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Shi L, Lin X, Tang B, Zhao R, Wang Y, Lin Y, Wu L, Zheng C, Zhu H. Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Sweet Potato ( Ipomoea batatas). Genes (Basel) 2024; 15:237. [PMID: 38397226 PMCID: PMC10887590 DOI: 10.3390/genes15020237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The LBD family is a plant-specific transcription factor family that plays an important role in a variety of biological processes. However, the function of IbLBD genes in sweet potato remains unclear. In this study, we identified a total of 53 IbLBD genes in sweet potato. Genetic structure showed that most of the IbLBD genes contained only two exons. Following the phylogenetic investigation, the IbLBD gene family was separated into Class I (45 members) and Class II (8) members. Both classes of proteins contained relatively conservative Motif1 and Motif2 domains. The chromosomal locations, gene duplications, promoters, PPI network, and GO annotation of the sweet potato LBD genes were also investigated. Furthermore, gene expression profiling and real-time quantitative PCR analysis showed that the expression of 12 IbLBD genes altered in six separate tissues and under various abiotic stresses. The IbLBD genes belonging to Class I were mostly expressed in the primary root, the pencil root, and the leaves of sweet potatoes, while the genes belonging to Class II were primarily expressed in the various sweet potato roots. The IbLBD genes belonging to Class I were mostly expressed in the primary root, the pencil root, and the leaves of sweet potatoes, while the genes belonging to Class II were primarily expressed in the fibrous root, pencil root, and tuber root.
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Affiliation(s)
- Lei Shi
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (L.S.); (X.L.); (B.T.); (Y.W.); (L.W.)
| | - Xiongjian Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (L.S.); (X.L.); (B.T.); (Y.W.); (L.W.)
| | - Binquan Tang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (L.S.); (X.L.); (B.T.); (Y.W.); (L.W.)
| | - Rong Zhao
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang 524088, China; (R.Z.); (Y.L.)
| | - Yichi Wang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (L.S.); (X.L.); (B.T.); (Y.W.); (L.W.)
| | - Yingyi Lin
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang 524088, China; (R.Z.); (Y.L.)
| | - Liangliang Wu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (L.S.); (X.L.); (B.T.); (Y.W.); (L.W.)
| | - Chao Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (L.S.); (X.L.); (B.T.); (Y.W.); (L.W.)
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (L.S.); (X.L.); (B.T.); (Y.W.); (L.W.)
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Jiang Q, Wu X, Zhang X, Ji Z, Cao Y, Duan Q, Huang J. Genome-Wide Identification and Expression Analysis of AS2 Genes in Brassica rapa Reveal Their Potential Roles in Abiotic Stress. Int J Mol Sci 2023; 24:10534. [PMID: 37445710 DOI: 10.3390/ijms241310534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
The ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) gene family plays a pivotal role in plant growth, induction of phytohormones, and the abiotic stress response. However, the AS2 gene family in Brassica rapa has yet to be investigated. In this study, we identified 62 AS2 genes in the B. rapa genome, which were classified into six subfamilies and distributed across 10 chromosomes. Sequence analysis of BrAS2 promotors showed that there are several typical cis-elements involved in abiotic stress tolerance and stress-related hormone response. Tissue-specific expression analysis showed that BrAS2-47 exhibited ubiquitous expression in all tissues, indicating it may be involved in many biological processes. Gene expression analysis showed that the expressions of BrAS2-47 and BrAS2-10 were significantly downregulated under cold stress, heat stress, drought stress, and salt stress, while BrAS2-58 expression was significantly upregulated under heat stress. RT-qPCR also confirmed that the expression of BrAS2-47 and BrAS2-10 was significantly downregulated under cold stress, drought stress, and salt stress, and in addition BrAS2-56 and BrAS2-4 also changed significantly under the three stresses. In addition, protein-protein interaction (PPI) network analysis revealed that the Arabidopsis thaliana genes AT5G67420 (homologous gene of BrAS2-47 and BrAS2-10) and AT3G49940 (homologous gene of BrAS2-58) can interact with NIN-like protein 7 (NLP7), which has been previously reported to play a role in resistance to adverse environments. In summary, our findings suggest that among the BrAS2 gene family, BrAS2-47 and BrAS2-10 have the most potential for the regulation of abiotic stress tolerance. These results will facilitate future functional investigations of BrAS2 genes in B. rapa.
