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The impact of hybridization on alternative splicing revealed by transcriptome analysis Baute, Gregory Joseph


Hybridization can result in offspring with transgressive traits when compared to the parents. These hybrid traits may have had an important role in plant evolution, they impact ecological fitness, and they have been exploited extensively in agricultural systems. Gene expression levels and patterns of small RNA expression as well as epigenetic modifications can be affected by hybridization. Alternative splicing (AS) is an important form of gene regulation, where multiple final transcript types are created from a single gene. AS is found in a large number of plant genes and has various functional consequences. Here changes in AS regulation upon hybridization have been assayed on a genome-wide scale using RNA-seq data from rice hybrids. AS was quantified in both parental genotypes and their reciprocal hybrids based on read coverage across genes as well as junction spanning reads. Of the over 24,000 AS events investigated, ~8% happen at different frequencies between the different subspecies. The majority of events in the hybrids occur at additive levels compared to their parents, although a large number of events (~9%) are at non-additive levels. Many nonadditive events in the hybrids are at levels equal to one parent. Several hundred AS events happen at higher or lower levels in at least one of the hybrids then in either parent, indicating transgressive AS. Some of these events, 48 in total, could be unique to the hybrids. The transgressively spliced events could contribute to the phenotype of the hybrids by altering the proteome through introducing different proteins, or via regulation of protein levels through nonsense-mediated decay. These data may also be useful in understanding the evolution of the regulation of AS.

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