Abstract
Background
The drought condition is responsible for considerable losses in soybean production, which in turn may result in billionaire losses. After drought perception, plants activate a cascade of protecting genes against water deficit (WD), many of which are responsive to abscisic acid, the most important phytohormone to plants’ adaptation. This work aimed to recover abscisic acid (ABA)-responsive differentially expressed genes (DEG) from an RNA-Seq, carried out from leaves and roots of drought-sensitive (BR16) and tolerant (Embrapa 48) soybean cultivars under mild (MiWD), moderate (MoWD), and severe (SWD) water-deficit treatments. Enriched ABA-responsive pathways important to drought tolerance in soybean were also identified.
Results
In drought-sensitive and tolerant soybean cultivars, approximately 75% of genes were identified as ABA-responsive by containing more than two ABRE (ABA-responsive elements) in the promoter region. Most of these genes were positively regulated. Roots were the tissue with more ABA-responsive genes and pathways triggered in response to WD in both cultivars, although, on the tolerant cultivar, these pathways were higher expressed. The most important enriched ABA pathways observed in the roots of both cultivars were involved in sugar and sulfur amino acid biosynthesis, osmoregulation, and crosstalk among ABA and ethylene, jasmonate, auxin, and cytokinin. Other pathways enriched were involved in phytoalexin production, ROS homeostasis, and membrane stability by glycerolipid and glycerophospholipid production. ABA-responsive genes were also ordered based on their expression profile in tissue and cultivar, and nine confidence groups could be observed. More than 80% of these clustered genes showed the same regulation profile under MiWd, MoWD, and SWD treatments. Activation of ABA biosynthesis under water deficit was validated by RT-qPCR by increasing the expression level of NCED3, an important enzyme in this pathway, and GOLS, a known ABA-responsive gene.
Conclusions
A robust catalog of ABA-responsive genes was made available in this work. Considering ABA’s role in drought-response mechanisms, the genes in the groups pointed out in this study would be reliable candidates to be used in strategies to develop soybean lines more tolerant to drought. This paper, presented for the first time, ABA-responsive genes and ABA-enriched pathways in contrasting soybean cultivars for drought tolerance.
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Availability of Data and Material
The datasets generated and/or analyzed during this study are available in the NCBI Sequence Read Archive (SRA) database (BioProject accession: PRJNA615913), https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=615913
Abbreviations
- ABA:
-
Abscisic acid
- ABRE:
-
Abscisic acid-responsive element
- ACS:
-
1-Aminocyclopropane-1-carboxylate synthase
- AP2:
-
Apetala2
- ARFs:
-
Auxin response factors
- At:
-
Arabidopsis thaliana
- ATAF1-2:
-
Arabidopsis transcription activation factor 1–2
- cDNA:
-
Complementary deoxyribonucleic acid
- CKK:
-
Cytokinin dehydrogenase
- CUC2:
-
Cup-shaped cotyledon
- DEGs:
-
Differentially expressed genes
- DNA:
-
Deoxyribonucleic acid
- DNAse:
-
Deoxyribonuclease
- DREB:
-
Dehydration-responsive element-binding protein
- E48:
-
Embrapa 48
- EREBPs:
-
Ethylene-responsive element binding proteins
- ERF:
-
Responsive factors of ethylene
- ET:
-
Ethylene
- Gm:
-
Glycine max
- GOLS:
-
Galactinol synthase
- HSFs:
-
Heat shock factors
- JA:
-
Jasmonic acid
- JAI3/JAZ:
-
Jasmonate-insensitive/jasmonate-zim
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- LEA:
-
Late embryogenesis abundant
- Log2 FC:
-
Log2 fold-change
- MiWD:
-
Mild water-deficit treatment
- MoWD:
-
Moderate water-deficit treatment
- mRNA:
-
Messenger ribonucleic acid
- NAC:
-
No apical meristem
- NADPH:
-
Nicotinamide adenine dinucleotide phosphate
- NCED3:
-
9-Cis-epoxycarotenoid dioxygenase
- NO:
-
Nitric oxide
- OST1:
-
Open stomata 1
- RFO:
-
Raffinose family oligosaccharide
- RIN:
-
RNA integrity number
- RNA:
-
Ribonucleic acid
- RNA-Seq:
-
RNA sequencing
- ROS:
-
Reactive oxygen species
- rRNA:
-
Ribosomal ribonucleic acid
- RT-qPCR:
-
Reverse transcriptase quantitative polymerase chain reaction
- SA:
-
Salicylic acid
- SWD:
-
Severe water-deficit treatment
- TFs:
-
Transcription factors
- TSS:
-
Transcription start site
- WD:
-
Water deficit.
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Acknowledgements
The authors would like to thank the Coordination for the Improvement of Higher Education Personnel (CAPES) for granting a master’s scholarship to DRM and a doctoral scholarship to JMK and DAB, and the Embrapa Soybean and Arthur Bernardes Foundation for granting a postdoctoral fellowship to MDCM.
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This research was funded by Embrapa (Brazilian Agricultural Research Corporation), CNPq (National Council for Scientific and Technological Development), and CAPES (Coordination for the Improvement of Higher Education Personnel).
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MDCM conceived and designed the study, performed data analysis and interpretation, and wrote the manuscript. RFP also conceived and designed the study, performed data analysis and results compilation, reviewed the manuscript, and provided scientific editing and language proofreading. EGB reviewed the manuscript and provided scientific editing and language proofreading. DAB, DRM, and SRRM were involved in the experiments and collecting of biological material in a greenhouse. LMMH and ALN are the principal researchers in the project and reviewed the final version of the manuscript. All authors have read and approved the final version of the article.
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Molinari, M.D.C., Fuganti-Pagliarini, R., de Amorim Barbosa, D. et al. Comparative ABA-Responsive Transcriptome in Soybean Cultivars Submitted to Different Levels of Drought. Plant Mol Biol Rep 41, 260–276 (2023). https://doi.org/10.1007/s11105-022-01364-4
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DOI: https://doi.org/10.1007/s11105-022-01364-4