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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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Yu J, Gao B, Li D, Li S, Chiang VL, Li W, Zhou C. Ectopic Expression of PtrLBD39 Retarded Primary and Secondary Growth in Populus trichocarpa. Int J Mol Sci 2024; 25:2205. [PMID: 38396881 PMCID: PMC10889148 DOI: 10.3390/ijms25042205] [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: 12/16/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Primary and secondary growth of trees are needed for increments in plant height and stem diameter, respectively, affecting the production of woody biomass for applications in timber, pulp/paper, and related biomaterials. These two types of growth are believed to be both regulated by distinct transcription factor (TF)-mediated regulatory pathways. Notably, we identified PtrLBD39, a highly stem phloem-specific TF in Populus trichocarpa and found that the ectopic expression of PtrLBD39 in P. trichocarpa markedly retarded both primary and secondary growth. In these overexpressing plants, the RNA-seq, ChIP-seq, and weighted gene co-expression network analysis (WGCNA) revealed that PtrLBD39 directly or indirectly regulates TFs governing vascular tissue development, wood formation, hormonal signaling pathways, and enzymes responsible for wood components. This regulation led to growth inhibition, decreased fibrocyte secondary cell wall thickness, and reduced wood production. Therefore, our study indicates that, following ectopic expression in P. trichocarpa, PtrLBD39 functions as a repressor influencing both primary and secondary growth.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Boyuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Danning Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
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Zhou F, Zhang H, Chen S, Fan C. Transcriptome analysis of the transition from primary to secondary growth of vertical stem in Eucalyptus grandis. BMC PLANT BIOLOGY 2024; 24:96. [PMID: 38331783 PMCID: PMC10851593 DOI: 10.1186/s12870-024-04731-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024]
Abstract
Eucalyptus was one of the most cultivated hardwood species worldwide, with rapid growth, good wood properties and a wide range of adaptability. Eucalyptus stem undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. In order to better understand the genetic regulation of secondary growth in Eucalyptus grandis, Transcriptome analyses in stem segments along a developmental gradient from the third internode to the eleventh internode of E. grandis that spanned primary to secondary growth were carried out. 5,149 genes that were differentially expressed during stem development were identified. Combining the trend analysis by the Mfuzz method and the module-trait correlation analysis by the Weighted Gene Co-expression Network Analysis method, a total of 70 differentially expressed genes (DEGs) selected from 868 DEGs with high connectivity were found to be closely correlated with secondary growth. Results revealed that the differential expression of these DEGs suggests that they may involve in the primary growth or secondary growth. AP1, YAB2 TFs and EXP genes are highly expressed in the IN3, whereas NAC, MYB TFs are likely to be important for secondary growth. These results will expand our understanding of the complex molecular and cellular events of secondary growth and provide a foundation for future studies on wood formation in Eucalyptus.
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Affiliation(s)
- Fangping Zhou
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of State Forestry Administration On Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Haonan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of State Forestry Administration On Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shanshan Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of State Forestry Administration On Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
- State Key Laboratory of Tree Genetics Breeding, Northeast Forestry University, Harbin, China
| | - Chunjie Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration On Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
- Yuelushan Laboratory, Central South University of Forestry and Technology, Changsha, Hunan, China.
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Derelli Tufekci E. Genome-wide identification and analysis of Lateral Organ Boundaries Domain ( LBD) transcription factor gene family in melon ( Cucumis melo L.). PeerJ 2023; 11:e16020. [PMID: 37790611 PMCID: PMC10544307 DOI: 10.7717/peerj.16020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/11/2023] [Indexed: 10/05/2023] Open
Abstract
Background Lateral Organ Boundaries Domain (LBD) transcription factor (TF) gene family members play very critical roles in several biological processes like plant-spesific development and growth process, tissue regeneration, different biotic and abiotic stress responses in plant tissues and organs. The LBD genes have been analyzed in various species. Melon (Cucumis melo L.), a member of the Cucurbitaceae family, is economically important and contains important molecules for nutrition and human health such as vitamins A and C, β-carotenes, phenolic acids, phenolic acids, minerals and folic acid. However, no studies have been reported so far about LBD genes in melon hence this is the first study for LBD genes in this plant. Results In this study, 40 melon CmLBD TF genes were identified, which were separated into seven groups through phylogenetic analysis. Cis-acting elements showed that these genes were associated with plant growth and development, phytohormone and abiotic stress responses. Gene Ontology (GO) analysis revealed that of CmLBD genes especially function in regulation and developmental processes. The in silico and qRT-PCR expression patterns demonstrated that CmLBD01 and CmLBD18 are highly expressed in root and leaf tissues, CmLBD03 and CmLBD14 displayed a high expression in male-female flower and ovary tissues. Conclusions These results may provide important contributions for future research on the functional characterization of the melon LBD gene family and the outputs of this study can provide information about the evolution and characteristics of melon LBD gene family for next studies.
