Transcriptome Analyses of Standing Genetic Variation and Phenotypic Plasticity in Conifer Trees

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Adaptability of plants and trees to accelerated climate warming and other environmental changes over the short term (decades to centuries) depends on their inherent phenotypic plasticity and standing genetic variation within existing populations. Recent studies show that a proportion of the genetic variants underlying complex phenotypes exert their effects through gene expression; so, discovering the genetic basis for the variation in transcript abundance is central to understanding phenotypic variation. My discovery research program aims to enhance our understanding of the conifer transcriptome as it relates to diversity and genetic architecture of complex traits. The proposal builds on my group's recent achievements including the development of large-scale RNA profiling capacity in conifer trees, discovery of extensive heritable variation in gene expression, discovery of transcriptional networks controlling metabolism, and an insect resistance gene. The short-term objectives presented in this proposal leverage transcriptome analyses to bridge between genetic diversity and phenotypes of adaptive significance in conifer trees, and aim to: 1. Characterize the diversity and genetic architecture of gene expression through haploid analyses 2. Investigate the impact of gene copy number varying on gene expression diversity 3. Investigate gene networks by eQTL analysis 4. Characterize transcriptional networks involving MYBs and their role in metabolic plasticity 5. Investigate regulatory mechanisms (micro RNAs) that influence cambial maturation and possible interactions with regulatory networks controlling metabolic plasticity 6. Link diversity in gene expression to mechanisms of adaptive significance for insect resistance The requested funds will support the training of six graduate students and four undergraduates. These funds will give present and future trainees access to cutting-edge technology - among the most advanced that are available anywhere for conifers - and enable the production of highly original contributions.