Bridging physiological and evolutionary time‐scales in a gene regulatory network

• Published in: The New phytologist Vol. 203; no. 2; pp. 685 - 696
• Main Authors: Marchand, Gwenaëlle, Huynh‐Thu, Vân Anh, Kane, Nolan C, Arribat, Sandrine, Varès, Didier, Rengel, David, Balzergue, Sandrine, Rieseberg, Loren H, Vincourt, Patrick, Geurts, Pierre, Vignes, Matthieu, Langlade, Nicolas B
• Format: Journal Article Web Resource
• Language: English
• Published: England William Wesley and Son 01-07-2014; New Phytologist Trust; Wiley Subscription Services, Inc; Wiley
• Subjects: Abscisic acid; abscisic acid (ABA); Abscisic Acid - genetics; Adaptation; Algorithms; Biological Evolution; Biologie végétale (sciences végétales, sylviculture, mycologie...); Biology; CLC-A chloride channel protein; Computer Science; Cultivars; Datasets; Differentiation; Drought; Droughts; dry environmental conditions; Evolution; evolutionary adaptation; F ST; Gene expression; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes; genetic differentiation; Genetic diversity; Genetic variation; Guard cells; Helianthus; Helianthus - genetics; Helianthus - physiology; Helianthus annuus; Hormones; humans; Identification; Inference; Life Sciences; Mathematics; Models, Genetic; network inference; Network topologies; NITRATE TRANSPORTER 1.1 (NRT1.1); nitrates; Nitrates - metabolism; physiological response; Physiological responses; Physiology; Phytobiology (plant sciences, forestry, mycology...); Plant Proteins - genetics; Plant Proteins - metabolism; Plants; Population genetics; regulator genes; Sciences du vivant; Sunflowers; Topology; Transcriptome; Transport; Vegetal Biology; CLC-A chloride channel protein; abscisic acid (ABA); drought; genetic differentiation; network inference; F ST; NITRATE TRANSPORTER 1.1 (NRT1.1)
• ISSN: 0028-646X; 1469-8137; 1469-8137
• DOI: 10.1111/nph.12818

Gene regulatory networks (GRNs) govern phenotypic adaptations and reflect the trade‐offs between physiological responses and evolutionary adaptation that act at different time‐scales. To identify patterns of molecular function and genetic diversity in GRNs, we studied the drought response of the common sunflower, Helianthus annuus, and how the underlying GRN is related to its evolution. We examined the responses of 32 423 expressed sequences to drought and to abscisic acid (ABA) and selected 145 co‐expressed transcripts. We characterized their regulatory relationships in nine kinetic studies based on different hormones. From this, we inferred a GRN by meta‐analyses of a Gaussian graphical model and a random forest algorithm and studied the genetic differentiation among populations (FST) at nodes. We identified two main hubs in the network that transport nitrate in guard cells. This suggests that nitrate transport is a critical aspect of the sunflower physiological response to drought. We observed that differentiation of the network genes in elite sunflower cultivars is correlated with their position and connectivity. This systems biology approach combined molecular data at different time‐scales and identified important physiological processes. At the evolutionary level, we propose that network topology could influence responses to human selection and possibly adaptation to dry environments.