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Affiliation(s)
- Ebru Derelli Tufekci
- Department of Field Crops, Food and Agriculture Vocational High School, Cankiri Karatekin University, Cankiri, Turkey
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Ma Y, Zhong M, Li J, Jiang Y, Zhou X, Justice Ijeoma C, Tang X, Chen S, Cao S. Genome Identification and Evolutionary Analysis of LBD Genes and Response to Environmental Factors in Phoebe bournei. Int J Mol Sci 2023; 24:12581. [PMID: 37628762 PMCID: PMC10454761 DOI: 10.3390/ijms241612581] [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: 03/29/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Phoebe bournei is nationally conserved in China due to its high economic value and positive effect on the ecological environment. P. bournei has an excellent wood structure, making it useful for industrial and domestic applications. Despite its importance, there are only a few studies on the lateral organ boundary domain (LBD) genes in P. bournei. The LBD gene family contributes to prompting rooting in multiple plant species and therefore supports their survival directly. To understand the LBD family in P. bournei, we verified its characteristics in this article. By comparing the sequences of Arabidopsis and identifying conserved domains and motifs, we found that there were 38 members of the LBD family in P. bournei, which were named PbLBD1 to PbLBD38. Through evolutionary analysis, we found that they were divided into two different populations and five subfamilies in total. The LBD gene family in P. bournei (Hemsl.) Yang species had two subfamilies, including 32 genes in Class I and 6 genes in Class II. It mainly consists of a Lateral Organ Boundary (LOB) conservative domain, and the protein structure is mostly "Y"-shaped. The gene expression pattern of the LBD gene family showed that the LBD genes were mainly expressed in lateral organs of plants, such as flowers and fruits. The response of LBD transcription factors to red and blue light was summarized, and several models of optogenetic expression regulation were proposed. The effect of regulatory mechanisms on plant rooting was also predicted. Moreover, quantitative real-time PCR (qRT-PCR) revealed that most PbLBDs were differentially expressed under cold, heat, drought, and salt stresses, indicating that PbLBDs might play different functions depending on the type of abiotic stress. This study provides the foundation for further research on the function of LBD in this tree species in the future.
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Affiliation(s)
- Yiming Ma
- International College, Fujian Agriculture and Forestry University, Fuzhou 350002, China (C.J.I.)
| | - Minchen Zhong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingshu Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiming Jiang
- Horticultrue College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuerong Zhou
- Commonwealth Scientific Industrial Research Organization (CSIRO) Agriculture Food, Canberra, ACT 2601, Australia;
| | - Chris Justice Ijeoma
- International College, Fujian Agriculture and Forestry University, Fuzhou 350002, China (C.J.I.)
| | - Xinghao Tang
- Fujian Academy of Forestry, Fuzhou 350002, China
| | - Shipin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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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:ijms24054644. [PMID: 36902075 PMCID: PMC10003661 DOI: 10.3390/ijms24054644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Jin Q, Yang Z, Yang W, Gao X, Liu C. Genome-Wide Identification and Analysis of Lbd Transcription Factor Genes in Jatropha curcas and Related Species. PLANTS 2022; 11:plants11182397. [PMID: 36145796 PMCID: PMC9504267 DOI: 10.3390/plants11182397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022]
Abstract
Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors that play important roles in organ development and stress response. However, the function of LBD genes has not been reported in Euphorbiaceae. In this paper, we used Jatropha curcas as the main study object and added rubber tree (Hevea brasiliensis), cassava (Manihot esculenta Crantz) and castor (Ricinus communis L.) to take a phylogenetic analysis of LBD genes. Of LBD, 33, 58, 54 and 30 members were identified in J. curcas, rubber tree, cassava and castor, respectively. The phylogenetic analysis showed that LBD members of Euphorbiaceae could be classified into two major classes and seven subclasses (Ia-Ie,IIa-IIb), and LBD genes of Euphorbiaceae tended to cluster in the same branch. Further analysis showed that the LBD genes of Euphorbiaceae in the same clade usually had similar protein motifs and gene structures, and tissue expression patterns showed that they also have similar expression profiles. JcLBDs in class Ia and Ie are mainly expressed in male and female flowers, and there are multiple duplication genes with similar expression profiles in these clades. It was speculated that they are likely to play important regulatory roles in flower development. Our study provided a solid foundation for further investigation of the role of LBD genes in the sexual differentiaion of J. curcas.
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Affiliation(s)
- Qi Jin
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Zitian Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Wenjing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiaoyang Gao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Changning Liu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
- Correspondence:
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Isolation and Characterization of an LBD Transcription Factor CsLBD39 from Tea Plant (Camellia sinensis) and Its Roles in Modulating Nitrate Content by Regulating Nitrate-Metabolism-Related Genes. Int J Mol Sci 2022; 23:ijms23169294. [PMID: 36012559 PMCID: PMC9409460 DOI: 10.3390/ijms23169294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Nitrate nitrogen is an important nitrogen source for tea plants’ growth and development. LBD transcription factors play important roles in response to the presence of nitrate in plants. The functional study of LBD transcription factors in tea plants remains limited. In this study, the LBD family gene CsLBD39 was isolated and characterized from tea plants. Sequence analysis indicated that CsLBD39 contained a highly conserved CX2CX6CX3CX domain. The phylogenetic tree assay showed that CsLBD39 belonged to class II subfamily of the LBD family. CsLBD39 was highly expressed in flowers and root; we determined that its expression could be induced by nitrate treatment. The CsLBD39 protein was located in the nucleus and has transcriptional activation activity in yeast. Compared with the wild type, overexpression of CsLBD39 gene in Arabidopsis resulted in smaller rosettes, shorter main roots, reduced lateral roots and lower plant weights. The nitrate content and the expression levels of genes related to nitrate transport and regulation were decreased in transgenic Arabidopsis hosting CsLBD39 gene. Compared with the wild type, CsLBD39 overexpression in transgenic Arabidopsis had smaller cell structure of leaves, shorter diameter of stem cross section, and slender and compact cell of stem longitudinal section. Under KNO3 treatment, the contents of nitrate, anthocyanins, and chlorophyll in leaves, and the content of nitrate in roots of Arabidopsis overexpressing CsLBD39 were reduced, the expression levels of nitrate transport and regulation related genes were decreased. The results revealed that CsLBD39 may be involved in nitrate signal transduction in tea plants as a negative regulator and laid the groundwork for future studies into the mechanism of nitrate response.
