Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

Abstract

Mol Gen Genomics (2005) 273: 54–65 DOI 10.1007/s00438-004-1095-4 O R I GI N A L P A P E R Daolin Fu AE Pe´ter Szu } cs AE Liuling Yan Marcelo Helguera AE Jeffrey S. Skinner Jarislav von Zitzewitz AE Patrick M. Hayes Jorge Dubcovsky Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat Received: 15 September 2004 / Accepted: 22 November 2004 / Published online: 3 February 2005 Springer-Verlag 2005 Abstract The broad adaptability of wheat and barley is in part attributable to their flexible growth habit, in that spring forms have recurrently evolved from the ancestral winter growth habit. In diploid wheat and barley growth habit is determined by allelic variation at the VRN-1 and/or VRN-2 loci, whereas in the polyploid wheat species it is determined primarily by allelic variation at VRN-1. Dominant Vrn-A1 alleles for spring growth habit are frequently associated with mutations in the promoter region in diploid wheat and in the A genome of common wheat. However, several dominant Vrn-A1, Vrn-B1, Vrn-D1 (common wheat) and Vrn-H1 (barley) alleles show no polymorphisms in the promoter region relative to their respective recessive alleles. In this study, we sequenced the complete VRN-1 gene from these accessions and found that all of them have large dele- tions within the first intron, which overlap in a 4-kb region. Furthermore, a 2.8-kb segment within the 4-kb region showed high sequence conservation among the different recessive alleles. PCR markers for these dele- tions showed that similar deletions were present in all the accessions with known Vrn-B1 and Vrn-D1 alleles, and in 51 hexaploid spring wheat accessions previously shown to have no polymorphisms in the VRN-A1 pro- moter region. Twenty-four tetraploid wheat accessions Communicated by W.R. McCombie D. Fu AE L. Yan AE J. Dubcovsky (&) Department of Plant Sciences, University of California, One Shields Av, Davis, CA 95616, USA P. Szu } cs Agricultural Research Institute of the Hungarian Academy of Sciences, 2462 Martonva´sa´r, Hungary M. Helguera EEA INTA Marcos Jua´rez, CC 21, 2580 Marcos Jua´rez, Argentina J. S. Skinner AE J. von Zitzewitz AE P. M. Hayes Department of Crop and Soil Science and Horticulture, Oregon State University, Corvallis, OR 97331, USA had a similar deletion in VRN-A1 intron 1. We hypothesize that the 2.8-kb conserved region includes regulatory elements important for the vernalization requirement. Epistatic interactions between VRN-H2 and the VRN-H1 allele with the intron 1 deletion suggest that the deleted region may include a recognition site for the flowering repression mediated by the product of the VRN-H2 gene of barley. Keywords Wheat AE Barley AE Vernalization AE VRN-1 AE Allelic variation Introduction Many cereal crops, such as wheat, barley and oat, are divided into spring and winter types based on their growth habit. Winter varieties require an extended per- iod of exposure to cold in order to flower, a process known as vernalization. Vernalization is defined as ‘‘the acquisition or acceleration of the ability to flower by a chilling treatment’’ (Chouard 1960). The physiology of vernalization has been studied extensively in cereals, but only a few genes from this molecular pathway are cur- rently known (Yan et al. 2003, 2004b). In wheat and barley, the determination of the ver- nalization requirement involves an epistatic interaction between the genetic loci VRN-1 and VRN-2 (Takahashi and Yasuda 1971; Tranquilli and Dubcovsky 2000). Positional cloning of these two genes from diploid wheat (Triticum monococcum L., 2n=14, genome A m A m ) re- vealed that VRN-1 encodes a MADS-box transcription factor that is orthologous to the Arabidopsis meristem identity gene APETALA1 (Yan et al. 2003), while the VRN-2 gene codes for a zinc finger-CCT domain tran- scription factor with no clear orthologues in Arabidopsis or rice (Yan et al. 2004b). The VRN-1 gene is dominant for the spring growth habit and it is up-regulated by vernalization in winter lines (Danyluk et al. 2003; Tre- vaskis et al. 2003; Yan et al. 2003), whereas the VRN-2