Fitness costs and benefits of gene expression plasticity in rice under drought

Abstract

Genome-wide gene expression changes in response to environmental variability have been widely documented, but we lack detailed and comprehensive understanding of the interplay between this form of phenotypic plasticity and natural selection. Selection on expression plasticity may be limited by environment-specific costs, and plasticity may in turn affect selection on baseline expression levels. Here, we address this fundamental issue by measuring selection on drought-induced plasticity of leaf transcripts in field-grown rice populations. Selection disfavored switching off housekeeping genes under drought. This stress-induced dysregulation did not constrain selection on baseline transcript levels, suggesting compensatory evolution may be possible. Selection rarely acted strongly on individual transcripts but worked polygenically on gradual (continuous) plasticity of co-expressed gene modules regulating photosynthesis via known drought-responsive transcription factors. Finally, selection was tied to inefficient gene architectural features and metabolic costs of expression. Our study provides a genome-wide view of costs and benefits of gene expression plasticity.

Systems genomics of salinity stress response in rice

“…Here, we use an integrative system genomics approach to comprehensively dissect the genome-wide molecular and phenotypic response to salinity stress in rice. This study builds on prior work by our group that examined selection on gene expression in rice in response to normal and dry conditions ( Ćalić et al, 2022 ; Groen et al, 2021 , 2020 ). Using genomic, transcriptomic, and phenotypic datasets obtained from 130 diverse accessions of rice subjected to moderate levels of salinity stress, we (i) explore the selection on gene expression variation under salinity stress, (ii) dissect the genetic architecture of gene expression variation under saline conditions, and (iii) identify genes, molecular pathways, and salt stress response traits as well as associated trade-offs in the saline environment.…”