Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybean
Abstract Background BBX genes are key players in the regulation of various developmental processes and stress responses, which have been identified and functionally characterized in many plant species. However, our understanding of BBX family was greatly limited in soybean. Results In this study, 59...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-12-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-09068-5 |
| _version_ | 1811292632868978688 |
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| author | Binghui Shan Guohua Bao Tianran Shi Lulu Zhai Shaomin Bian Xuyan Li |
| author_facet | Binghui Shan Guohua Bao Tianran Shi Lulu Zhai Shaomin Bian Xuyan Li |
| author_sort | Binghui Shan |
| collection | DOAJ |
| description | Abstract Background BBX genes are key players in the regulation of various developmental processes and stress responses, which have been identified and functionally characterized in many plant species. However, our understanding of BBX family was greatly limited in soybean. Results In this study, 59 BBX genes were identified and characterized in soybean, which can be phylogenetically classified into 5 groups. GmBBXs showed diverse gene structures and motif compositions among the groups and similar within each group. Noticeably, synteny analysis suggested that segmental duplication contributed to the expansion of GmBBX family. Moreover, our RNA-Seq data indicated that 59 GmBBXs showed different transcript profiling under salt stress, and qRT-PCR analysis confirmed their expression patterns. Among them, 22 GmBBXs were transcriptionally altered with more than two-fold changes by salt stress, supporting that GmBBXs play important roles in soybean tolerance to salt stress. Additionally, Computational assay suggested that GmBBXs might potentially interact with GmGI3, GmTOE1b, GmCOP1, GmCHI and GmCRY, while eight types of transcription factors showed potentials to bind the promoter regions of GmBBX genes. Conclusions Fifty-nine BBX genes were identified and characterized in soybean, and their expression patterns under salt stress and computational assays suggested their functional roles in response to salt stress. These findings will contribute to future research in regard to functions and regulatory mechanisms of soybean BBX genes in response to salt stress. |
| first_indexed | 2024-04-13T04:49:15Z |
| format | Article |
| id | doaj.art-e0d9f618d0ee4548bd836f6db0cd0370 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T04:49:15Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e0d9f618d0ee4548bd836f6db0cd03702022-12-22T03:01:46ZengBMCBMC Genomics1471-21642022-12-0123111710.1186/s12864-022-09068-5Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybeanBinghui Shan0Guohua Bao1Tianran Shi2Lulu Zhai3Shaomin Bian4Xuyan Li5College of Plant Science, Jilin UniversityCollege of Plant Science, Jilin UniversityCollege of Plant Science, Jilin UniversityCollege of Plant Science, Jilin UniversityCollege of Plant Science, Jilin UniversityCollege of Plant Science, Jilin UniversityAbstract Background BBX genes are key players in the regulation of various developmental processes and stress responses, which have been identified and functionally characterized in many plant species. However, our understanding of BBX family was greatly limited in soybean. Results In this study, 59 BBX genes were identified and characterized in soybean, which can be phylogenetically classified into 5 groups. GmBBXs showed diverse gene structures and motif compositions among the groups and similar within each group. Noticeably, synteny analysis suggested that segmental duplication contributed to the expansion of GmBBX family. Moreover, our RNA-Seq data indicated that 59 GmBBXs showed different transcript profiling under salt stress, and qRT-PCR analysis confirmed their expression patterns. Among them, 22 GmBBXs were transcriptionally altered with more than two-fold changes by salt stress, supporting that GmBBXs play important roles in soybean tolerance to salt stress. Additionally, Computational assay suggested that GmBBXs might potentially interact with GmGI3, GmTOE1b, GmCOP1, GmCHI and GmCRY, while eight types of transcription factors showed potentials to bind the promoter regions of GmBBX genes. Conclusions Fifty-nine BBX genes were identified and characterized in soybean, and their expression patterns under salt stress and computational assays suggested their functional roles in response to salt stress. These findings will contribute to future research in regard to functions and regulatory mechanisms of soybean BBX genes in response to salt stress.https://doi.org/10.1186/s12864-022-09068-5SoybeanBBX familyPhylogenetic evolutionSalt stressGene expressionPrediction of protein interaction |
| spellingShingle | Binghui Shan Guohua Bao Tianran Shi Lulu Zhai Shaomin Bian Xuyan Li Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybean BMC Genomics Soybean BBX family Phylogenetic evolution Salt stress Gene expression Prediction of protein interaction |
| title | Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybean |
| title_full | Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybean |
| title_fullStr | Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybean |
| title_full_unstemmed | Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybean |
| title_short | Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybean |
| title_sort | genome wide identification of bbx gene family and their expression patterns under salt stress in soybean |
| topic | Soybean BBX family Phylogenetic evolution Salt stress Gene expression Prediction of protein interaction |
| url | https://doi.org/10.1186/s12864-022-09068-5 |
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