Differentially Expressed Genes during Flowering and Grain Filling in Common Bean (Phaseolus vulgaris) Grown under Drought Stress Conditions

Abstract

Drought stress, particularly during the flowering and grain-filling stages of growth, contributes to serious yield loss in common bean (Phaseolus vulgaris L.). The aim of this study was to identify genes induced in response to drought stress using transcriptome analysis of contrasting genotypes. Using leaf tissues of tolerant (BAT 477) and susceptible common bean genotypes (Pérola), collected at the flowering and grain-filling stages, four complementary deoxyribonucleic acid representational difference analysis subtractive libraries were constructed and then sequenced. A total of 7,203 (77.6 %) sequences with an average sequence size of 570 bp were considered valid, for a combined 4 Mbp sequence. According to a differential display analysis, 802 expressed sequence tags, distributed across 67 contigs, were differentially expressed by the tolerant (37 contigs) and susceptible genotypes (30 contigs) after identification under drought conditions during the two investigated plant developmental stages. Of these differential contigs, the 13 most frequent genes were exclusive to the tolerant genotype. Based on BLAST2GO, 73 % of the gene sequences were annotated and 12 % showed mapping results, with the highest similarity rate corresponding to Glycine max (41 %). According to gene ontology functional analysis, 48 % of the sequences were attributed to cell metabolic processes. Overall, 8.3 % of the transcribed sequences exhibited similarity to transcription factors, predominantly those of the AP2-EREBP family (97.8 %). Of the target sequences validated by quantitative real-time polymerase chain reaction, most genes showed an expression level that agreed with that predicted by in silico analysis. Thus, the drought transcriptome dataset is a valuable Electronic supplementary material The online version of this article

Greater water availability increases the water use efficiency and productivity of corn and bean species grown in secondary crop systems

“…According to Müller et al (2014), drought stress, particularly during flowering and grain-filling stages of growth, contributes to serious yield losses in bean plants. Global climate change is predicted to increase ambient temperatures as well as the frequency and severity of drought in various growing regions that are highly dependent on maize (Campos et al, 2004;Sicher et al, 2011).…”

Functional Genomics of Biotic and Abiotic Stresses in Phaseolus vulgaris

“…These gene products protect the plant against the damages caused by drought stress and are divided into different classes: osmoprotectors (amino acids, dimethyl-sulfonyl compounds, mannitol, sorbitol, complex carbohydrates); enzymatic and non-enzymatic ROS scavengers; LEA proteins; heat-shock proteins; ion transporters; fatty acid desaturases; aquaporins; signaling components (homologous to histidine kinases, MAP kinases, Ca At the transcriptional level, expressed sequence tags (EST) sequencing has been widely used to discover and identify genes potentially involved in drought stress response [73,74]. Therefore, by using a great amount of transcriptome profiling methods, researchers are being able to contrast genotypes with different potential for drought tolerance, thus increasing the already large datasets of candidate genes for using in studies regarding the improvement of drought stress in plants.…”

“…Suppressive subtractive hybridization (SSH) method has been successfully used to construct cDNA libraries enriched in transcripts that are differentially expressed in target tissues, developmental stages, and specific treatments in various biological systems [74,75]. The SSH method [76] consists on the hybridization of one cDNA population (tester -sample whose genetic profile is of interest, e.g., drought-tolerant genotype), with an excess of cDNA from a control population (driver -usually drought-susceptible genotype or well-watered control), followed by the separation of the nonhybridized molecules (target genes -the ones of interest) from the hybridized ones (what is common for both samples).…”

“…Recently, the use of SSH library technique combined with new high-throughput NGS-sequencing technologies [74][75][76][77][78][79][80]81] has provided evidence for solving this issue since they are more able to achieve sample saturation. In RNA-Seq technologies, saturation could be reached when an increment in the number of reads does not result in additional true expressed transcripts being detected or in more features called as differentially expressed when two or more conditions are compared [82].…”

RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

“…Transcriptome profi les under drought response have been analyzed in horticultural plants that are vulnerable to drought such as potato ( Solanum tubersosum ) (Massa et al 2013 ;Zhang et al 2014 ), rice ( Oriza sativa ) (Zong et al 2013 ), and common beans ( Phaseolus vulgaris ) (Müller et al 2013 ). Similarly, several drought-tolerant species such as Agave deserti and Agave tequilana have been studied based on RNA-seq experiments (Gross et al 2013 ).…”