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Lei X, Liu Z, Xie Q, Fang J, Wang C, Li J, Wang C, Gao C. Construction of two regulatory networks related to salt stress and lignocellulosic synthesis under salt stress based on a Populus davidiana × P. bolleana transcriptome analysis. PLANT MOLECULAR BIOLOGY 2022; 109:689-702. [PMID: 35486290 DOI: 10.1007/s11103-022-01267-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Construction of ML-hGRN for the salt pathway in Populus davidiana × P. bolleana. Construction of ML-hGRN for the lignocellulosic pathway in Populus davidiana × P. bolleana under salt stress. Many woody plants, including Populus davidiana × P. bolleana, have made great contributions to human production and life. High salt is one of the main environmental factors that restricts the growth of poplar. This study found that high salt could induce strong biochemical changes in poplar. To detect the effect of salt treatment on gene expression, 18 libraries were sequenced on the Illumina sequencing platform. The results identified a large number of early differentially expressed genes (DEGs) and a small number of late DEGs, which indicated that most of the salt response genes of poplar were early response genes. In addition, 197 TFs, including NAC, ERF, and other TFs related to salt stress, were differentially expressed during salt treatment, which indicated that these TFs may play an important role in the salt stress response of poplar. Based on the RNA-seq analysis results, multilayered hierarchical gene regulatory networks (ML-hGRNs) of salt stress- and lignocellulosic synthesis-related DEGs were constructed using the GGM algorithm. The lignocellulosic synthesis regulatory network under salt stress revealed that lignocellulosic synthesis might play an important role in the process of salt stress resistance. Furthermore, the NAC family transcription factor PdbNAC83, which was found in the upper layer in both pathways, was selected to verify the accuracy of the ML-hGRNs. DAP-seq showed that the binding site of PdbNAC83 included a "TT(G/A)C(G/T)T" motif, and ChIP-PCR further verified that PdbNAC83 can regulate the promoters of at least six predicted downstream genes (PdbNLP2-2, PdbZFP6, PdbMYB73, PdbC2H2-like, PdbMYB93-1, PdbbHLH094) by binding to the "TT(G/A)C(G/T)T" motif, which indicates that the predicted regulatory network diagram obtained in this study is relatively accurate. In conclusion, a species-specific salt response pathway might exist in poplar, and this finding lays a foundation for further study of the regulatory mechanism of the salt stress response and provides new clues for the use of genetic engineering methods to create high-quality and highly resistant forest germplasms.
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Affiliation(s)
- Xiaojin Lei
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Zhongyuan Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Qingjun Xie
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Jiaru Fang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Chunyao Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Jinghang Li
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China.
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Sivanesan I, Nayeem S, Venkidasamy B, Kuppuraj SP, RN C, Samynathan R. Genetic and epigenetic modes of the regulation of somatic embryogenesis: a review. Biol Futur 2022; 73:259-277. [DOI: 10.1007/s42977-022-00126-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/16/2022] [Indexed: 01/17/2023]
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11
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Sun X, Wu W, Yang Y, Wilson I, Shao F, Qiu D. Genome-Wide Identification of m6A Writers, Erasers and Readers in Poplar 84K. Genes (Basel) 2022; 13:genes13061018. [PMID: 35741780 PMCID: PMC9223284 DOI: 10.3390/genes13061018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
N6-methyladenosine (m6A) RNA modification is a conserved mechanism to regulate gene expression that plays vital roles in the development of plants. However, the m6A RNA modification in forest trees remains limited. Here, we performed a complete analysis of m6A writers, erasers and readers in Poplar 84K, including gene location, gene structures, conserved motifs, phylogenetic relationships, promoter analysis, expression profiles and the homology modeling. We have identified 61 m6A pathway genes in Poplar 84K (Populus alba × Populus glandulosa), including 14 m6A writers, 14 m6A erasers and 33 m6A readers. Phylogenetic analysis indicated that the m6A writers and erasers were clustered into four groups and m6A readers were clustered into two groups. Promoter analysis showed that m6A pathway genes were mainly responsive to low oxygen followed by ABA and ethylene. The expression of the identified m6A pathway genes showed tissue-specific expression patterns in leaves, xylem, phloem and roots. Moreover, 17 genes were significantly up-regulated and 13 genes were significantly down-regulated in poplar overexpressing the transcription factor LBD15. Homology modeling and molecular docking results suggested that PagFIP37b was most likely to be regulated by LBD15, and the qPCRshowed that PagFIP37b were up-regulated in the LBD15-oe plants. The results provide insights that aid in the future elucidation of the functions of these m6A pathway genes and the epigenetic regulation mechanism of these genes in Poplar 84K.
