Genomic reshuffling in advanced lines of hexaploid tritordeum

Genomic restructuring was detected in newly synthesized tritordeum by molecular and cytogenetic tools. Genomic stability is expected for advanced tritordeum lines (H(ch)H(ch)AABB; 2n = 42) with multiple generations of self-fertilization. This study intends to confirm or decline this hypothesis by characterizing three advanced tritordeum lines and their parental species using cytogenetics, inter-simple sequence repeat (ISSR) and retrotransposon-based markers. Mitotic chromosomes of each tritordeum line were hybridized with six synthetic oligonucleotide probes using non-denaturing fluorescence in situ hybridization. Polymorphic hybridization patterns and structural rearrangements involving SSR regions were detected. The same chromosome spreads were re-hybridized with genomic DNA of Hordeum chilense Roem. et Schult. and the 45S ribosomal DNA (rDNA) sequence pTa71. These FISH experiments allowed for parental genome discrimination, identification of nucleolar chromosomes, and detection of structural rearrangements, mostly involving rDNA loci. The chromosomes bearing SSR hybridization signals and/or chromosomes involved in structural rearrangements were identified. ISSR, retrotransposon-microsatellite amplified polymorphism, inter-retrotransposon amplified polymorphism and inter-primer binding site markers evidenced genomic reshuffling in all tritordeum lines relative to their parents. Line HT28 was considered the most genetically stable. This work demonstrated that cytogenetic and molecular monitoring of tritordeum is needed, even after several self-fertilization generations, to guarantee the selection of the most stable lines for improvement and sustainable agriculture.