Abstract
The basic helix loop helix (bHLH) transcription factor comprises one of the largest plant-specific transcriptional regulators in plant growth and development that response to biotic and abiotic stresses. Many members of bHLH play essential roles in the growth of root hair and response to drought, salt, and cold stresses. The family of bHLH genes has been found in many species; nevertheless, the barrel medic and alfalfa species still have a minute gap of bHLH new members thus far. This research aims to identify members of the bHLH family in barrel medic and alfalfa and elucidate their expression pattern level, network analysis, predictive 3D modeling and phylogenetic relationships. Here, we identified and characterized the bHLH gene family in both barrel medic and alfalfa plants and their genes expression response to drought, salinity, and cold stresses. A total of 159 MtbHLH and 133 MsbHLH genes were identified and characterized, divided into 18 subgroups and 17 subgroups, respectively. As a ubiquitous and popular method, neighbor-joining clustering was used. Based on the phylogenetic analyses, the VIII and IX subfamily and X subfamily were selected as the stress-related subfamily in these two species. The 154 MtbHLH genes were progressively distributed on the 8 chromosomes and 23 tandem duplicated genes, and 44 duplicated genes segments were detected in MtbHLH family. The analyses of gene ontology discovered the bHLH predominantly functions in protein and DNA binding in these two species. The results of Ka/Ks were < 1, which showed that the most orthologous of the bHLH gene values was found between A. thaliana and M. truncatula species. Remarkably, 7 MtbHLH and 10 MsbHLH genes were selected and validated with qRT-PCR after the treatment’s samples sampled under stressed abiotic conditions. The similar expression patterns between M. truncatula and M. sativa L have demonstrated identical expression patterns level in the root, and contrasting patterns in the stems and leaves were diverse. It was highlighted that the gene expression analyses of 17 bHLH genes were up-regulated to stresses, respectively, apart from some genes that were timely trended down-regulated to control (0 h). This study provided a concise understanding of the tissue specific of bHLH gene functions in genome-wide levels under drought, salt, and cold stresses. Our analyses provide the first insights onto the M. truncatula and M. sativa L evolution that contributes to molecular breeding for improving plant yield and stress tolerance.
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Abbreviations
- TFs:
-
Transcription factors
- bHLH:
-
Basic helix-loop-helix
- GRAVY:
-
Grand average of hydropathicity
- pI:
-
Isoelectric point
- CDS:
-
Coding sequences
- HMM:
-
Hidden Markov Model
- MW:
-
Molecular weight
- qRT-PCR:
-
Quantitative real-time PCR
- GO:
-
Gene ontology
- Mt:
-
Medicago truncatula
- Ms:
-
Medicago sativa L
- CDD:
-
Conserved domain
- HLH:
-
Helix-loop-helix
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This research was supported by the 111 Project (B12002), the Fundamental Research Funds for the Central Universities (lzujbky-2020-18), the National Natural Science Foundation of China (31502000), and the Special Funding for Open and Shared Large-Scale Instruments and Equipments of Lanzhou University (LZU-GXJJ-2019C041).
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WL and BN conceived and designed research. BN, XJ, XM, XS, and XF performed the experiments. NB, XM, and WL draw figures and tables, and analyzed the data. BN and WL wrote the manuscript. All the authors read and approved the manuscript.
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Ndayambaza, B., Jin, X., Min, X. et al. Genome-Wide Identification and Expression Analysis of the Barrel Medic (Medicago truncatula) and Alfalfa (Medicago sativa L.) Basic Helix-Loop-Helix Transcription Factor Family Under Salt and Drought Stresses. J Plant Growth Regul 40, 2058–2078 (2021). https://doi.org/10.1007/s00344-020-10252-8
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DOI: https://doi.org/10.1007/s00344-020-10252-8