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Affiliation(s)
- Qiwei Jiang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Xiaoyu Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Xiaoyu Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Zhaojing Ji
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Yunyun Cao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Qiaohong Duan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Jiabao Huang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
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Jiang X, Cui H, Wang Z, Kang J, Yang Q, Guo C. Genome-Wide Analysis of the LATERAL ORGAN BOUNDARIES Domain ( LBD) Members in Alfalfa and the Involvement of MsLBD48 in Nitrogen Assimilation. Int J Mol Sci 2023; 24:4644. [PMID: 36902075 PMCID: PMC10003661 DOI: 10.3390/ijms24054644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 03/04/2023] Open
Abstract
The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a transcription factor family specific to the land plants, have been implicated in multiple biological processes including organ development, pathogen response and the uptake of inorganic nitrogen. The study focused on LBDs in legume forage Alfalfa. The genome-wide analysis revealed that in Alfalfa 178 loci across 31 allelic chromosomes encoded 48 unique LBDs (MsLBDs), and the genome of its diploid progenitor M. sativa spp. Caerulea encoded 46 LBDs. Synteny analysis indicated that the expansion of AlfalfaLBDs was attributed to the whole genome duplication event. The MsLBDs were divided into two major phylogenetic classes, and the LOB domain of the Class I members was highly conserved relative to that of the Class II. The transcriptomic data demonstrated that 87.5% of MsLBDs were expressed in at least one of the six test tissues, and Class II members were preferentially expressed in nodules. Moreover, the expression of Class II LBDs in roots was upregulated by the treatment of inorganic nitrogen such as KNO3 and NH4Cl (0.3 mM). The overexpression of MsLBD48, a Class II member, in Arabidopsis resulted in growth retardance with significantly declined biomass compared with the non-transgenic plants, and the transcription level of the genes involved in nitrogen uptake or assimilation, including NRT1.1, NRT2.1, NIA1 and NIA2 was repressed. Therefore, the LBDs in Alfalfa are highly conserved with their orthologs in embryophytes. Our observations that ectopic expression of MsLBD48 inhibited Arabidopsis growth by repressing nitrogen adaption suggest the negative role of the transcription factor in plant uptake of inorganic nitrogen. The findings imply the potential application of MsLBD48 in Alfalfa yield improvement via gene editing.
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Affiliation(s)
- Xu Jiang
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Huiting Cui
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Qingchuan Yang
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Changhong Guo
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
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Transcription Factor IAA27 Positively Regulates P Uptake through Promoted Adventitious Root Development in Apple Plants. Int J Mol Sci 2022; 23:ijms232214029. [PMID: 36430505 PMCID: PMC9695701 DOI: 10.3390/ijms232214029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Phosphate (P) deficiency severely limits the growth and production of plants. Adventitious root development plays an essential role in responding to low phosphorus stress for apple plants. However, the molecular mechanisms regulating adventitious root growth and development in response to low phosphorus stress have remained elusive. In this study, a mutation (C-T) in the coding region of the apple AUXIN/INDOLE-3-ACETIC ACID 27 (IAA27) gene was identified. MdIAA27T-overexpressing transgenic apple improved the tolerance to phosphorus deficiency, which grew longer and denser adventitious roots and presented higher phosphorous content than the control plants under low phosphorus conditions, while the overexpression of MdIAA27C displayed the opposite trend. Moreover, the heterologous overexpression of MdIAA27 in tobacco yielded the same results, supporting the aforementioned findings. In vitro and in vivo assays showed that MdIAA27 directly interacted with AUXIN RESPONSE FACTOR (ARF8), ARF26 and ARF27, which regulated Small Auxin-Up RNA 76 (MdSAUR76) and lateral organ boundaries domain 16 (MdLBD16) transcription. The mutation in IAA27 resulted in altered interaction modes, which in turn promoted the release of positive ARFs to upregulate SAUR76 and LBD16 expression in low phosphorus conditions. Altogether, our studies provide insights into how the allelic variation of IAA27 affects adventitious root development in response to low phosphorus stress.
