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Regulation of gene expression in invasive and non-invasive Compositae weeds Bell, Graeme Douglas Milton

Abstract

Gene expression divergence between populations has been linked to adaptive morphological evolution and is thought to be a factor in the invasive success of certain weedy plants. Understanding the genetic basis of these regulatory changes can identify genes that have been under selection during adaptation to a new environment or new species interactions. A high-throughput sequencing approach was used to study the regulatory basis (cis and/or trans) of gene expression differences between native and invasive populations of Cirsium arvense (Canada thistle) by exploring patterns of differential gene expression and sequence variation. Parent and hybrid allele-specific expression ratios were compared to infer the relative effects of cis- and trans-regulatory change. Genes differentially regulated in cis are considered candidate genes involved in adaptation or weediness because there is evidence for selection acting primarily on cis-regulatory variation. Illumina sequencing of cDNA libraries derived from parents and hybrid pools resulted in a total of 82,713,256 paired-end (2x100bp) reads and 83.4% of these were mapped to a reference C. arvense transcriptome of 88,374 unigene sequences. Expression analysis and variant (SNPs and Indel) calling was performed to score the nature of regulatory divergence for the first 900 contigs, representing ~1% of the total dataset. Of the 40 high-confidence cases, 7 showed cis-effects, 6 showed trans-effects, 9 had varying degrees of both cis and trans, and 18 showed non-intermediate hybrid effects. A set of contigs that had high similarity to 63 known or confirmed stress-related genes, previously identified in studies of sunflower and Canada thistle, was also assayed for allelic imbalance. Of these, 2 cases showed a cis-effect, 2 showed both cis- and trans-effects, and 2 revealed hybrid effects. Contig 23614, an auxin-response transcription factor, was differentially regulated due to cis-effects and has been previously confirmed as drought-stress gene in both sunflower and C. arvense. This research identifies changes in gene expression that are driven by differential selective pressures in native and invasive populations. It also advances our understanding of the nature of genetic changes that drive gene expression evolution.

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