Genome-Wide Identification of <i>bHLH</i> Transcription Factor in <i>Medicago sativa</i> in Response to Cold Stress
Alfalfa represents one of the most important legume forages, and it is also applied as an organic fertilizer to improve soil quality. However, this perennial plant is native to warmer temperate regions, and its valuable cold-acclimation-related regulatory mechanisms are still less known. In higher p...
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| Format: | Article |
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MDPI AG
2022-12-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/12/2371 |
| _version_ | 1797457739148951552 |
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| author | Guangjun Li Lei Jin Song Sheng |
| author_facet | Guangjun Li Lei Jin Song Sheng |
| author_sort | Guangjun Li |
| collection | DOAJ |
| description | Alfalfa represents one of the most important legume forages, and it is also applied as an organic fertilizer to improve soil quality. However, this perennial plant is native to warmer temperate regions, and its valuable cold-acclimation-related regulatory mechanisms are still less known. In higher plants, the <i>bHLH</i> transcription factors play pleiotropic regulatory roles in response to abiotic stresses. The recently released whole genome sequencing data of alfalfa allowed us to identify 469 <i>MsbHLHs</i> by multi-step homolog search. Herein, we primarily identified 65 <i>MsbHLH</i> genes that significantly upregulated under cold stress, and such <i>bHLHs</i> were classified into six clades according to their expression patterns. Interestingly, the phylogenetic analysis and conserved motif screening of the cold-induced <i>MsbHLHs</i> showed that the expression pattern is relatively varied in each <i>bHLH</i> subfamily, this result indicating that the 65 <i>MsbHLHs</i> may be involved in a complex cold-responsive regulatory network. Hence, we analyzed the TFBSs at promoter regions that unraveled a relatively conserved TFBS distribution with genes exhibiting similar expression patterns. Eventually, to verify the core components involved in long-term cold acclimation, we examined transcriptome data from a freezing-tolerant species (cv. Zhaodong) in the field and compared the expression of cold-sensitive/tolerant subspecies of alfalfa, giving 11 bHLH as candidates, which could be important for further cold-tolerance enhancement and molecular breeding through genetic engineering in alfalfa. |
| first_indexed | 2024-03-09T16:27:16Z |
| format | Article |
| id | doaj.art-38a3fb709cdc405aa67d54d23b941815 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T16:27:16Z |
| publishDate | 2022-12-01 |
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| record_format | Article |
| series | Genes |
| spelling | doaj.art-38a3fb709cdc405aa67d54d23b9418152023-11-24T15:05:50ZengMDPI AGGenes2073-44252022-12-011312237110.3390/genes13122371Genome-Wide Identification of <i>bHLH</i> Transcription Factor in <i>Medicago sativa</i> in Response to Cold StressGuangjun Li0Lei Jin1Song Sheng2College of Forest, Central South University of Forestry and Technology, Changsha 410004, ChinaCollege of Forest, Central South University of Forestry and Technology, Changsha 410004, ChinaCollege of Forest, Central South University of Forestry and Technology, Changsha 410004, ChinaAlfalfa represents one of the most important legume forages, and it is also applied as an organic fertilizer to improve soil quality. However, this perennial plant is native to warmer temperate regions, and its valuable cold-acclimation-related regulatory mechanisms are still less known. In higher plants, the <i>bHLH</i> transcription factors play pleiotropic regulatory roles in response to abiotic stresses. The recently released whole genome sequencing data of alfalfa allowed us to identify 469 <i>MsbHLHs</i> by multi-step homolog search. Herein, we primarily identified 65 <i>MsbHLH</i> genes that significantly upregulated under cold stress, and such <i>bHLHs</i> were classified into six clades according to their expression patterns. Interestingly, the phylogenetic analysis and conserved motif screening of the cold-induced <i>MsbHLHs</i> showed that the expression pattern is relatively varied in each <i>bHLH</i> subfamily, this result indicating that the 65 <i>MsbHLHs</i> may be involved in a complex cold-responsive regulatory network. Hence, we analyzed the TFBSs at promoter regions that unraveled a relatively conserved TFBS distribution with genes exhibiting similar expression patterns. Eventually, to verify the core components involved in long-term cold acclimation, we examined transcriptome data from a freezing-tolerant species (cv. Zhaodong) in the field and compared the expression of cold-sensitive/tolerant subspecies of alfalfa, giving 11 bHLH as candidates, which could be important for further cold-tolerance enhancement and molecular breeding through genetic engineering in alfalfa.https://www.mdpi.com/2073-4425/13/12/2371<i>bHLH</i><i>Medicago sativa</i> L.cold stressexpression profilingtranscription factor binding sites (TFBS) |
| spellingShingle | Guangjun Li Lei Jin Song Sheng Genome-Wide Identification of <i>bHLH</i> Transcription Factor in <i>Medicago sativa</i> in Response to Cold Stress Genes <i>bHLH</i> <i>Medicago sativa</i> L. cold stress expression profiling transcription factor binding sites (TFBS) |
| title | Genome-Wide Identification of <i>bHLH</i> Transcription Factor in <i>Medicago sativa</i> in Response to Cold Stress |
| title_full | Genome-Wide Identification of <i>bHLH</i> Transcription Factor in <i>Medicago sativa</i> in Response to Cold Stress |
| title_fullStr | Genome-Wide Identification of <i>bHLH</i> Transcription Factor in <i>Medicago sativa</i> in Response to Cold Stress |
| title_full_unstemmed | Genome-Wide Identification of <i>bHLH</i> Transcription Factor in <i>Medicago sativa</i> in Response to Cold Stress |
| title_short | Genome-Wide Identification of <i>bHLH</i> Transcription Factor in <i>Medicago sativa</i> in Response to Cold Stress |
| title_sort | genome wide identification of i bhlh i transcription factor in i medicago sativa i in response to cold stress |
| topic | <i>bHLH</i> <i>Medicago sativa</i> L. cold stress expression profiling transcription factor binding sites (TFBS) |
| url | https://www.mdpi.com/2073-4425/13/12/2371 |
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