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Affiliation(s)
- Xiaochen Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
| | - Wenli Wu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
| | - Yanfang Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
| | - Iain Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Fenjuan Shao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
- Correspondence: ; Tel.: +86-10-62889641; Fax: +86-10-62872015
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
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Zhan N, Shang X, Wang Z, Xie Y, Liu G, Wu Z. Screening cellulose synthesis related genes of EgrEXP and EgrHEX in Eucalyptus grandis. Gene 2022; 824:146396. [PMID: 35278632 DOI: 10.1016/j.gene.2022.146396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/19/2022] [Accepted: 03/04/2022] [Indexed: 11/04/2022]
Abstract
Eucalyptus (including Eucalyptus grandis) is an excellent wood forest tree species that provides a large number of plant fiber raw materials for the paper and timber industries. Cellulose, an essential structural component in plant cell walls, is a renewable biomass resource that plays a very important role in nature. There is still a lack of research on the role of gene regulation in cellulose synthesis. To study the genes of cellulose synthesis, the wood chemical indexes of Eucalyptus grandis were analyzed by taking three different parts from the main stem of Eucalyptus grandis as raw materials. The results showed that the cellulose content in the middle of the trunk was significantly higher than that at the chest diameter and at the upper part of the trunk. A total of 296 differentially expressed genes (DEGs) were obtained from the three site by transcriptome, and 19 key candidate genes were related to the synthesis of cellulose in Eucalyptus grandis. EgrEXP1 and EgrHEX4 were overexpressed in 84 K poplar, the content of cellulose and lignin in genetically modified plants was significantly higher than that of wild type 84 K poplar. Also, the average plant height and average root count were significantly higher than those of control plants, and the average diameter of the middle and stem bases were significantly larger than those of control plants. In this study, the genes related to cellulose synthesis in Eucalyptus grandis are studied, which serve as a strong foundation for understanding the molecular regulation of cellulose synthesis in plants.
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Affiliation(s)
- Ni Zhan
- China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang 524022, Guangdong, China; Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Xiuhua Shang
- China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang 524022, Guangdong, China
| | - Zhen Wang
- Guangdong Lingnan Institute Survey and Design Co., LTD, Guangzhou 510000, Guangdong, China
| | - Yaojian Xie
- China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang 524022, Guangdong, China
| | - Guo Liu
- China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang 524022, Guangdong, China
| | - Zhihua Wu
- China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang 524022, Guangdong, 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: 7] [Impact Index Per Article: 3.5] [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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Feng S, Shi J, Hu Y, Li D, Guo L, Zhao Z, Lee GS, Qiao Y. Genome-Wide Analysis of Soybean Lateral Organ Boundaries Domain Gene Family Reveals the Role in Phytophthora Root and Stem Rot. FRONTIERS IN PLANT SCIENCE 2022; 13:865165. [PMID: 35599907 PMCID: PMC9116278 DOI: 10.3389/fpls.2022.865165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/16/2022] [Indexed: 06/15/2023]
Abstract
The plant-specific lateral organ boundaries (LOB) domain (LBD) proteins, a family of transcription factors, play important roles in plant growth and development, as well as in responses to various stresses. However, little is known about the functions of LBD genes in soybean (Glycine max). In this study, we investigated the evolution and classification of the LBD family in soybean by a phylogenetic tree of the LBD gene family from 16 species. Phylogenetic analysis categorized these proteins into two classes (Class I and Class II) with seven subgroups. Moreover, we found that all the 18 LBD ancestors in angiosperm were kept in soybean, common bean genomes, and genome-wide duplication, suggesting the main force for the expansion of LBD from common bean to soybean. Analysis of gene expression profiling data indicated that 16 GmLBD genes were significantly induced at different time points after inoculation of soybean plants (cv. Huachun 6) with Phytophthora sojae (P. sojae). We further assessed the role of four highly upregulated genes, GmLBD9, GmLBD16, GmLBD23, and GmLBD88, in plant defense in soybean hairy roots using the transient overexpression and knockdown assays. The results showed that GmLBD9 and GmLBD23 negatively regulate plant immunity against P. sojae, whereas GmLBD16 and GmLBD88 positively manipulate plant immunity against P. sojae. Collectively, our findings expand our knowledge of the origin and evolution of the GmLBD gene family in soybean and promote the potential application of these genes in soybean genetic improvement.
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Affiliation(s)
- Siqi Feng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jinxia Shi
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yongkang Hu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Die Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Liang Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhibo Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Gang-Seob Lee
- National Institute of Agricultural Science, Jeonju, South Korea
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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15
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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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16
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Yu J, Zhou C, Li D, Li S, Jimmy Lin YC, Wang JP, Chiang VL, Li W. A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa. PLANT COMMUNICATIONS 2022; 3:100250. [PMID: 35059630 PMCID: PMC8760142 DOI: 10.1016/j.xplc.2021.100250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/10/2021] [Accepted: 10/19/2021] [Indexed: 05/29/2023]
Abstract
Tension wood (TW) is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses (e.g., bending). The genetic regulation that underlies this important mechanism remains poorly understood. Here, we used laser capture microdissection of stem xylem cells coupled with full transcriptome RNA-sequencing to analyze TW formation in Populus trichocarpa. After tree bending, PtrLBD39 was the most significantly induced transcription factor gene; it has a phylogenetically paired homolog, PtrLBD22. CRISPR-based knockout of PtrLBD39/22 severely inhibited TW formation, reducing cellulose and increasing lignin content. Transcriptomic analyses of CRISPR-based PtrLBD39/22 double mutants showed that these two genes regulate a set of TW-related genes. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify direct targets of PtrLBD39. We integrated transcriptomic analyses and ChIP-seq assays to construct a transcriptional regulatory network (TRN) mediated by PtrLBD39. In this TRN, PtrLBD39 directly regulates 26 novel TW-responsive transcription factor genes. Our work suggests that PtrLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Danning Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan 10617, China
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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17
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Christie N, Mannapperuma C, Ployet R, van der Merwe K, Mähler N, Delhomme N, Naidoo S, Mizrachi E, Street NR, Myburg AA. qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE). BMC Bioinformatics 2021; 22:595. [PMID: 34911434 PMCID: PMC8672637 DOI: 10.1186/s12859-021-04514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking. RESULTS We have developed qtlXplorer ( https://eucgenie.org/QTLXplorer ) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. CONCLUSIONS qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.
