RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations

Abstract

Hybridization 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 less than 1.25× fold-changes. More unigenes had higher expression in the invasive parent (P1) than the noninvasive parent (P2). Of those that were divergently expressed between parents, 10% showed additive and 81% showed nonadditive (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 single-nucleotide polymorphism 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 with nonadditive inheritance patterns. This study explores the nature of, and types of mechanisms underlying, expression changes that occur in upon intraspecific hybridization in natural populations.

Keywords: Cirsium; Compositae; gene expression; gene regulation; hybrids; intraspecific hybridization.

Fig. 1.—

Expression divergence between native and invasive parents of Cirsium arvense. (A) Volcano plot summarizes normalized expression for all contigs that passed the filter for minimum coverage. Vertical lines indicate 2-fold changes in expression, and the horizontal line shows the threshold for significant test results (FDR: 0.5%). (B) A histogram shows the direction and magnitude of expression changes at contigs exhibiting parental expression divergence; positive log₂(P₁/P₂) values indicate that the invasive parent (P₁) has higher expression than the native parent (P₂), whereas negative values show that P₂ > P₁.

Fig. 2.—

Modes of hybrid expression inheritance are investigated for the 68,746 contigs that passed the filter for minimum expression. (A) A scatterplot comparing total expression between Hyb_Avg and P₁ (x axis), and between Hyb_Avg and P₂ (y axis), enabled sorting of contigs into their modes of expression inheritance as described in text. (B) and (C) Total expression (log₂ normalized read counts) is compared between hybrid and invasive and native parents, left to right, respectively. Barplots (D) and (E) further explore the cases of parental dominance in hybrid expression patterns.

Fig. 3.—

(A) Absolute magnitude (fold-change) of parental divergence resulting from cis- and trans-effects. (B) A box-and-whisker plot showing the percent of cis-effects for genes binned based on the magnitude of expression divergence between parents. (C) Scatterplot showing relative allelic expression levels in parents and hybrids; results used to sort genes into categories based on their mechanism of regulatory evolution as described in Materials and Methods. Scatterplots (D) and (E) compare parental and hybrid allelic expression for alleles P₁ and P₂, respectively.

Fig. 4.—

Box-and-whisker plots compare the relative contribution of cis-effects (% cis) underlying regulatory divergence between sets of genes categorized by (A) additive versus nonadditive and (B) transgressive versus nontransgressive modes of expression inheritance.