Evolutionary Analyses of Gene Expression Divergence in Panicum hallii : Exploring Constitutive and Plastic Responses Using Reciprocal Transplants

Bhaskara, Govinal Badiger; Haque, Taslima; Bonnette, Jason E.; Napier, Joseph D.; Bauer, Diane; Schmutz, Jeremy; Juenger, Thomas E.; Josephs, ed., Emily

doi:10.1093/molbev/msad210

Title: Evolutionary Analyses of Gene Expression Divergence in Panicum hallii : Exploring Constitutive and Plastic Responses Using Reciprocal Transplants

Journal Article · 19 September 2023 · Molecular Biology and Evolution

DOI: https://doi.org/10.1093/molbev/msad210 · OSTI ID:2280395

;

; Bonnette, Jason E.; Napier, Joseph D.; Bauer, Diane;

;

; Josephs, ed., Emily

Abstract The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified FST–QST outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis–environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.

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Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0014156; SC0021126; AC02-05CH11231

OSTI ID:: 2280395

Alternate ID(s):: OSTI ID: 2472340

Journal Information:: Molecular Biology and Evolution, Journal Name: Molecular Biology and Evolution Journal Issue: 10 Vol. 40; ISSN 0737-4038

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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