set of selected genes detecting SFPs showed association of 52.6% SFPs analyzed with actual sequence polymorphisms in the probe sets. Gene ontology analysis of the genes detecting SFPs provided a set of candidate genes that may have association with drought tolerance. These candidate genes are useful resource for undertaking the gene expression analysis as well develop- ment of functional markers for both basic and applied research, especially for drought tolerance in pigeonpea improvement. Acknowledgements Authors are thankful to the CGIAR Generation Challenge Programme (GCP) for providing financial support to conduct this research. Microarray data were generated by the Genomics Core facility at the Institute for Integrative Genome Biology of the University of California, Riverside (USA). 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