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

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)...

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Published inGenetics and molecular biology Vol. 43; no. 1; p. e20180259
Main Authors Pereira, Wendell Jacinto, Melo, Arthur Tavares de Oliveira, Coelho, Alexandre Siqueira Guedes, Rodrigues, Fabiana Aparecida, Mamidi, Sujan, Alencar, Sérgio Amorim de, Lanna, Anna Cristina, Valdisser, Paula Arielle Mendes Ribeiro, Brondani, Claudio, Nascimento-Júnior, Ivanildo Ramalho do, Borba, Tereza Cristina de Oliveira, Vianello, Rosana Pereira
Format Journal Article
LanguageEnglish
Portuguese
Published Brazil Sociedade Brasileira de Genetica 01.01.2020
Sociedade Brasileira de Genética
Subjects
Beans
BIOCHEMISTRY & MOLECULAR BIOLOGY
Damage tolerance
Drought resistance
functional genomics
Gene expression
Genes
GENETICS & HEREDITY
Genomes
Genotypes
Germplasm
Isoforms
Kinases
Leaves
Oxidation
Oxidation-reduction potential
Oxidative stress
Phaseolus vulgaris
Plant Genetics
Plant tissues
Ribonucleic acid
RNA
Single Nucleotide Polymorphism (SNP)
Sulfur
Transcription
water deficit
water deficit
functional genomics
Phaseolus vulgaris
Single Nucleotide Polymorphism (SNP)
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Summary: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.
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Author’s contributions: RPV, SAA, FAR and CB conceived and designed the study. FAR conducted the hydroponic
physiological data. PAMRV performed qPCR experiments. WJP, ATOM, ASGC, SM, SAA and
Conflicts of interest: The authors declare that they have no competing interests.
wrote the manuscript. All authors read and approved the final version of the manuscript.
TCOB performed the analysis of the RNA-Seq data. WJP, ATOM and ASGC contributed to the
interpretation of the RNA-Seq analysis. ACL interpreted the annotation results. WJP, CB and RPV
experiment and took the physiological data. IRN-J performed statistical analyses of the
ISSN:1415-4757
1678-4685
1678-4685
DOI:10.1590/1678-4685-GMB-2018-0259