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Affiliation(s)
- Nanette Christie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 907 81, Umeå, Sweden
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Karen van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Niklas Mähler
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 907 81, Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 907 81, Umeå, Sweden.
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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18
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Teng R, Wu Z, Xu S, Hou H, Zhang D, Chen F, Teng N. A Novel Lateral Organ Boundary-domain Factor CmLBD2 Positively Regulates Pollen Development by Activating CmACOS5 in Chrysanthemum morifolium. PLANT & CELL PHYSIOLOGY 2021; 62:1687-1701. [PMID: 34370862 DOI: 10.1093/pcp/pcab124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Male sterility, as a common reproductive characteristic in plants, plays an important role in breeding, in which pollen abortion is a key factor leading to male sterility. Here, based on a low expression level gene CmACOS5 in transcriptome of pollen abortive chrysanthemum, a new transcription factor CmLBD2 of the Lateral Organ Boundaries Domain family, which could bind the promoter of CmACOS5 by yeast one-hybrid library was screened. This study revealed the origin and expression pattern of CmLBD2 in chrysanthemum and verified the functions of two genes in pollen development by transgenic means. Inhibiting the expression of CmACOS5 or CmLBD2 can lead to a large reduction in pollen and even abortion in chrysanthemum. Using yeast one-/two-hybrid, electrophoretic mobility shift assays, and luciferase reporter assays, it was verified that CmLBD2 directly binds to the promoter of CmACOS5. These results suggest that LBD2 is a novel, key transcription factor regulating pollen development. This result will provide a new research background for enriching the function of LBD family proteins and also lay a new foundation for the breeding of male sterile lines and the mechanism of pollen development.
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Affiliation(s)
- Renda Teng
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Ze Wu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Sujuan Xu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Huizhong Hou
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Dehua Zhang
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Fadi Chen
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Nianjun Teng
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
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Expression Patterns and Regulation of Non-Coding RNAs during Synthesis of Cellulose in Eucalyptus grandis Hill. FORESTS 2021. [DOI: 10.3390/f12111565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cellulose, an essential structural component in the plant cell wall and a renewable biomass resource, plays a significant role in nature. Eucalyptus’s excellent timber tree species (including Eucalyptus grandis Hill) provide many raw materials for the paper and wood industries. The synthesis of cellulose is a very complex process involving multiple genes and regulated by various biological networks. However, research on regulating associated genes and non-coding RNAs during cellulose synthesis in E. grandis remains lacking. In this study, the wood anatomical characteristics and chemical indexes of E. grandis were analyzed by taking three different parts (diameter at breast height (DBH), middle and upper part of the trunk) from the main stem of E. grandis as raw materials. The role of non-coding RNAs (Long non-coding RNA, lncRNA; Micro RNA, miRNA; Circle RNA, circRNA) on regulating candidate genes was presented, and the network map of ceRNA (Competing endogenous RNA) regulation during wood cellulose biosynthesis of E. grandis was constructed. The transcriptome sequencing of nine samples obtained from the trunk of the immature xylem in E. grandis at DBH, middle and upper parts had a 95.81 G clean reading, 57,480 transcripts, 7365 lncRNAs, and 5180 circRNAs. Each sample had 172–306 known miRNAs and 1644–3508 new miRNAs. A total of 190 DE-lncRNAs (Differentially expressed long non-coding RNAs), 174 DE-miRNAs (Differentially expressed micro RNAs), and 270 DE-circRNAs (Differentially expressed circle RNAs) were obtained by comparing transcript expression levels. Four lncRNAs and nine miRNAs were screened out, and the ceRNA regulatory network was constructed. LncRNA1 and lncRNA4 regulated the genes responsible for cellulose synthesis in E. grandis, which were overexpressed in 84K (Populus Alba × Populus glandulosa) poplar. The cellulose and lignin content in lncRNA4-oe were significantly higher than wild type 84K poplar and lncRNA1-oe. The average plant height, middle and basal part of the stem diameter in lncRNA4-oe were significantly higher than the wild type. However, there was no significant difference between the growth of lncRNA1-oe and the wild type. Further studies are warranted to explore the molecular regulatory mechanism of cellulose biosynthesis in Eucalyptus species.