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Zhang C, Zhu P, Zhang M, Huang Z, Hippolyte AR, Hou Y, Lou X, Ji K. Identification, Classification and Characterization of LBD Transcription Factor Family Genes in Pinus massoniana. Int J Mol Sci 2022; 23:13215. [PMID: 36362005 PMCID: PMC9658656 DOI: 10.3390/ijms232113215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 09/11/2024] Open
Abstract
Transcription factors (TFs) are a class of proteins that play an important regulatory role in controlling the expression of plant target genes by interacting with downstream regulatory genes. The lateral organ boundary (LOB) structural domain (LBD) genes are a family of genes encoding plant-specific transcription factors that play important roles in regulating plant growth and development, nutrient metabolism, and environmental stresses. However, the LBD gene family has not been systematically identified in Pinus massoniana, one of the most important conifers in southern China. Therefore, in this study, we combined cell biology and bioinformatics approaches to identify the LBD gene family of P. massoniana by systematic gene structure and functional evolutionary analysis. We obtained 47 LBD gene family members, and all PmLBD members can be divided into two subfamilies, (Class I and Class II). By treating the plants with abiotic stress and growth hormone, etc., under qPCR-based analysis, we found that the expression of PmLBD genes was regulated by growth hormone and abiotic stress treatments, and thus this gene family in growth and development may be actively involved in plant growth and development and responses to adversity stress, etc. By subcellular localization analysis, PmLBD is a nuclear protein, and two of the genes, PmLBD44 and PmLBD45, were selected for functional characterization; secondly, yeast self-activation analysis showed that PmLBD44, PmLBD45, PmLBD46 and PmLBD47 had no self-activating activity. This study lays the foundation for an in-depth study of the role of the LBD gene family in other physiological activities of P. massoniana.
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Affiliation(s)
| | | | | | | | | | | | | | - Kongshu Ji
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Wang H, Han X, Fu X, Sun X, Chen H, Wei X, Cui S, Liu Y, Guo W, Li X, Xing J, Zhang Y. Overexpression of TaLBD16-4D alters plant architecture and heading date in transgenic wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:911993. [PMID: 36212357 PMCID: PMC9533090 DOI: 10.3389/fpls.2022.911993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Lateral organ boundaries domain (LBD) proteins, a class of plant-specific transcription factors with a special domain of lateral organ boundaries (LOB), play essential roles in plant growth and development. However, there is little known about the functions of these genes in wheat to date. Our previous study demonstrated that TaLBD16-4D is conducive to increasing lateral root number in wheat. In the present work, we further examined important agronomical traits of the aerial part of transgenic wheat overexpressing TaLBD16-4D. Interestingly, it was revealed that overexpressing TaLBD16-4D could lead to early heading and multiple alterations of plant architecture, including decreased plant height, increased flag leaf size and stem diameter, reduced spike length and tillering number, improved spike density and grain width, and decreased grain length. Moreover, auxin-responsive experiments demonstrated that the expression of TaLBD16-4D in wild-type (WT) wheat plants showed a significant upregulation through 2,4-D treatment. TaLBD16-4D-overexpression lines displayed a hyposensitivity to 2,4-D treatment and reduced shoot gravitropic response. The expressions of a set of auxin-responsive genes were markedly different between WT and transgenic plants. In addition, overexpressing TaLBD16-4D affected the transcript levels of flowering-related genes (TaGI, TaCO1, TaHd1, TaVRN1, TaVRN2, and TaFT1). Notably, the expression of TaGI, TaCO1, TaHd1, TaVRN1, and TaFT1 displayed significant upregulation under IAA treatment. Collectively, our observations indicated that overexpressing TaLBD16-4D could affect aerial architecture and heading time possibly though participating in the auxin pathway.
