Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean.

Wendell Jacinto Pereira,Ivanildo Ramalho Do Nascimento-Júnior,Claudio Brondani,Sérgio Amorim De Alencar,Tereza Cristina De Oliveira Borba,Fabiana Aparecida Rodrigues,Paula Arielle Mendes Ribeiro Valdisser,Alexandre Siqueira Guedes Coelho,Anna Cristina Lanna,Arthur Tavares De Oliveira Melo,Sujan Mamidi,Rosana Pereira Vianello

doi:10.1590/1678-4685-gmb-2018-0259

Abstract

Genes related to the response to drought stress in leaf and root tissue of drought-susceptible (DS) and tolerant (DT) genotypes were characterized by RNA-Seq. In total, 54,750 transcripts, representative of 28,590 genes, were identified; of these, 1,648 were of high-fidelity (merge of 12 libraries) and described for the first time in the Andean germplasm. From the 1,239 differentially expressed genes (DEGs), 458 were identified in DT, with a predominance of genes in categories of oxidative stress, response to stimulus and kinase activity. Most genes related to oxidation-reduction terms in roots were early triggered in DT (T75) compared to DS (T150) suggestive of a mechanism of tolerance by reducing the damage from ROS. Among the KEGG enriched by DEGs up-regulated in DT leaves, two related to the formation of Sulfur-containing compounds, which are known for their involvement in tolerance to abiotic stresses, were common to all treatments. Through qPCR, 88.64% of the DEGs were validated. A total of 151,283 variants were identified and functional effects estimated for 85,780. The raw data files were submitted to the NCBI database. A transcriptome map revealed new genes and isoforms under drought. These results supports a better understanding of the drought tolerance mechanisms in beans.

Highlights

Drought has become increasingly intense and worrisome because the worldwide demand for agricultural products is expected to increase over the coming decade (FAO Land and Water, 2013)
From the Kyoto Encyclopedia of Genes and Genomes (KEGG), 70 metabolic pathways were identified for newly identified genes, and 97 metabolic pathways for differentially expressed genes (DEGs). These results provide a broad overview of transcriptional regulation in response to drought, enriching the public database of genes potentially involved in abiotic stress
A more uniform water stress can facilitate the discovery of more related genes and, the recognition of mechanisms more directly involved in the response to the environmental change

Summary

Introduction

Drought has become increasingly intense and worrisome because the worldwide demand for agricultural products is expected to increase over the coming decade (FAO Land and Water, 2013). Climate changes have imposed selective pressure on genetic diversity plays an important role in the adaptive response to environmental changes (Ravenscroft et al, 2015). This directional selection pressure provides an increased allelic frequency that is most advantageous for the adaptive response (Jump et al, 2009; Anderson et al, 2012). Plants under drought stress activate different mechanisms of resistance, maintaining a balance to optimize yield and survive (Zhang, 2007)

Methods

Results

Discussion

Conclusion