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Han Z, Yang T, Guo Y, Cui WH, Yao LJ, Li G, Wu AM, Li JH, Liu LJ. The transcription factor PagLBD3 contributes to the regulation of secondary growth in Populus. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7092-7106. [PMID: 34313722 DOI: 10.1093/jxb/erab351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
LATERAL ORGAN BOUNDARIES DOMAIN (LBD) genes encode plant-specific transcription factors that participate in regulating various developmental processes. In this study, we genetically characterized PagLBD3 encoding an important regulator of secondary growth in poplar (Populus alba × Populus glandulosa). Overexpression of PagLBD3 increased stem secondary growth in Populus with a significantly higher rate of cambial cell differentiation into phloem, while dominant repression of PagLBD3 significantly decreased the rate of cambial cell differentiation into phloem. Furthermore, we identified 1756 PagLBD3 genome-wide putative direct target genes (DTGs) through RNA sequencing (RNA-seq)-coupled DNA affinity purification followed by sequencing (DAP-seq) assays. Gene Ontology analysis revealed that genes regulated by PagLBD3 were enriched in biological pathways regulating meristem development, xylem development, and auxin transport. Several central regulator genes for vascular development, including PHLOEM INTERCALATED WITH XYLEM (PXY), WUSCHEL RELATED HOMEOBOX4 (WOX4), Secondary Wall-Associated NAC Domain 1s (SND1-B2), and Vascular-Related NAC-Domain 6s (VND6-B1), were identified as PagLBD3 DTGs. Together, our results indicate that PagLBD3 and its DTGs form a complex transcriptional network to modulate cambium activity and phloem/xylem differentiation.
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Affiliation(s)
- Zhen Han
- College of Forestry, State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Tong Yang
- College of Forestry, State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Ying Guo
- College of Forestry, State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Wen-Hui Cui
- College of Forestry, State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Li-Juan Yao
- College of Forestry, State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Gang Li
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Ji-Hong Li
- College of Forestry, State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Li-Jun Liu
- College of Forestry, State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, Shandong Agriculture University, Taian, Shandong 271018, China
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Kunej U, Jakše J, Radišek S, Štajner N. Identification and Characterization of Verticillium nonalfalfae-Responsive MicroRNAs in the Roots of Resistant and Susceptible Hop Cultivars. PLANTS (BASEL, SWITZERLAND) 2021; 10:1883. [PMID: 34579416 PMCID: PMC8471970 DOI: 10.3390/plants10091883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
MicroRNAs are 21- to 24-nucleotide-long, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. They can modulate various biological processes, including plant response and resistance to fungal pathogens. Hops are grown for use in the brewing industry and, recently, also for the pharmaceutical industry. Severe Verticillium wilt caused by the phytopathogenic fungus Verticillium nonalfalfae, is the main factor in yield loss in many crops, including hops (Humulus lupulus L.). In our study, we identified 56 known and 43 novel miRNAs and their expression patterns in the roots of susceptible and resistant hop cultivars after inoculation with V. nonalfalfae. In response to inoculation with V. nonalfalfae, we found five known and two novel miRNAs that are differentially expressed in the susceptible cultivar and six known miRNAs in the resistant cultivar. Differentially expressed miRNAs target 49 transcripts involved in protein localization and pigment synthesis in the susceptible cultivar, whereas they are involved in transcription factor regulation and hormone signalling in the resistant cultivar. The results of our study suggest that the susceptible and resistant hop cultivars respond differently to V. nonalfalfae inoculation at the miRNA level and that miRNAs may contribute to the successful defence of the resistant cultivar.
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Affiliation(s)
- Urban Kunej
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Sebastjan Radišek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, 3310 Žalec, Slovenia;
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
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Xu J, Hu P, Tao Y, Song P, Gao H, Guan Y. Genome-wide identification and characterization of the Lateral Organ Boundaries Domain ( LBD) gene family in polyploid wheat and related species. PeerJ 2021; 9:e11811. [PMID: 34447619 PMCID: PMC8364319 DOI: 10.7717/peerj.11811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/27/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. METHODS Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a-e, II a and II b). RESULTS The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.