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Affiliation(s)
- Huifang Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofan Han
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofeng Fu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xinling Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Hailong Chen
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xirui Wei
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Shubin Cui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yiguo Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Weiwei Guo
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Ximei Li
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yumei Zhang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
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Xiong J, Zhang W, Zheng D, Xiong H, Feng X, Zhang X, Wang Q, Wu F, Xu J, Lu Y. ZmLBD5 Increases Drought Sensitivity by Suppressing ROS Accumulation in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2022; 11:1382. [PMID: 35631807 PMCID: PMC9144968 DOI: 10.3390/plants11101382] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Drought stress is known to significantly limit crop growth and productivity. Lateral organ boundary domain (LBD) transcription factors-particularly class-I members-play essential roles in plant development and biotic stress. However, little information is available on class-II LBD genes related to abiotic stress in maize. Here, we cloned a maize class-II LBD transcription factor, ZmLBD5, and identified its function in drought stress. Transient expression, transactivation, and dimerization assays demonstrated that ZmLBD5 was localized in the nucleus, without transactivation, and could form a homodimer or heterodimer. Promoter analysis demonstrated that multiple drought-stress-related and ABA response cis-acting elements are present in the promoter region of ZmLBD5. Overexpression of ZmLBD5 in Arabidopsis promotes plant growth under normal conditions, and suppresses drought tolerance under drought conditions. Furthermore, the overexpression of ZmLBD5 increased the water loss rate, stomatal number, and stomatal apertures. DAB and NBT staining demonstrated that the reactive oxygen species (ROS) decreased in ZmLBD5-overexpressed Arabidopsis. A physiological index assay also revealed that SOD and POD activities in ZmLBD5-overexpressed Arabidopsis were higher than those in wild-type Arabidopsis. These results revealed the role of ZmLBD5 in drought stress by regulating ROS levels.
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Affiliation(s)
- Jing Xiong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Weixiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Dan Zheng
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Hao Xiong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Xuanjun Feng
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang 611130, China
| | - Xuemei Zhang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Qingjun Wang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang 611130, China
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Tian Y, Han X, Qu Y, Zhang Y, Rong H, Wu K, Xu L. Genome-Wide Identification of the Ginkgo ( Ginkgo biloba L.) LBD Transcription Factor Gene and Characterization of Its Expression. Int J Mol Sci 2022; 23:ijms23105474. [PMID: 35628284 PMCID: PMC9141976 DOI: 10.3390/ijms23105474] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors involved in various transcriptional regulation processes. We identified a total of 37 GbLBD genes in ginkgo, and based on gene structure and phylogenetic analysis, the GbLBD gene family was classified into class I (33, with the largest number of Id genes (16)) and class II (4). The ginkgo LBD gene was also analyzed regarding its chromosomal distributions, gene duplications, promoters, and introns/exons. In addition, gene expression profiling and real-time quantitative PCR analysis showed that the expression of 14 GbLBD genes differed in six different tissues and three developmental stages. The GbLBD gene of class II were highly expressed relative to the class I gene in all tissues and developmental stages, while class Id gene were generally at low levels or were not expressed, especially in seed developmental stages. The expression pattern analysis of cold/drought treatment and IAA/ABA hormone treatment showed that abiotic stress treatment could significantly induce the expression of GbLBD gene, of which class II genes played a key role in stress treatment. Our study provides a solid foundation for further evolutionary and functional analysis of the ginkgo LBD gene family.
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Affiliation(s)
| | | | | | | | | | | | - Li’an Xu
- Correspondence: ; Tel.: +86-25-8542-7882
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Jia R, Li C, Wang Y, Qin X, Meng L, Sun X. Genome-Wide Analysis of LBD Transcription Factor Genes in Dendrobiumcatenatum. Int J Mol Sci 2022; 23:ijms23042089. [PMID: 35216201 PMCID: PMC8877895 DOI: 10.3390/ijms23042089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) gene family comprises plant-specific transcription factors that control cell proliferation and differentiation during growth and development in many plant species. However, to date, no studies of the LBD gene family in Dendrobium catenatum have been reported. In this study, a genome-wide analysis of LBD genes was performed in D. catenatum and 24 LBD genes were identified. The genes were classified into two classes (I and II) based on phylogenetic relationships and motif structure. Subcellular localization analysis for DcaLBD6 and DcaLBD18 from class I and DcaLBD37 and DcaLBD41 from class II revealed that the proteins were localized in the nucleus. Transient expression analysis of DcaLBD6, DcaLBD18, DcaLBD37, and DcaLBD41 indicated that class I and class II members have opposite roles in regulating VASCULAR-RELATED NAC-DOMAIN 7 (VND7) expression. DcaLBD genes showed diverse expression patterns in response to different phytohormone treatments. Heat maps revealed diverse patterns of DcaLBD gene expression in different organs. These results lay the foundation for further detailed studies of the LBD gene family in D. catenatum.
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Affiliation(s)
- Ru Jia
- School of Life Sciences, Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China;
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
| | - Cheng Li
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhua Wang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangshi Qin
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
| | - Lihua Meng
- School of Life Sciences, Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China;
- Correspondence: (L.M.); (X.S.); Tel.: +86-871-65230873 (X.S.)
| | - Xudong Sun
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- Correspondence: (L.M.); (X.S.); Tel.: +86-871-65230873 (X.S.)
