SHORT COMMUNICATION Development and validation of a PCR-based functional marker system for the major wide-compatible gene locus S5 in rice R. M. Sundaram • K. Sakthivel • A. S. Hariprasad • M. S. Ramesha • B. C. Viraktamath • C. N. Neeraja • S. M. Balachandran • N. Shobha Rani • P. Revathi • P. Sandhya • Y. Hari Received: 17 December 2009 / Accepted: 8 July 2010 / Published online: 21 July 2010 Ó Springer Science+Business Media B.V. 2010 Abstract The major wide-compatibility gene locus S5 in rice (Oryza sativa L.) located on chromosome 6 has been recently cloned and a 136-bp deletion in the candidate gene encoding aspartyl protease has been characterized to be specific for wide-compatible varieties, while many single nucleotide polymor- phisms have been identified at S5 between indica and japonica rice types. In the present study, we designed a PCR-based multiplex functional marker system targeting the deletion and the SNPs for precise determination of the allelic status at S5. By deploying the marker system, the allelic status at the S5 locus in 584 rice genotypes has been assayed. A total of 116 genotypes, including 11 cultivars, two known wide- compatible varieties, 48 IRRI germplasm lines, 12 Indian aromatic rice genotypes, 37 restorer lines and six breeding lines, have been identified to possess the 136-bp deletion specific for the neutral allele at S5. The marker system was able to clearly distinguish indica and japonica alleles from the neutral allele and has been validated in a mapping population derived from the three-way cross IR36/Dular//Akihikari, which segregated for spikelet sterility/fertility. The functional marker system targeting S5 developed in the present study will be very useful in rapid identi- fication of wide-compatible genotypes, in predicting the success of inter-subspecific crosses and in targeted introgression of the wide-compatible allele of S5 into elite indica and japonica rice varieties. Keywords Oryza sativa  Rice  Wide compatibility  Hybrid sterility  S5  Functional marker  Neutral allele Exploitation of strong heterosis noticed in inter- subspecific hybrids is considered to be an important strategy for developing high-yielding rice (Oryza sativa L.) hybrids. A major difficulty encountered in the development of such inter-subspecific hybrids is the partial hybrid sterility (HS) frequently observed in most indica/japonica crosses (Kato et al. 1928). A special class of rice germplasm, known as wide- compatible varieties (WCVs), can produce hybrids with normal fertility when crossed with both indica and japonica (Ikehashi and Araki 1984). Realizing the importance of WCVs in overcoming HS, studies have been conducted to reveal the genetic basis of wide compatibility in rice. More than 28 genes were R. M. Sundaram, K. Sakthivel, and A. S. Hariprasad have contributed equally. Electronic supplementary material The online version of this article (doi:10.1007/s11032-010-9482-5) contains supplementary material, which is available to authorized users. R. M. Sundaram (&)  K. Sakthivel  A. S. Hariprasad  M. S. Ramesha  B. C. Viraktamath  C. N. Neeraja  S. M. Balachandran  N. Shobha Rani  P. Revathi  P. Sandhya  Y. Hari Crop Improvement Section, Directorate of Rice Research, Rajendranagar, Hyderabad 500030, India e-mail: rms_28@rediffmail.com 123 Mol Breeding (2010) 26:719–727 DOI 10.1007/s11032-010-9482-5