Alternative Splicing of Duplicated Genes in Polyploid Brassica napus

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Polyploids, organisms with an extra set of chromosomes, are common among plants and many crop plants are polyploids. The formation of polyploids often involves hybridization (crossing) between two species followed by chromosome doubling. Polyploidy can lead to novel morphological and developmental characteristics, larger cell sizes, and new gene functions and expression patterns. The long-term goals of my research program are to understand the consequences of polyploidy on the evolution, expression, splicing, and function of duplicated genes. We study evolutionarily recent polyploid plants, as well as genes derived from ancient polyploidy events that occurred millions of years ago to determine the long-term outcomes of duplicate gene evolution. The goal of this research proposal is to understand the consequences of polyploidy on gene expression with a focus on patterns of RNA splicing (alternative splicing) in response to environmental stress conditions. Brassica napus (canola) polyploids will be compared with their diploid parental species, B. rapa and B. oleracea. Stress treatments will include heat, cold, drought, and salt. To examine the effects of each stress treatment on RNA expression and splicing, the RNA will be sequenced with a high-throughput method that provides sequences of entire transcripts (isoforms). The data will be analyzed with computational approaches. The proposed research will provide insights into differences in transcript isoforms between duplicated genes in the polyploids, as well as reveal how the polyploids compare with their diploid parental species. In addition, RNA splicing patterns in genes duplicated by a much older polyploidy during the evolutionary history of the Brassica lineage will be analyzed to assess changes in transcript isoforms on a longer-term evolutionary time scale. This research is likely to have an impact on the fields of plant genomics, plant molecular biology, and molecular evolution. Some duplicate genes play a role in specifying traits of agronomic importance in plants. Some RNA splicing patterns in duplicated genes may be involved in conferring traits selected for during plant breeding. In particular, polyploid canola (Brassica napus) is very important to Canada's economy and food supply and what is learned from studying RNA splicing in canola may lead to improvement of this crop plant.