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10
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Huang B, Huang Z, Ma R, Ramakrishnan M, Chen J, Zhang Z, Yrjälä K. Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis). BMC PLANT BIOLOGY 2021; 21:296. [PMID: 34182934 PMCID: PMC8240294 DOI: 10.1186/s12870-021-03078-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/26/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Moso bamboo, the fastest growing plant on earth, is an important source for income in large areas of Asia, mainly cultivated in China. Lateral organ boundaries domain (LBD) proteins, a family of transcription factors unique to plants, are involved in multiple transcriptional regulatory pathways and play important roles in lateral organ development, pathogen response, secondary growth, and hormone response. The LBD gene family has not previously been characterized in moso bamboo (Phyllostachys edulis). RESULTS In this study, we identified 55 members of the LBD gene family from moso bamboo and found that they were distributed non-uniformly across its 18 chromosomes. Phylogenetic analysis showed that the moso bamboo LBD genes could be divided into two classes. LBDs from the same class share relatively conserved gene structures and sequences encoding similar amino acids. A large number of hormone response-associated cis-regulatory elements were identified in the LBD upstream promoter sequences. Synteny analysis indicated that LBDs in the moso bamboo genome showed greater collinearity with those of O. sativa (rice) and Zea mays (maize) than with those of Arabidopsis and Capsicum annuum (pepper). Numerous segmental duplicates were found in the moso bamboo LBD gene family. Gene expression profiles in four tissues showed that the LBD genes had different spatial expression patterns. qRT-PCR assays with the Short Time-series Expression Miner (STEM) temporal expression analysis demonstrated that six genes (PeLBD20, PeLBD29, PeLBD46, PeLBD10, PeLBD38, and PeLBD06) were consistently up-regulated during the rapid growth and development of bamboo shoots. In addition, 248 candidate target genes that function in a variety of pathways were identified based on consensus LBD binding motifs. CONCLUSIONS In the current study, we identified 55 members of the moso bamboo transcription factor LBD and characterized for the first time. Based on the short-time sequence expression software and RNA-seq data, the PeLBD gene expression was analyzed. We also investigated the functional annotation of all PeLBDs, including PPI network, GO, and KEGG enrichment based on String database. These results provide a theoretical basis and candidate genes for studying the molecular breeding mechanism of rapid growth of moso bamboo.
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Affiliation(s)
- Bin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang Province, People's Republic of China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High efficiency Utilization, Zhejiang A&F University, Zhejiang, China
| | - Zhinuo Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang Province, People's Republic of China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High efficiency Utilization, Zhejiang A&F University, Zhejiang, China
| | - Ruifang Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang Province, People's Republic of China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High efficiency Utilization, Zhejiang A&F University, Zhejiang, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jialu Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang Province, People's Republic of China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High efficiency Utilization, Zhejiang A&F University, Zhejiang, China
| | - Zhijun Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang Province, People's Republic of China.
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High efficiency Utilization, Zhejiang A&F University, Zhejiang, China.
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang Province, People's Republic of China.
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland.
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Wang Z, Zhang R, Cheng Y, Lei P, Song W, Zheng W, Nie X. Genome-Wide Identification, Evolution, and Expression Analysis of LBD Transcription Factor Family in Bread Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:721253. [PMID: 34539714 PMCID: PMC8446603 DOI: 10.3389/fpls.2021.721253] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/09/2021] [Indexed: 05/04/2023]
Abstract
The lateral organ boundaries domain (LBD) genes, as the plant-specific transcription factor family, play a crucial role in controlling plant architecture and stress tolerance. Although it has been thoroughly characterized in many species, the LBD family was not well studied in wheat. Here, the wheat LBD family was systematically investigated through an in silico genome-wide search method. A total of 90 wheat LBD genes (TaLBDs) were identified, which were classified into class I containing seven subfamilies, and class II containing two subfamilies. Exon-intron structure, conserved protein motif, and cis-regulatory elements analysis showed that the members in the same subfamily shared similar gene structure organizations, supporting the classification. Furthermore, the expression patterns of these TaLBDs in different types of tissues and under diverse stresses were identified through public RNA-seq data analysis, and the regulation networks of TaLBDs involved were predicted. Finally, the expression levels of 12 TaLBDs were validated by quantitative PCR (qPCR) analysis and the homoeologous genes showed differential expression. Additionally, the genetic diversity of TaLBDs in the landrace population showed slightly higher than that of the genetically improved germplasm population while obvious asymmetry at the subgenome level. This study not only provided the potential targets for further functional analysis but also contributed to better understand the roles of LBD genes in regulating development and stress tolerance in wheat and beyond.
