The strength and pattern of natural selection on gene expression in rice

Simon C. Groen, Irina Ćalić, Zoé Joly-Lopez, Adrian E. Platts, Jae Young Choi, Mignon Natividad, Katherine Dorph, William M. Mauck, Bernadette Bracken, Carlo Leo U. Cabral, Arvind Kumar, Rolando O. Torres, Rahul Satija, Georgina Vergara, Amelia Henry, Steven J. Franks and Michael D. Purugganan ()
Additional contact information
Simon C. Groen: New York University
Irina Ćalić: Fordham University
Zoé Joly-Lopez: New York University
Adrian E. Platts: New York University
Jae Young Choi: New York University
Mignon Natividad: International Rice Research Institute
Katherine Dorph: New York University
William M. Mauck: New York Genome Center
Bernadette Bracken: New York University
Carlo Leo U. Cabral: International Rice Research Institute
Arvind Kumar: International Rice Research Institute
Rolando O. Torres: International Rice Research Institute
Rahul Satija: New York University
Georgina Vergara: International Rice Research Institute
Amelia Henry: International Rice Research Institute
Steven J. Franks: Fordham University
Michael D. Purugganan: New York University

Nature, 2020, vol. 578, issue 7796, 572-576

Abstract: Abstract Levels of gene expression underpin organismal phenotypes1,2, but the nature of selection that acts on gene expression and its role in adaptive evolution remain unknown1,2. Here we assayed gene expression in rice (Oryza sativa)3, and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts4,5. Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions. Overall, more transcripts are conditionally neutral (2.83%) than are antagonistically pleiotropic6 (0.04%), and transcripts that display lower levels of expression and stochastic noise7–9 and higher levels of plasticity9 are under stronger selection. Selection strength was further weakly negatively associated with levels of cis-regulation and network connectivity9. Our multivariate analysis suggests that selection acts on the expression of photosynthesis genes4,5, but that the efficacy of selection is genetically constrained under drought conditions10. Drought selected for earlier flowering11,12 and a higher expression of OsMADS18 (Os07g0605200), which encodes a MADS-box transcription factor and is a known regulator of early flowering13—marking this gene as a drought-escape gene11,12. The ability to estimate selection strengths provides insights into how selection can shape molecular traits at the core of gene action.

Date: 2020
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DOI: 10.1038/s41586-020-1997-2

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