PAG 2013, San Diego, CA Strimagdo: diploid and tetraploid oat transcriptome interactions in a synthetic hexaploid oat Emir Islamovic1, Rob Reid2, Raad Gharaibeh2, Cory Brouwer2, Jessica A. Schlueter2, Shannon D. Schlueter2, Gongshe Hu1, Robert Campbell1, Irene Shackelford1, Gideon Ladizinsky3, Eric N. Jellen4, Jeff Maughan4, Rachel Redman5, Melissa Coon4, Joseph Lutz6, Lane Johnson6, Rebekah E. Oliver6, Ryan H. Brown6 and Eric W. Jackson6, (1)USDA-ARS, Aberdeen, ID, (2)University of North Carolina at Charlotte, Charlotte, NC, (3)The Hebrew University of Jerusalem, Israel, (4)Brigham Young University, Provo, UT, (5)University of Utah, UT, (6)General Mills, Kannapolis, NC ABSTRACT The genomic origins of the natural hexaploid oat Avena sativa are still uncertain. However, it is certain that the evolution of hexaploid oats, whether through allopolyploidy (merging of different oat genomes) or autopolyploidy (duplication of existing oat genomes) or a combination of both, required the existence of two genomes (tetraploid) prior to addition of another genome (diploid) in a common nucleus. The advantage of an additional genome had to be immediate for this new species to survive and this advantage had to be a product of altered “tetraploid” gene expression. In this study, we compared transcriptomes of diploid oat, tetraploid oat and a merged diploid/tetraploid in a synthetic hexaploid oat to elucidate genome interactions and alterations to gene expression. Briefly, a synthetic hexaploid oat, ASASCCDDM (2n=42), was previously generated by hybridization of Avena strigosa diploid oat, ASAS (2n=14), and Avena magna tetraploid oat, CCDDM (2n=28), in Gideon Ladizinsky's oat genetics program. RNA was extracted from immature seed embryos and each transcriptome was assembled de novo using RNA-Seq. We will discuss gene expression, gene silencing and derepression, and present possible underlying mechanisms of this phenomenon.
“Talking Genomes” - Transcriptome comparison of diploid, tetraploid and newly synthesized hexaploid oat Robert W. Reid1, Emir Islamovic2, Raad Gharaibeh1, Cory Brouwer1, Jessica Schlueter1, Shannon Schlueter1, Gongshe Hu2, Robert Campbell2, Irene Shackelford2, Gideon Ladizinsky3, Rick Jellen4, Jeff Maughan4, Rachel Redman Hulse5, Melissa Coon Fogarty4, Lane Johnson6, Rebekah Oliver6, Ryan Brown6, Joe Lutz6, Eric Jackson6 Poster P0299 Our study showed that newly synthesized hexaploid, with 39497 gene candidates, maintained a similar transcriptome, about 80%, as combined Avena magna and Avena strigosa transcriptomes, with 49983 gene candidates. This suggests that diploid and tetraploid genomes mostly conserved their gene expression after merging into a new hexaploid state. Interestingly, the similarity of transcriptomes between evolved oat genome (Leggett) and newly merged hexaploid is also about 80%. This leaves 20% of transcriptome differences to be explained by either directed genetic or epigenetic changes. Current thought is that the genetic and epigenetic repatterning of transcriptome is programmed rather than a chaotic response to the new merger, suggesting allopolyploidy being sensed by cell machinery and triggering a complex but methodical cellular response, which is observed in transcriptome changes. 25 million reads per sample
