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Research Article
Xiaojun Nie
State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling712100, Shaanxi, China
Corresponding Author
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This work is licensed under a CC BY 4.0 License. Read Full License
Background: The LBD (lateral organ boundaries)-domain transcription factor is one unique gene family in plants, playing the crucial role in regulating plant architecture as well as stress tolerance. Although LBD family has been thoroughly characterized in many species, it is not well studied in wheat.
Results: In this study, the in silico genome-wide analysis was performed and a total of 90 LBD proteins were identified in wheat (TaLBDs). Phylogenetic analysis classified them into two major groups, of which Class I contained 8 subfamily (IA-IH), and Class II include 2 subfamily (IIA-B). Exon-intron structure, conserved protein motif and cis-regulatory elements analysis showed that the members in the subfamily shared similar gene structure organizations, supporting the classification. Furthermore, these TaLBDs mainly interacted with the genes related to signal transduction cascades and they were also targeted by miRNAs to form the sophisticated regulation network. Then, the tissue-specific and stress-responsive TaLBD genes were identified through RNA-seq analysis. Finally, the expression of 12 TaLBDs were selected to validate by QPCR analysis and the homoeologous genes showed significantly differential expression, suggesting subfunctionalization of them has occurred. In addition, the genetic diversity of TaLBDs in wheat landrace showed slight higher than that of variety while obvious asymmetry at subgenome level.
Conclusions: This study reported the composition, structure, evolution and expression patterns of LBD family in wheat, which will provide potential target genes for further functional analysis and also shed light on the role of LBD gene playing in regulating development and stresses tolerance in wheat and beyond.
Keywords
LBD gene family, Abiotic stress, Expression profiles, Genetic variation, Wheat
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No competing interests reported.
This is a list of supplementary files associated with this preprint. Click to download.
- SupplementaryFigures.docx
Figure S1. Protein sequence alignment of TaLBD genes by DNAMAN. The highlighted blue dots showed the conserved signature motif. Figure S2. The distribution of cis-elements in 90 TaLBDs promoter regions.
- SupplementaryTables.xlsx
Table S1. Cis-elements organizations of TaLBD genes. Table S2. Cis-elements statistics of TaLBD genes. Table S3. SNP number found in the wheat LBD genes. Table S4. Pi valure of the wheat LBD genes. Table S5. Accession number and samples information of RNA-seq data using in this study. Table S6. The primers used in this study.
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research Article
Xiaojun Nie
State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling712100, Shaanxi, China
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 28 Jan, 2021
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: The LBD (lateral organ boundaries)-domain transcription factor is one unique gene family in plants, playing the crucial role in regulating plant architecture as well as stress tolerance. Although LBD family has been thoroughly characterized in many species, it is not well studied in wheat.
Results: In this study, the in silico genome-wide analysis was performed and a total of 90 LBD proteins were identified in wheat (TaLBDs). Phylogenetic analysis classified them into two major groups, of which Class I contained 8 subfamily (IA-IH), and Class II include 2 subfamily (IIA-B). Exon-intron structure, conserved protein motif and cis-regulatory elements analysis showed that the members in the subfamily shared similar gene structure organizations, supporting the classification. Furthermore, these TaLBDs mainly interacted with the genes related to signal transduction cascades and they were also targeted by miRNAs to form the sophisticated regulation network. Then, the tissue-specific and stress-responsive TaLBD genes were identified through RNA-seq analysis. Finally, the expression of 12 TaLBDs were selected to validate by QPCR analysis and the homoeologous genes showed significantly differential expression, suggesting subfunctionalization of them has occurred. In addition, the genetic diversity of TaLBDs in wheat landrace showed slight higher than that of variety while obvious asymmetry at subgenome level.
Conclusions: This study reported the composition, structure, evolution and expression patterns of LBD family in wheat, which will provide potential target genes for further functional analysis and also shed light on the role of LBD gene playing in regulating development and stresses tolerance in wheat and beyond.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
No competing interests reported.
This is a list of supplementary files associated with this preprint. Click to download.
- SupplementaryFigures.docx
Figure S1. Protein sequence alignment of TaLBD genes by DNAMAN. The highlighted blue dots showed the conserved signature motif. Figure S2. The distribution of cis-elements in 90 TaLBDs promoter regions.
- SupplementaryTables.xlsx
Table S1. Cis-elements organizations of TaLBD genes. Table S2. Cis-elements statistics of TaLBD genes. Table S3. SNP number found in the wheat LBD genes. Table S4. Pi valure of the wheat LBD genes. Table S5. Accession number and samples information of RNA-seq data using in this study. Table S6. The primers used in this study.
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