RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids

Cirsium arvenseHybridization is a prominent process among natural plant populations that can result in phenotypic novelty, heterosis, and changes in gene expression. The effects of intraspecific hybridization on F1 hybrid gene expression were investigated using parents from divergent, natural populations of Cirsium arvense, an invasive Compositae weed.

Using an RNA-seq approach, the expression of 68,746 unigenes was quantified in parents and hybrids. The expression levels of 51% of transcripts differed between parents, a majority of which had <1.25x fold-changes. More unigenes had higher expression in the invasive parent (P1) than the non-invasive parent (P2). Of those that were divergently expressed between parents, 10% showed additive and 81% showed non-additive (transgressive or dominant) modes of gene action in the hybrids. A majority of the dominant cases had P2-like expression patterns in the hybrids. Comparisons of allele-specific expression also enabled a survey of cis- and trans-regulatory effects. Cis- and trans-regulatory divergence was found at 70% and 68% of 62,281 informative SNP sites, respectively. Of the 17% of sites exhibiting both cis- and trans- effects, a majority (70%) had antagonistic regulatory interactions (cis x trans); trans-divergence tended to drive higher expression of the P1 allele whereas cis-divergence tended to increase P2 transcript abundance. Trans-effects correlated more highly than cis- with parental expression divergence and accounted for a greater proportion of the regulatory divergence at sites with additive compared to non-additive inheritance patterns. This study explores the nature of, and types of mechanisms underlying, expression changes that occur in upon intraspecific hybridization in natural populations.

  • Bell GD, Kane NC, Rieseberg LH, Adams KL. (2013) RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations. Genome Biol Evol [Epub ahead of print]. [abstract]
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