J Appl Genetics (2011) 52:313–318 DOI 10.1007/s13353-011-0049-x PLANT GENETICS ∙ SHORT COMMUNICATION DArT markers tightly linked with the Rfc1 gene controlling restoration of male fertility in the CMS-C system in cultivated rye (Secale cereale L.) Stefan Andrzej Stojałowski & Paweł Milczarski & Monika Hanek & Hanna Bolibok-Brągoszewska & Beata Myśków & Andrzej Kilian & Monika Rakoczy-Trojanowska Received: 19 December 2010 / Revised: 7 April 2011 / Accepted: 13 April 2011 / Published online: 11 May 2011 # The Author(s) 2011. This article is published with open access at SpringerLink.com Abstract The Rfc1 gene controls restoration of male fertility in rye (Secale cereale L.) with sterility-inducing cytoplasm CMS-C. Two populations of recombinant inbred lines (RIL) were used in this study to identify DArT markers located on the 4RL chromosome, in the close vicinity of the Rfc1 gene. In the population developed from the 541×2020LM inter- cross, numerous markers tightly linked with the restorer gene were identified. This group contained 91 DArT markers and three SCARs additionally analyzed in the study. All these markers were mapped in the distance not exceeding 6 cM from the gene of interest. In the second mapping population (541×Ot1-3 intercross), only 9 DArT markers located closely to the Rfc1 gene were identified. Five of these DArT markers were polymorphic in both populations. Keywords Cytoplasmic male sterility . Genetic mapping . Restorer gene . Rye Rye (Secale cereale L.) is a crop of a great importance in the north-east part of Europe due to its tolerance to low temperatures in winter, aluminum ions in the soil and other S. A. Stojałowski (*) : P. Milczarski : M. Hanek : B. Myśków Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, Poland e-mail: sstojalowski@zut.edu.pl H. Bolibok-Brągoszewska : M. Rakoczy-Trojanowska Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Warsaw, Poland A. Kilian Diversity Arrays Technology P/L, Yarralumla, Canberra, Australia environmental stresses often occurring in this region. The breeding progress recently achieved in hybrids is signifi- cantly higher than in population cultivars of rye (Geiger 2007). This leads to a regular increase of the growing areas of hybrid cultivars in European countries. Generally, the breeding of rye hybrids is based on the Pampa sterility-inducing cytoplasm (CMS-P). The use of an alternative type of CMS in practice is strongly recommen- ded for reducing risks arising from plasmotype uniformity (Morgenstern and Geiger 1982; Adolf and Winkel 1985; Geiger et al. 1995). One of potentially applicable sources of CMS in rye is the C cytoplasm (CMS-C) discovered by Łapiński (1972) in the old Polish cultivar ‘Smolickie’. In consideration of the low frequency of sterility alleles in populations of cultivated rye, development of new non- restorer lines in the CMS-C system can be significantly facilitated by the application of marker assisted selection (MAS). The main gene controlling restoration of male fertility in the C cytoplasm (Rfc1) is located on the 4RL chromosome (Stojałowski et al. 2004) and some molecular markers linked with this locus were identified (Stojałowski et al. 2005; Hackauf et al. 2009). Recently a high density genetic map of rye was developed by Bolibok- Brągoszewska et al. (2009) with the use of Diversity Array Technology (DArT). This study was aimed at identification of new markers based on Diversity Array Technology which are tightly linked to the Rfc1 gene. Two mapping populations composed of recombinant inbred lines (RILs) were used in the study. First population consisted of 92 RILs of F5 generation developed from the cross between the inbred lines: 541 (non-restorer) and 2020LM (restorer). The second population contained 144 RILs (F9) originating from the cross between the same non- restorer line 541 and the restorer Ot1-3. The origin of