P0299
“Talking Genomes” - Transcriptome Comparison of Diploid, Tetraploid and Newly Synthesized Hexaploid Oat
“Talking Genomes” - Transcriptome Comparison of Diploid, Tetraploid and Newly Synthesized Hexaploid Oat
Date: Monday, January 14, 2013
Room: Grand Exhibit Hall
Allopolyploids are polyploids with chromosomes derived from different species and, in plants, they have been examples of evolutionary success. The selective advantage of multiple genomes can be studied by generating newly synthesized allopolyploid plants. In this study, a synthetic hexaploid oat was generated (ASASCCDDM) by hybridization of Avena strigosa diploid oat, ASAS(2n=14), and Avena magna tetraploid oat, CCDDM (2n=28). We compared transcriptome of diploid, tetraploid and newly synthesized hexaploid oat in order to elucidate genome interactions affecting gene expression and consequently, a production of favorable trait. We also compared transcriptome of newly synthesized hexaploid oat (ASASCCDDM) to cultivatedAvena sativa (AACCDD) in attempt to elucidate effects of recent genome interaction vs. evolved genome interaction on gene expression.
A transcriptome for each of the four strains was assembled de novo using RNA-seq (Illumina HiSeq, paired end) at immature embryo seed stage. Genes were annotated by using a novel step down method where candidate genes were blasted to the nearest phylogenetic plant model in a descending manner until a match was found. Microsatellite analysis, gene coexpression and Gene Ontology assignment were then used to compare and highlight the differences on these oat strains, showing the effects of genomes on overall gene expression. This research was funded by the General Mills, Inc.