Theor Appl Genet (2008) 117:273–281 DOI 10.1007/s00122-008-0772-9 123 ORIGINAL PAPER The origin of the C-genome and cytoplasm of Avena polyploids N. Nikoloudakis · A. Katsiotis Received: 3 December 2007 / Accepted: 9 April 2008 / Published online: 8 May 2008  Springer-Verlag 2008 Abstract The contribution of C-genome diploid species to the evolution of polyploid oats was studied using C- genome ITS-speciWc primers. SCAR analysis among Avena accessions conWrmed the presence of C-genome ITS1-5.8S- ITS2 sequences in the genome of AACC and AACCDD polyploids. In situ hybridization and screening of more than a thousand rRNA clones in Avena polyploid species con- taining the C-genome revealed substantial C-genome rRNA sequence elimination. C-genome clones sequenced and Maximum Likelihood Parsimony analysis revealed close proximity to Avena ventricosa ITS1-5.8S-ITS2 sequences, providing strong evidence of the latter’s active role in the evolution of tetraploid and hexaploid oats. In addition, cloning and sequencing of the chloroplastic trnL intron among the most representative Avena species veriWed the maternal origin of A-genome for the AACC interspeciWc hybrid formation, which was the genetic bridge for the establishment of cultivated hexaploid oats. Introduction Genus Avena L. (Poaceae) belongs to the tribe Aveneae and contains diploid, tetraploid and hexaploid species, with the basic chromosome number seven (x = 7). All diploid spe- cies contain either the A-genome or the C-genome, which are also present in the AABB/AACC tetraploid and AACCDD hexaploid species. No diploid species have been found containing either the B-genome or the D-genome (Rajhathy and Thomas 1974). In addition, minor genic diVerences have been reported between the A-genome, B-genome and D-genome (Oinuma 1952; Leggett and Markhand 1995; Katsiotis et al. 1997; Linares et al. 1998; Irigoyen et al. 2001), justifying the proposed genomic designation of A’ for the B-genome and A” for the D-genome (Leggett and Markhand 1995; Katsiotis et al. 2000; Loskutov 2008). High chromosome aYnity between the abovementioned genomes complicates the unravelling of the phylogeny and the identiWcation of ancestral species for Avena polyploids. Molecular markers such as RFLPs, RAPDs, AFLPs and SSRs (O’Donoughue et al. 1995; Alicchio et al. 1995; Ron- ald et al. 1997; Kianian et al. 1999; Jin et al. 1999; Nocelli et al. 1999; Li et al. 2000; Drossou et al. 2004) have ade- quately described species and genome relationships, but there is little information concerning phylogenetic studies. Recently, Nikoloudakis et al. (2008) were able to reveal the association of A. longiglumis Dur. and A. strigosa Scheb. to AACC and AACCDD polyploids, by using the Internal Transcribed Spacers (ITS) and the Inter-Genic Spacer (IGS) nucleotide polymorphism. However, identiWcation of the C-genome species contributing to the speciation of the cultivating oat was not possible. It is noteworthy that during all of the abovementioned studies (molecular markers and nucleotide sequences), it has been observed that all Avena allopolyploids cluster with the A-genome diploids, leading to the conclusion that the C-genome has undergone major genomic alterations. In addition, dominance of the A-genome over the C-genome rRNA sequences and sequence elimination of the latter (Jellen et al. 1994; Fominaya et al. 1995; Yang et al. 1999; Shelukhina et al. 2007) complicates phylogenies. As a result, C-genome ancestry in polyploids remains uncertain. Furthermore, there is no available information based on Communicated by J. S. (Pat) Heslop-Harrison. N. Nikoloudakis · A. Katsiotis (&) Plant Breeding and Biometry Laboratory, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece e-mail: katsioti@aua.gr