Funct Integr Genomics (2011) 11:651–657 DOI 10.1007/s10142-011-0227-2 SHORT COMMUNICATION Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.) Rachit K. Saxena & Xinping Cui & Vivek Thakur & Barbara Walter & Timothy J. Close & Rajeev K. Varshney Received: 6 January 2011 / Revised: 13 April 2011 / Accepted: 17 April 2011 / Published online: 6 May 2011 # The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Single feature polymorphisms (SFPs) are microarray-based molecular markers that are detected by hybridization of DNA or cRNA to oligonucleotide probes. With an objective to identify the potential polymorphic markers for drought tolerance in pigeonpea [Cajanus cajan (L.) Millspaugh], an important legume crop for the semi- arid tropics but deficient in genomic resources, Affymetrix Genome Arrays of soybean (Glycine max), a closely related species of pigeonpea were used on cRNA of six parental genotypes of three mapping populations of pigeonpea segregating for agronomic traits like drought tolerance and pod borer (Helicoverpa armigiera) resistance. By using robustified projection pursuit method on 15 pair-wise comparisons for the six parental genotypes, 5,692 SFPs were identified. Number of SFPs varied from 780 (ICPL 8755 × ICPL 227) to 854 (ICPL 151 ×ICPL 87) per parental combination of the mapping populations. Randomly select- ed 179 SFPs were used for validation by Sanger sequencing and good quality sequence data were obtained for 99 genes Electronic supplementary material The online version of this article (doi:10.1007/s10142-011-0227-2) contains supplementary material, which is available to authorized users. R. K. Saxena : V. Thakur : R. K. Varshney (*) International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India e-mail: r.k.varshney@cgiar.org X. Cui : B. Walter : T. J. Close University of California, Riverside, CA 92521, USA R. K. Varshney CGIAR- Generation Challenge Programme (GCP), c/o CIMMYT, 06600, Mexico DF, Mexico of which 75 genes showed sequence polymorphisms. While associating the sequence polymorphisms with SFPs detected, true positives were observed for 52.6% SFPs detected. In terms of parental combinations of the mapping populations, occurrence of true positives was 34.48% for ICPL 151× ICPL 87, 41.86% for ICPL 8755 ×ICPL 227, and 81.58% for ICP 28 ×ICPW 94. In addition, a set of 139 candidate genes that may be associated with drought tolerance has been identified based on gene ontology analysis of the homologous pigeonpea genes to the soybean genes that detected SFPs between the parents of the mapping populations segregating for drought tolerance. Keywords Single feature polymorphism . Microarray . Robustified projection pursuit . Molecular markers . Legumes Introduction Pigeonpea [Cajanus cajan (L.) Millspaugh], with a genome size 858 Mbp and 11 pairs of chromosomes, is a major grain legume crop in the tropical and subtropical regions of the world. However, the crop productivity of pigeonpea has remained stagnant less than 1 ton per hectares for last 40 years as the crop is exposed to several biotic (e.g., Fusarium wilt, sterility mosaic disease, and pod borer) and abiotic (drought, salinity, and water logging) stresses. As genomics-assisted breeding has been very successful in several temperate cereals (Varshney et al. 2006) and some legume species like soybean (Varshney et al. 2010), the pigeonpea crop has remained untouched with genomics research. For instance, until recently a few hundred simple sequence repeat (SSR) markers were available (Burns et al. 2001; Odeny et al. 2007; Saxena et al. 2010a,b), some