A transcriptomic atlas facilitating systems biology approaches in pea

Abstract Pea is a model organism in biology and an agronomic crop, entering the genomics era. Although RNA‐sequencing (RNA‐seq) has become the main transcriptomic approach in biology, there is currently no genome‐wide expression atlas covering a wide range of biological conditions for this species. Here, we generate a transcriptomic atlas in Pisum sativum by integrating 149 publicly available RNA‐seq libraries, covering 10 cultivars, and a comprehensive collection of plant organs and several environmental stress conditions (heat, low temperature, nutrient, and water deficit). As proof of concept, we first verified the expression profiles of key gene families, such as sugar transporters and transcription factors (TF), across this transcriptomic atlas. Using a systems biology approach, we then inferred a regulatory network of genes responsive to water deficit, from which we predicted putative TF‐target interactions, including genes encoding monosaccharide transporter PsSTP13.2 and sugar facilitator PsSWEET6 . Finally, we exploited our meta‐analysis to identify new reference genes with stable expression based on their coefficient of variation. Ten reference genes were validated by quantitative PCR across various biological samples, including different pea varieties, organs, and stress conditions (water deficit and fungal pathogen infection). Three reference genes ( Psat6g102320 , Psat6g163160 , and Psat7g253080 ) outperformed the expression stability of common housekeeping genes ( TFIIA , PPIIA , and β‐tubulin ). Altogether, this atlas opens new avenues of integrative research in the genomics and systems biology era of legume crops.