DNA analysis and Avena genomes

Abstract

Molecular analysis and characterization of the four Avena genomes (A, B, C and D) is a powerful and promising tool towards understanding species and genome relationships (Katsiotis et al 1997, 2000) which are not yet fully resolved. In a recent study we reported on the resolving power of RAPD (Random Amplified Polymorphic DNA) and AFLP (Amplified Fragment Length Polymorphism) markers in 18 Avena taxa (Drossou et al. 2004). In the present study we extend our investigations on several genome and/or taxonspecific RAPD markers and their organisation. Twelve genome and/or taxon-specific RAPD markers were extracted from agarose gels and cloned. At least five clones per marker were sequenced. These sequences were aligned using CLUSTALW and their similarity homology to other previously characterised sequences was checked by FASTA. For each set of sequences, primer pairs were designed and SCAR (Sequence Characterised Amplified Regions) markers were produced. Sequencing of the cloned RAPD markers revealed that four RAPD markers contained a single sequence family while the rest were comprised of two or three different families, confirming the co-migration of different sequence families sharing similar sizes in RAPDs. The SCAR markers revealed the presence of certain sequence families in more species and genomes than the RAPD markers indicated. The information from the sequence divergence of the RAPD markers and the SCARs suggests that the modified A genome species are separated mainly due to structural rearrangements, in contrast to the major genetic differences between the A and C genomes. Drossou, A. et al. 2004. Theoretical and Applied Genetics In Press; Katsiotis, A. et al. 1997. Annals of Botany 79:103-109; Katsiotis, A. et al. 2000. Annals of Botany 86:1135-1142.