ORIGINAL PAPER A. Tondelli Æ E. Francia Æ D. Barabaschi Æ A. Aprile J. S. Skinner Æ E. J. Stockinger Æ A. M. Stanca N. Pecchioni Mapping regulatory genes as candidates for cold and drought stress tolerance in barley Received: 27 July 2005 / Accepted: 24 October 2005 / Published online: 29 November 2005 Ó Springer-Verlag 2005 Abstract Cereal crop yield is greatly affected in many growing areas by abiotic stresses, mainly low tempera- ture and drought. In order to find candidates for the tolerance genes for these stresses, 13 genes encoding for transcription factors and upstream regulators were screened by amplification and SSCP on six parental genotypes of three barley mapping populations (‘Nure’ · ‘Tremois’, ‘Proctor’ · ‘Nudinka’, and ‘Step- toe’ · ‘Morex’), and mapped as newly developed STS, SNP, and SSCP markers. A new consensus function map was then drawn using the three maps above, including 16 regulatory candidate genes (CGs). The positions of barley cold and drought tolerance quanti- tative trait loci (QTLs) presently described in the liter- ature were added to the consensus map to find positional candidates from among the mapped genes. A cluster of six HvCBF genes co-mapped with the Fr-H2 cold tol- erance QTL, while no QTLs for the same trait were positioned on chromosome 7H, where two putative barley regulators of CBF expression, ICE1 and FRY1, found by homology search, were mapped in this work. These observations suggest that CBF gene(s) themselves, rather than their two regulators, are at present the best candidates for cold tolerance. Four out of 12 drought tolerance QTLs of the consensus map are associated with regulatory CGs, on chromosomes 2H, 5H, and 7H, and two QTLs with effector genes, on chromosomes 5H and 6H. The results obtained could be used to guide MAS applications, allowing introduction into an ideal genotype of favourable alleles of tolerance QTLs. Keywords Candidate genes Æ Stress tolerance Æ CBF Æ ICE1 Æ FRY1 Abbreviations CG: Candidate gene Æ QTL: Quantitative trait locus Æ TF: Transcription factor Æ COR: Cold regulated gene Æ STS: Sequence tagged site Æ SNP: Single nucleotide polymorphism Æ SSCP: Single strand conformation polymorphism Æ CAPS: Cleaved amplified polymorphic sequence Æ ARMS: Amplification refractory mutation system Introduction During their evolution, plants have acquired adaptive strategies to cope with abiotic stresses. Throughout domestication and breeding, man has driven the genetic improvement of crops towards high yields in different environments. These two facts notwithstanding, crop yield is greatly affected in many growing areas by abiotic stresses such as low temperature and drought. Among cereals, barley (Hordeum vulgare L.) can be considered a good genetic model for its tribe (Triticeae) to study plant response to adverse environmental conditions. Its inbreeding behaviour and diploidy make the genetic studies easy to perform; its wide range of adaptability, the availability of a wide range of genetic stocks, and the extended colinearity with other members of the tribe are additional advantages as a model (Hayes et al. 2003). Electronic Supplementary Material Supplementary material is available for this article at http://www.dx.doi.org/10.1007/s00122- 005-0144-7 and is accessible for authorized users. Communicated by J. W. Snape A. Tondelli Æ E. Francia Æ A. Aprile Æ A. M. Stanca D. Barabaschi Æ N. Pecchioni (&) CRA Istituto Sperimentale per la Cerealicoltura, Sezione di Fiorenzuola d’Arda (PC), 29017 Fiorenzuola d’Arda, Italy E-mail: pecchioni.nicola@unimore.it Tel.: +39-522-522003 Fax: +39-522-522053 D. Barabaschi Æ N. Pecchioni Facolta` di Agraria, Universita` di Modena e Reggio, 42100 Reggio Emilia, Italy J. S. Skinner Departments of Horticulture and Crop and Soil Science, Oregon State University, Corvallis, OR OR-97331, USA E. J. Stockinger Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH OH-44691, USA Theor Appl Genet (2006) 112: 445–454 DOI 10.1007/s00122-005-0144-7