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Affiliation(s)
- Jun Xu
- Henan Institute of Science and Technology, Xinxiang, China
| | - Ping Hu
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Ye Tao
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Puwen Song
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Huanting Gao
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Yuanyuan Guan
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
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Marcianò D, Ricciardi V, Marone Fassolo E, Passera A, Bianco PA, Failla O, Casati P, Maddalena G, De Lorenzis G, Toffolatti SL. RNAi of a Putative Grapevine Susceptibility Gene as a Possible Downy Mildew Control Strategy. FRONTIERS IN PLANT SCIENCE 2021; 12:667319. [PMID: 34127927 PMCID: PMC8196239 DOI: 10.3389/fpls.2021.667319] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/20/2021] [Indexed: 05/07/2023]
Abstract
Downy mildew, caused by the oomycete Plasmopara viticola, is one of the diseases causing the most severe economic losses to grapevine (Vitis vinifera) production. To date, the application of fungicides is the most efficient method to control the pathogen and the implementation of novel and sustainable disease control methods is a major challenge. RNA interference (RNAi) represents a novel biotechnological tool with a great potential for controlling fungal pathogens. Recently, a candidate susceptibility gene (VviLBDIf7) to downy mildew has been identified in V. vinifera. In this work, the efficacy of RNAi triggered by exogenous double-stranded RNA (dsRNA) in controlling P. viticola infections has been assessed in a highly susceptible grapevine cultivar (Pinot noir) by knocking down VviLBDIf7 gene. The effects of dsRNA treatment on this target gene were assessed by evaluating gene expression, disease severity, and development of vegetative and reproductive structures of P. viticola in the leaf tissues. Furthermore, the effects of dsRNA treatment on off-target (EF1α, GAPDH, PEPC, and PEPCK) and jasmonic acid metabolism (COI1) genes have been evaluated. Exogenous application of dsRNA led to significant reductions both in VviLBDIf7 gene expression, 5 days after the treatment, and in the disease severity when artificial inoculation was carried out 7 days after dsRNA treatments. The pathogen showed clear alterations to both vegetative (hyphae and haustoria) and reproductive structures (sporangiophores) that resulted in stunted growth and reduced sporulation. Treatment with dsRNA showed signatures of systemic activity and no deleterious off-target effects. These results demonstrated the potential of RNAi for silencing susceptibility factors in grapevine as a sustainable strategy for pathogen control, underlying the possibility to adopt this promising biotechnological tool in disease management strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Silvia Laura Toffolatti
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy
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Wang H, Xie Y, Liu W, Tao G, Sun C, Sun X, Zhang S. Transcription factor LkWOX4 is involved in adventitious root development in Larix kaempferi. Gene 2020; 758:144942. [PMID: 32640309 DOI: 10.1016/j.gene.2020.144942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 06/20/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
WUSCHEL-related homeobox4 (WOX4) plays important roles in vascular formation and adventitious root (AR) development. Here, we cloned the WOX4 from the AR of Larix kaempferi, whose cDNA is 1452 bp in length and encodes 483 amino acids. LkWOX4 is mainly expressed in the layer formation area of the stem at 10 days after cutting and its expression levels in the middles and ends of the ARs were higher than that in the AR tips. The fused protein LkWOX4-GFP localized in the nucleus. The heterologous overexpression of LkWOX4 in 84 K poplar significantly increased AR numbers and decreased AR lengths. In LkWOX4 plants, the endogenous jasmonic acid and abscisic acid contents significantly decreased in stems, while the auxin, jasmonic acid and abscisic acid contents significantly increased in ARs. RNA-Seq of those LkWOX4 overexpression poplar plants showed that the expression of plant hormone signaling genes (ARF2, ARF3, ARF7 and ARF18), rooting-related transcription factors (WOX5, LBD29 and SCR) and root development-related genes (CYCD3, GRF1 and TAA1) were affected. Moreover, we found that LkWOX4 interacts with LkPAT18, LkACBP6, and LkCIP7 using yeast two hybrid screening. Thus, we found LkWOX4 involves in the AR initiation and development, which might be regulated through the IAA, JA and ABA signaling pathways.
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Affiliation(s)
- Hongming Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; College of Bioengineering and Biotechnology, Tianshui Normal University, Gansu 741000, China
| | - Yunhui Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh 27695, USA
| | - Guiyun Tao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xiaomei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
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Huang X, Yan H, Liu Y, Yi Y. Genome-wide analysis of LATERAL ORGAN BOUNDARIES DOMAIN-in Physcomitrella patens and stress responses. Genes Genomics 2020; 42:651-662. [PMID: 32279230 DOI: 10.1007/s13258-020-00931-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/31/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND LBDs, as the plant-specific gene family, play essential roles in lateral organ development, plant regeneration, as well as abiotic stress and pathogen response. However, the number and characteristic of LBD genes in Pyscomitrella patens were still obscure. OBJECTIVE This study was performed to identify the LBD family gene in moss and to determine the expression profiles of LBDs under the abiotic and pathogen stress. METHODS Complete genome sequences and transcriptomes of P. patens were downloaded from the Ensembl plant database. The hidden Markov model-based profile of the conserved LOB domain was submitted as a query to identify all potential LOB domain sequences with HMMER software. Expression profiles of PpLBDs were obtained based on the GEO public database and qRT-PCR analysis. RESULTS In this study, a total of 31 LBDs were identified in the P. patens genome, divided into two classes based on the presence of the leucine zipper-like coiled-coil motif. A phylogenetic relationship was obtained between 31 proteins from P. patens and 43 proteins from the Arabidopsis thaliana genome, providing insights into their conserved and potential functions. Furthermore, the exon-intron organization of each PpLBD were analyzed. All PpLBD contain the conserved DNA binding motif (CX2CX6CX3C zinc finger-like motif), and were predicted to be located in cell nuclear. The 31 PpLBD genes were unevenly assigned to 18 out of 27 chromosomes based on the physical positions. Among these genes, PpLBD27 was not only remarkably highest expressed in desiccation, but also a susceptible gene to pathogens through jasmonic acid-mediated signaling pathway. Most of PpLBDs were up-regulated with the treatment of mannitol. These results showed they were differentially induced and their potential functions in the environmental stimulus of the early terrestrial colonizers. CONCLUSION Despite significant differences in the life cycle in P. patens and flowering plants, their functions involved in abiotic and biotic stress-regulated by LBDs have been identified and appear to be conserved in the two lineages. These results provided a comprehensive analysis of PpLBDs and paved insights into studies aimed at a better understanding of PpLBDs.