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Affiliation(s)
- Zhenyu Wang
- 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, Yangling, China
| | - Ruoyu Zhang
- 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, Yangling, China
| | - Yue Cheng
- 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, Yangling, China
| | - Pengzheng Lei
- 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, Yangling, China
| | - Weining Song
- 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, Yangling, China
- Australia-China Joint Research Centre for Abiotic and Biotic Stress Management in Agriculture, Horticulture and Forestry, Yangling, China
| | - Weijun Zheng
- 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, Yangling, China
- *Correspondence: Weijun Zheng
| | - 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, Yangling, China
- Xiaojun Nie
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12
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Iwakawa H, Takahashi H, Machida Y, Machida C. Roles of ASYMMETRIC LEAVES2 (AS2) and Nucleolar Proteins in the Adaxial-Abaxial Polarity Specification at the Perinucleolar Region in Arabidopsis. Int J Mol Sci 2020; 21:E7314. [PMID: 33022996 PMCID: PMC7582388 DOI: 10.3390/ijms21197314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Leaves of Arabidopsis develop from a shoot apical meristem grow along three (proximal-distal, adaxial-abaxial, and medial-lateral) axes and form a flat symmetric architecture. ASYMMETRIC LEAVES2 (AS2), a key regulator for leaf adaxial-abaxial partitioning, encodes a plant-specific nuclear protein and directly represses the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). How AS2 could act as a critical regulator, however, has yet to be demonstrated, although it might play an epigenetic role. Here, we summarize the current understandings of the genetic, molecular, and cellular functions of AS2. A characteristic genetic feature of AS2 is the presence of a number of (about 60) modifier genes, mutations of which enhance the leaf abnormalities of as2. Although genes for proteins that are involved in diverse cellular processes are known as modifiers, it has recently become clear that many modifier proteins, such as NUCLEOLIN1 (NUC1) and RNA HELICASE10 (RH10), are localized in the nucleolus. Some modifiers including ribosomal proteins are also members of the small subunit processome (SSUP). In addition, AS2 forms perinucleolar bodies partially colocalizing with chromocenters that include the condensed inactive 45S ribosomal RNA genes. AS2 participates in maintaining CpG methylation in specific exons of ETT/ARF3. NUC1 and RH10 genes are also involved in maintaining the CpG methylation levels and repressing ETT/ARF3 transcript levels. AS2 and nucleolus-localizing modifiers might cooperatively repress ETT/ARF3 to develop symmetric flat leaves. These results raise the possibility of a nucleolus-related epigenetic repression system operating for developmental genes unique to plants and predict that AS2 could be a molecule with novel functions that cannot be explained by the conventional concept of transcription factors.
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Affiliation(s)
- Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
| | - Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan;
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
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Zhang Y, Li Z, Ma B, Hou Q, Wan X. Phylogeny and Functions of LOB Domain Proteins in Plants. Int J Mol Sci 2020; 21:ijms21072278. [PMID: 32224847 PMCID: PMC7178066 DOI: 10.3390/ijms21072278] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
Lateral organ boundaries (LOB) domain (LBD) genes, a gene family encoding plant-specific transcription factors, play important roles in plant growth and development. At present, though there have been a number of genome-wide analyses on LBD gene families and functional studies on individual LBD proteins, the diverse functions of LBD family members still confuse researchers and an effective strategy is required to summarize their functional diversity. To further integrate and improve our understanding of the phylogenetic classification, functional characteristics and regulatory mechanisms of LBD proteins, we review and discuss the functional characteristics of LBD proteins according to their classifications under a phylogenetic framework. It is proved that this strategy is effective in the anatomy of diverse functions of LBD family members. Additionally, by phylogenetic analysis, one monocot-specific and one eudicot-specific subclade of LBD proteins were found and their biological significance in monocot and eudicot development were also discussed separately. The review will help us better understand the functional diversity of LBD proteins and facilitate further studies on this plant-specific transcription factor family.
