Journal Article

Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use

Morais Carbonell, Sérgio Augusto, Chiorato, Alisson Fernando, Silva, Daiana Alves da, Tsai, Siu Mui, Esteves, José Antonio de Fatima, Recchia, Gustavo Henrique, da Silva Andrade, Sónia Cristina

2019

Overview

Common bean is a highly important food in tropical regions, where most production occurs on small farms with limited use of technology and, consequently, greater vulnerability to abiotic stresses such as nutritional stress. Usually phosphorus (P) is the most limiting nutrient for crop growth in these regions. The aim of this study was to characterize the gene expression profiles of the genotypes of common bean IAC Imperador (P-responsive) and DOR 364 (P-unresponsive) under different P concentrations using RNA-seq transcriptome sequencing technology. Plants were grown hydroponically, with application of two P concentrations (4.00 mg L-1 restrictive level and 8.00 mg L-1 control level). Differential expression analyses, annotation, and functional classification were performed comparing genotypes within each P rate administered and comparing each genotype response to the different P levels. Considering differential expression analyses within genotypes, IAC Imperador exhibited 1538 up-regulated genes under P restriction and 1679 up-regulated genes in the control, while DOR 364 exhibited 13 up-regulated genes in the control and only 2 up-regulated genes under P restriction, strongly corroborating P-unresponsiveness of this genotype. Genes related to phosphorus restriction were identified among the differentially expressed genes, including transcription factors such as WRKY, ERF, and MYB families, phosphatase related genes such as pyrophosphatase, acid phosphatase, and purple acid phosphatase, and phosphate transporters. The enrichment test for the P restriction treatment showed 123 enriched gene ontologies (GO) for IAC Imperador, while DOR 364 enriched only 24. Also, the enriched GO correlated with P metabolism, compound metabolic processes containing phosphate, nucleoside phosphate binding, phosphorylation, and also response to stresses. Thus, this study proved to be informative to phosphorus limitation in common bean showing global changes at transcript level.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Acid phosphatase / Acids / Agricultural production / Analysis / Analysis of Variance / Annotations / Bioinformatics / Biology / Biology and life sciences / Common beans / Crop growth / Crops / Down-Regulation - drug effects / Down-Regulation - genetics / Efficiency / Enrichment / Farms / Food production / Gene expression / Gene Expression Regulation, Plant - drug effects / Gene sequencing / Genes / Genetic aspects / Genomes / Genomics / Genotype & phenotype / Genotypes / Hydroponics / Metabolism / Morphology / Nutrient deficiency / Phaseolus - drug effects / Phaseolus - genetics / Phaseolus - growth & development / Phaseolus vulgaris / Phosphates / Phosphorus / Phosphorus (Nutrient) / Phosphorus - pharmacology / Phosphorylation / Physical Sciences / Physiology / Plant growth / Plant Roots - drug effects / Plant Roots - genetics / Plant Shoots - drug effects / Plant Shoots - genetics / Purple acid phosphatase / Pyrophosphatase / Quantitative Trait, Heritable / Ribonucleic acid / RNA / RNA sequencing / Small farms / Stresses / Technology / Transcription factors / Transcription Factors - metabolism / Transcriptome - drug effects / Transcriptome - genetics / Tropical environment / Tropical environments / Up-Regulation - drug effects / Up-Regulation - genetics