title: Transcriptome sequencing reveals population differentiation in gene expression linked to functional traits and environmental gradients in the South African shrub Protea repens.
abstract: Understanding the environmental and genetic mechanisms underlying locally adaptive trait variation across the ranges of species is a major focus of evolutionary biology. Combining transcriptome sequencing with common garden experiments on populations spanning geographical and environmental gradients holds promise for identifying such mechanisms. The South African shrub Protea repens displays diverse phenotypes in the wild along drought and temperature gradients. We grew plants from seeds collected at 19 populations spanning this species' range, and sequenced the transcriptomes of these plants to reveal gene pathways associated with adaptive trait variation. We related expression in co-expressed gene networks to trait phenotypes measured in the common garden and to source population climate. We found that expression in gene networks correlated with source-population environment and with plant traits. In particular, the activity of gene networks enriched for growth related pathways correlated strongly with source site minimum winter temperature and with leaf size, stem diameter and height in the garden. Other gene networks with enrichments for photosynthesis related genes showed associations with precipitation. Our results strongly suggest that this species displays population-level differences in gene expression that have been shaped by source population site climate, and that are reflected in trait variation along environmental gradients.
authors.affiliation: Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
authors.forename: Melis
authors.initials: M
authors.lastname: Akman
authors.affiliation: Department of Biological Sciences, Nicholls State University, PO Box 2021, Thibodaux, LA, 70310, USA.
authors.forename: Jane E
authors.initials: JE
authors.lastname: Carlson
authors.affiliation: Department of Ecology & Evolutionary Biology, University of Connecticut, U-3043, Storrs, CT, 06269-3043, USA.
authors.forename: Kent E
authors.identifier: http://orcid.org/0000-0003-4312-3804
authors.initials: KE
authors.lastname: Holsinger
authors.affiliation: Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Latimer
mesh_terms: D050260:Carbohydrate Metabolism / Q000235:genetics; D002473:Cell Wall / Q000378:metabolism; D002980:Climate; D004777:Environment; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D006019:Glycolysis / Q000235:genetics; D010788:Photosynthesis / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D054046:Plant Stomata / Q000033:anatomy & histology; D039105:Proteaceae / Q000235:genetics*; D019655:Quantitative Trait, Heritable; D011891:Rain; D012621:Seasons; D017423:Sequence Analysis, RNA; D013696:Temperature; D059467:Transcriptome / Q000235:genetics*
chemical_list: D010940:Plant Proteins
keywords: Protea repens (sugarbush); common garden; functional traits; local adaptation; population-level transcriptome sequencing; precipitation; temperature; the Greater Cape Floristic Region