PLANT GENETICS • SHORTCOMMUNICATION A doubled haploid rye linkage map with a QTL affecting α-amylase activity Teija Tenhola-Roininen & Ruslan Kalendar & Alan H. Schulman & Pirjo Tanhuanpää Received: 2 December 2010 / Revised: 13 January 2011 / Accepted: 14 January 2011 / Published online: 1 February 2011 # Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2011 Abstract A rye doubled haploid (DH) mapping population (Amilo × Voima) segregating for pre-harvest sprouting (PHS) was generated through anther culture of F 1 plants. A linkage map was constructed using DHs, to our knowledge, for the first time in rye. The map was composed of 289 loci: amplified fragment length polymorphism (AFLP), micro- satellite, random amplified polymorphic DNA (RAPD), retrotransposon-microsatellite amplified polymorphism (RE- MAP), inter-retrotransposon amplified polymorphism (IRAP), inter-simple sequence repeat (ISSR) and sequence- related amplified polymorphism (SRAP) markers, and extended altogether 732 cM (one locus in every 2.5 cM). All of the seven rye chromosomes and four unplaced groups were formed. Distorted segregation of markers (P ≤ 0.05) was detected on all chromosomes. One major quantitative trait locus (QTL) affecting α-amylase activity was found, which explained 16.1% of phenotypic variation. The QTL was localized on the long arm of chromosome 5R. Microsatellites SCM74, RMS1115, and SCM77, nearest to the QTL, can be used for marker-assisted selection as a part of a rye breeding program to decrease sprouting damage. Keywords Microsatellite . Pre-harvest sprouting . Retrotransposon . Secale cereale L. . Segregation distortion . Sequence-related amplified polymorphism Pre-harvest sprouting (PHS) leads to significant economic losses worldwide in cereal production, especially in wheat and rye (e.g., wheat: Humphreys and Noll 2002). In areas such as Finland, where crops must be harvested during rainy seasons, PHS is especially common, because cool, wet weather favors germination (Nyachiro et al. 2002; Chono et al. 2006). The most widely used parameters for PHS determination are Hagberg falling number and α- amylase activity, which are inversely correlated (Hagberg 1960; Perten 1964). Several quantitative trait loci (QTLs) for α-amylase activity as well as other QTLs involved in controling sprouting resistance have been found in rye (Masoj ć et al. 1999; Masoj ć and Milczarski 2005; Twardowska et al. 2005; Masojć et al. 2007; Masojć and Milczarski 2009; Masojć et al. 2009). Doubled haploid (DH) populations are excellent material for genetic mapping and QTL studies (Forster and Thomas 2004), and they have been used especially in self- pollinating species. The present study was carried out to construct the first linkage map of out-crossing rye using DHs, and to characterize QTL(s) affecting α-amylase activity. A rye DH population (89 individuals) derived from the cross of two DH parents, the sprouting-resistant Polish cv. Amilo and the susceptible Finnish cv. Voima, was used for mapping studies. The population was developed from F 1 plants through anther culture, as explained by Tenhola- Roininen et al. (2006). Several various marker types were used in the mapping studies (Table 1). Amplified fragment length polymorphism (AFLP) analyses were performed with minor modifications according to the procedure developed by Vos et al. (1995). Random amplified polymorphic DNA (RAPD) amplifica- tions were carried out as described by Tenhola-Roininen and Tanhuanpää (2010). Sixty-nine microsatellites from rye T. Tenhola-Roininen (*) : A. H. Schulman : P. Tanhuanpää Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, Myllytie 1, 31600 Jokioinen, Finland e-mail: teija.tenhola-roininen@mtt.fi R. Kalendar : A. H. Schulman MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland J Appl Genetics (2011) 52:299–304 DOI 10.1007/s13353-011-0029-1