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Title: Polyploidization as a Retraction Force in Plant Genome Evolution: Sequence Rearrangements in Triticale

Author
item BENITO, MIGUEL - UNIV OF LISBON, PORTUGAL
item PEREIRA, H - UNIV OF LISBON, PORTUGAL
item ROCHETA, MARGARIDA - UNIV OF LISBON, PORTUGAL
item Gustafson, J
item VIEGAS, WANDA - UNIV OF LISBON, PORTUGAL
item SILVA, MANUELA - UNIV OF LISBON, PORTUGAL

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/18/2007
Publication Date: 1/2/2008
Citation: Benito, M., Pereira, H.S., Rocheta, M., Gustafson, J.P., Viegas, W., Silva, M. 2008. Polyploidization as a Retraction Force in Plant Genome Evolution: Sequence Rearrangements in Triticale. PLoS One. Available at: http//www.plosone.org/doi/pone.0001402.

Interpretive Summary: Triticale is a new cereal produced by crossing wheat and rye and is an important addition to the agricultural repertoire designed to meet the needs of many regions of the world for feed, forage, and sustainable cropping systems. Triticale also plays a direct role in the improvement of wheat in that it can serve as a source of rye value-added trait gene complexes that are missing in wheat, but can be manipulated into wheat; e.g., fungal disease resistance and abiotic stress tolerances. However, wheat and rye exhibit an enormous evolutionary variation, which plays an active role in limiting our ability to manipulate rye gene complexes for improving wheat. Two important questions are; 1) how formation of the wheat-rye hybrid affects parental gene expression in this new species, and 2) what significance does this process have on the utilization of rye gene complexes for wheat improvement? This study was designed to compare the molecular structure of an existing USDA-ARS triticale and its original wheat and rye parents. The approach was designed to make use of existing molecular markers to analyze genome changes in the triticale by comparing the parents and the hybrid. The results of this study clearly showed that during polyploid formation, many wheat and rye gene complexes were rearranged when they were placed together in a triticale, and in some cases rye gene complexes were silenced (i.e., not expressed), or were completely missing (i.e., had been deleted from the triticale). The results clearly demonstrated that, in triticale, the rye genome and gene complexes were significantly more affected than the wheat genome. The results will enable scientists to better design strategies for the successful manipulation of desirable rye value-added trait gene complexes in our quest for improved wheat production.

Technical Abstract: Polyploidization is a major evolutionary process in plants where hybridization and chromosome doubling induce enormous genomic stress and restructuring. Here, we show that PCR-based molecular marker techniques involving retrotransposons and microsatellites are extremely powerful tools to uncover polyploidization induced genetic restructuring events. Inter Retrotransposons Amplified Polymorphism (IRAP), Retrotransposons Microsatellite Amplified Polymorphism (REMAP) and Inter Simple Sequence Repeat (ISSR) produced consistent and reproducible banding profiles for wheat, rye and triticale. Comparative analysis of banding profiles between the primary triticale and their wheat and rye direct progenitors uncovered nearly 40% of the sequences analyzed were rearranged in the polyploid. The majority of these modifications were due to modification and/or loss of rye sequences, the progenitor with the largest genome complement. Sequence analysis of lost genomic fragments showed these to be Retrotransposon-related as well as coding sequences. A few novel sequences absent inform both parents were also identified in the polyploid, and sequence analysis of one triticale-specific fragment showed that it was microsatellite related. Fluorescent in situ hybridization (FISH) with REMAP products demonstrated retrotransposon and/or microsatellite flanking sequences to be distributed throughout all rye chromosomes, with preferential accumulation in the heterochromatic sub-telomeric regions. The molecular and cytogenetic data suggested that the majority of sequence modification and/or loss observed in the triticale analyzed could be attributable to rye heterochromatic domains. Therefore, genome size as well as chromatin condensation may play an important role on the origin of genomic rearrangements mediating the evolutionary processes involved in polyploidization in wheat/rye hybrids.