Alternative Splicing and Long Non-coding RNAs in Polyploids

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Polyploids, organisms with an extra set of chromosomes, are common among plants and several crop plants are polyploid. Polyploidy can lead to novel morphological and developmental characteristics, larger cell sizes, and new gene functions and expression patterns. The formation of polyploids often involves hybridization (crossing) between two species followed by chromosome doubling. The goal of this research is to understand the consequences of polyploidy on gene expression with a focus on patterns of RNA splicing (alternative splicing) and long noncoding RNAs (genes whose products act as RNAs instead of as proteins). Expression and RNA splicing patterns of genes in Brassica napus (canola) polyploids will be compared with their diploid parents in response to stress conditions. Stress treatments will be done with heat, cold, and drought. RNA expression and splicing patterns will be examined on a genome-wide scale with high-throughput sequencing and computational analyses. Long noncoding RNA genes will be identified in Brassica species. Then their expression patterns will be assayed with high throughput sequencing in Brassica napus polyploids and their diploid parents to show how expression of this class of genes changes upon polyploidy. Duplicated long noncoding RNA genes, and their gene family histories, will be characterized in Arabidopsis thaliana and Brassica species, and the features will be compared with protein coding genes.The proposed research will provide the first insights into differences in RNA splicing patterns between duplicated genes in polyploid plants in response to stress conditions on a genome-wide scale. Also it will provide the first information about long noncoding RNA expression in polyploids. This research is likely to have a considerable 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, as well as gene regulation by long noncoding RNAs, may be involved in conferring traits selected for during plant breeding. In particular, polyploid canola (Brassica napus) is important to Canada's economy and food supply and what is learned from studying RNA splicing and long noncoding RNAs in canola may lead to improvement of this crop plant. Understanding how RNA splicing patterns can change gene expression and function, as well as how long noncoding RNAs regulate gene expression, may lead to using RNA splicing and noncoding RNAs as tools for biotechnology applications to design crops with altered expression of genes of interest to create or improve desired characteristics.