I am currently finishing my PhD at University of Colorado in Nolan Kane's lab. I got my start in plant biology as an undergrad doing summer field ecology research at the Rocky Mountain Biological Laboratory in Gothic, Colorado. Now my interests include population genomics, gene regulatory evolution, adaptation, domestication, and mating system evolution. My dissertation is focused on the evolution and diversity of North American blue flax (Linum lewisii) and supports an effort to domesticate this species as a new perennial oilseed crop. In grad school I've also worked on evolutionary genetics on Cannabis and sunflower (Helianthus).
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Gene expression and alternative splicing contribute to adaptive divergence of sunflower ecotypes
PETER INNES
, APRIL M. GOEBL, CHRIS C.R. SMITH, KAYLEE ROSENBERGER, NOLAN KANE
Ecology and Evolutionary Biology Department, University of Colorado, 1900 Pleasant Street, Boulder, Colorado 80309, USA
Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that specific regulatory mechanisms contribute to adaptive divergence of populations. The post-transcriptional regulatory mechanism of alternative splicing (AS) plays an important role in both plant development and abiotic stress response, making it a compelling potential target of natural selection. Here we examine whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation among ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how the sequence divergence landscape, including large chromosomal inversions, corresponds to divergence in transcript levels and isoform proportions and find evidence for both cis- and trans-regulation. Our results emphasize that alternative splicing has been an underappreciated mechanism involved in adaptive evolution at short time scales.