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Affiliation(s)
- Yuwen Zhang
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Ziwen Li
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Biao Ma
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
- Correspondence: or ; Tel.: +86-10-6299-5866
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14
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Yu Q, Hu S, Du J, Yang Y, Sun X. Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var . rapa. PLANT DIVERSITY 2020; 42:52-60. [PMID: 32140637 PMCID: PMC7046510 DOI: 10.1016/j.pld.2019.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 11/15/2019] [Accepted: 11/28/2019] [Indexed: 05/23/2023]
Abstract
The Lateral Organ Boundaries Domain (LBD) genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species. However, members of the LBD gene family have yet to be identified in Brassica rapa var. rapa. In the present study, fifty-nine LBD genes were identified and distributed on 10 chromosomes. The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa; the theoretical pI for these proteins varies from 4.83 to 9.68. There were 17 paralogous gene pairs in the BrrLBD family, suggesting that the amplification of the BrrLBD gene family involved large-scale gene duplication events. Members of the BrrLBD family were divided into 7 subclades (class I a to e, class II a and b). Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs. The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR (qRT-PCR). Most BrrLBD genes in the same subclade had similar gene expression profiles. However, the expression patterns of 7 genes differed from their duplicates, indicating that although the gene function of most BrrLBD genes has been conserved, some BrrLBD genes may have undergone evolutionary change.
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Affiliation(s)
- Qin Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Simin Hu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiancan Du
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xudong Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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15
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Liu H, Cao M, Chen X, Ye M, Zhao P, Nan Y, Li W, Zhang C, Kong L, Kong N, Yang C, Chen Y, Wang D, Chen Q. Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Solanum tuberosum. Int J Mol Sci 2019; 20:ijms20215360. [PMID: 31661866 PMCID: PMC6861928 DOI: 10.3390/ijms20215360] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/13/2019] [Accepted: 10/22/2019] [Indexed: 11/16/2022] Open
Abstract
Lateral organ boundaries domain (LBD) proteins belong to a particular class of transcription factors of lateral organ boundary (LOB) specific domains that play essential roles in plant growth and development. However, a potato phylogenetic analysis of the LBD family has not been fully studied by scholars and researchers. In this research, bioinformatics methods and the growth of potatoes were used to identify 43 StLBD proteins. We separated them into seven subfamilies: Ia, Ib, Ic, Id, Ie, IIa and IIb. The number of amino acids encoded by the potato LBD family ranged from 94 to 327. The theoretical isoelectric point distribution ranged from 4.16 to 9.12 Kda, and they were distributed among 10 chromosomes. The results of qRT-PCR showed that the expression levels of StLBD2-6 and StLBD3-5 were up-regulated under drought stress in the stem. The expression levels of StLBD1-5 and StLBD2-6 were down-regulated in leaves. We hypothesized that StLBD1-5 was down-regulated under drought stress, and that StLBD2-6 and StLBD3-5 up-regulation might help to maintain the normal metabolism of potato and enhance the potatoes’ resistance to drought.
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Affiliation(s)
- Hengzhi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Minxuan Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xiaoli Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Minghui Ye
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Peng Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yunyou Nan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Wan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lingshuang Kong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Nana Kong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chenghui Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Dongdong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Qin Chen
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
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16
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Teng RM, Wang YX, Wang WL, Li H, Shen W, Zhuang J. Genome-wide identification, classification and expression pattern of LBD gene family in Camellia sinensis. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1521303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Rui-Min Teng
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wen-Li Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wei Shen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Lu Q, Shao F, Macmillan C, Wilson IW, van der Merwe K, Hussey SG, Myburg AA, Dong X, Qiu D. Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:124-136. [PMID: 28499078 PMCID: PMC5785364 DOI: 10.1111/pbi.12754] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/16/2017] [Accepted: 05/01/2017] [Indexed: 05/16/2023]
Abstract
Lateral Organ Boundaries Domain (LBD) proteins are plant-specific transcription factors playing crucial roles in growth and development. However, the function of LBD proteins in Eucalyptus grandis remains largely unexplored. In this study, LBD genes in E. grandis were identified and characterized using bioinformatics approaches. Gene expression patterns in various tissues and the transcriptional responses of EgLBDs to exogenous hormones were determined by qRT-PCR. Functions of the selected EgLBDs were studied by ectopically overexpressing in a hybrid poplar (Populus alba × Populus glandulosa). Expression levels of genes in the transgenic plants were investigated by RNA-seq. Our results showed that there were forty-six EgLBD members in the E. grandis genome and three EgLBDs displayed xylem- (EgLBD29) or phloem-preferential expression (EgLBD22 and EgLBD37). Confocal microscopy indicated that EgLBD22, EgLBD29 and EgLBD37 were localized to the nucleus. Furthermore, we found that EgLBD22, EgLBD29 and EgLBD37 were responsive to the treatments of indol-3-acetic acid and gibberellic acid. More importantly, we demonstrated EgLBDs exerted different influences on secondary growth. Namely, 35S::EgLBD37 led to significantly increased secondary xylem, 35S::EgLBD29 led to greatly increased phloem fibre production, and 35S::EgLBD22 showed no obvious effects. We revealed that key genes related to gibberellin, ethylene and auxin signalling pathway as well as cell expansion were significantly up- or down-regulated in transgenic plants. Our new findings suggest that LBD genes in E. grandis play important roles in secondary growth. This provides new mechanisms to increase wood or fibre production.
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Affiliation(s)
- Qiang Lu
- State Key Laboratory of Tree Genetics and BreedingThe Research Institute of ForestryChinese Academy of ForestryBeijingChina
| | - Fenjuan Shao
- State Key Laboratory of Tree Genetics and BreedingThe Research Institute of ForestryChinese Academy of ForestryBeijingChina
| | | | | | - Karen van der Merwe
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI)Genomics Research Institute (GRI)University of PretoriaPretoriaSouth Africa
| | - Steven G. Hussey
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI)Genomics Research Institute (GRI)University of PretoriaPretoriaSouth Africa
| | - Alexander A. Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI)Genomics Research Institute (GRI)University of PretoriaPretoriaSouth Africa
| | - Xiaomei Dong
- State Key Laboratory of Agrobiotechnology and National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and BreedingThe Research Institute of ForestryChinese Academy of ForestryBeijingChina
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Grimplet J, Pimentel D, Agudelo-Romero P, Martinez-Zapater JM, Fortes AM. The LATERAL ORGAN BOUNDARIES Domain gene family in grapevine: genome-wide characterization and expression analyses during developmental processes and stress responses. Sci Rep 2017; 7:15968. [PMID: 29162903 PMCID: PMC5698300 DOI: 10.1038/s41598-017-16240-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) constitute a family of plant-specific transcription factors with key roles in the regulation of plant organ development, pollen development, plant regeneration, pathogen response, and anthocyanin and nitrogen metabolisms. However, the role of LBDs in fruit ripening and in grapevine (Vitis vinifera L.) development and stress responses is poorly documented. By performing a model curation of LBDs in the latest genome annotation 50 genes were identified. Phylogenetic analysis showed that LBD genes can be grouped into two classes mapping on 16 out of the 19 V. vinifera chromosomes. New gene subclasses were identified that have not been characterized in other species. Segmental and tandem duplications contributed significantly to the expansion and evolution of the LBD gene family in grapevine as noticed for other species. The analysis of cis-regulatory elements and transcription factor binding sites in the VviLBD promoter regions suggests the involvement of several hormones in the regulation of LBDs expression. Expression profiling suggest the involvement of LBD transcription factors in grapevine development, berry ripening and stress responses. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming to clarify mechanisms responsible for the onset of fruit ripening and fruit defense strategies.
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Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC-Universidad de La Rioja-Gobierno de La Rioja), 26006, Logroño, Spain
| | - Diana Pimentel
- Universidade de Lisboa, Faculdade de Ciências de Lisboa, BioISI, Campo Grande, 1749-016, Lisboa, Portugal
| | - Patricia Agudelo-Romero
- Universidade de Lisboa, Faculdade de Ciências de Lisboa, BioISI, Campo Grande, 1749-016, Lisboa, Portugal.,The UWA Institute of Agriculture, The University of Western Australia, M082 Perth, 6009, Australia and the ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M316 Perth, Perth, 6009, Australia
| | - Jose Miguel Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (CSIC-Universidad de La Rioja-Gobierno de La Rioja), 26006, Logroño, Spain
| | - Ana Margarida Fortes
- Universidade de Lisboa, Faculdade de Ciências de Lisboa, BioISI, Campo Grande, 1749-016, Lisboa, Portugal.
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