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Affiliation(s)
- Xiaolong Huang
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Mountainous Karst Area of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
- School of Life Sciences, Guizhou Normal University, Huaxi District, Guiyang, 550001, Guizhou, China
| | - Huiqing Yan
- School of Life Sciences, Guizhou Normal University, Huaxi District, Guiyang, 550001, Guizhou, China.
| | - Yanjing Liu
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Mountainous Karst Area of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
- School of Life Sciences, Guizhou Normal University, Huaxi District, Guiyang, 550001, Guizhou, China
| | - Yin Yi
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Mountainous Karst Area of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
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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: 34] [Impact Index Per Article: 8.5] [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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Yu J, Xie Q, Li C, Dong Y, Zhu S, Chen J. Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium. PLANTA 2020; 251:81. [PMID: 32185507 DOI: 10.1007/s00425-020-03364-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/13/2020] [Indexed: 05/16/2023]
Abstract
A comprehensive account of the LBD gene family of Gossypium was provided in this work. Expression analysis and functional characterization revealed that LBD genes might play different roles in G. hirsutum and G. barbadense. The Lateral Organ Boundaries Domain (LBD) proteins comprise a plant-specific transcription factor family, which plays crucial roles in physiological processes of plant growth, development, and stress tolerance. In the present work, a systematical analysis of LBD gene family from two allotetraploid cotton species, G. hirsutum and G. barbadense, together with their genomic donor species, G. arboreum and G. raimondii, was conducted. There were 131, 128, 62, and 68 LBDs identified in G. hirsutum, G. barbadense, G. arboreum and G. raimondii, respectively. The LBD proteins could be classified into two main classes, class I and class II, based on the structure of their lateral organ boundaries domain and traits of phylogenetic tree, and class I was further divided into five subgroups. The gene structure and motif composition analyses conducted in both G. hirsutum and G. barbadense revealed that LBD genes kept relatively conserved within the subfamilies. Synteny analysis suggested that segmental duplication acted as an important mechanism in expansion of the cotton LBD gene family. Cis-element analysis predicated the possible functions of LBD genes. Public RNA-seq data were investigated to analyze the expression patterns of cotton LBD genes in various tissues as well as gene expression under abiotic stress treatments. Furthermore, RT-qPCR results found that GhLBDs had various expression regulation under MeJA treatments. Expression analysis indicated the differential functions of cotton LBD genes in response to abiotic stress and hormones.
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Affiliation(s)
- Jingwen Yu
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qianwen Xie
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Li
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yating Dong
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shuijin Zhu
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Jinhong Chen
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Lu J, Liu JN, Sarsaiya S, Duns GJ, Han J, Jin L, Chen J. Phenotypic and Transcriptomic Analysis of Two Pinellia ternata Varieties T2 line and T2Plus line. Sci Rep 2020; 10:4614. [PMID: 32165650 PMCID: PMC7067869 DOI: 10.1038/s41598-020-61512-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/21/2020] [Indexed: 11/09/2022] Open
Abstract
Pinellia (Pinellia ternata (Thunb.) Breit.), as important medicinal plant, has been used to treat various ailments for a long time. The sixteen ploid plant (2n = 16 * 13 = 208) Pinellia T2Plus line was obtained from an octoploid (2n = 8 * 13 = 104) T2 line by chromosome-doubling technique. Compared with T2 line, the content of various medicinal components (polysaccharide, guanosine, adenosine and ephedrine) was increased in T2Plus line. In this study, the transcriptome of T2 line and T2Plus line were characterized by RNA sequencing (RNA-seq) technology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis on differential expressed unigenes (DEGs) revealed that multiple metabolic pathway were enriched significantly, such as 'Starch and sucrose metabolism', 'Purine metabolism', 'Photosynthesis' and six transcription factors (MYB, WRKY, bHLH, lateral organ boundaries domain (LBD), homeodomain-zipper (HD-ZIP) and Ethylene-responsive factor (ERF)) play a key role in difference of transcriptome between T2 line and T2Plus line. These metabolic pathways and transcription factors may play an important role in the difference of medicinal components and epigenetic features between these two Pinellia cultivars. This conclusion provides a robust theoretical basis for the mechanism of the formation of medicinal ingredients in Pinellia cultivars.
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Affiliation(s)
- Jun Lu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Jiangsu, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Jian Ning Liu
- KeGene Science & Technology Co. Ltd., Nantianmen Middle Road, Tai'an, 271018, China
| | - Surendra Sarsaiya
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Gregory Joseph Duns
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Jiangsu, China
- AirChem Consulting and Research, London, Ontario, N5X OE2, Canada
| | - Jing Han
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Jiangsu, China
| | - Leilei Jin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Jiangsu, China
| | - Jishuang Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Jiangsu, China.
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, 563000, Guizhou, China.
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Xie T, Zeng L, Chen X, Rong H, Wu J, Batley J, Jiang J, Wang Y. Genome-Wide Analysis of the Lateral Organ Boundaries Domain Gene Family in Brassica Napus. Genes (Basel) 2020; 11:genes11030280. [PMID: 32155746 PMCID: PMC7140802 DOI: 10.3390/genes11030280] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 02/08/2023] Open
Abstract
The plant specific LATERAL ORGAN BOUNDARIES (LOB)-domain (LBD) proteins belong to a family of transcription factors that play important roles in plant growth and development, as well as in responses to various stresses. However, a comprehensive study of LBDs in Brassica napus has not yet been reported. In the present study, 126 BnLBD genes were identified in B. napus genome using bioinformatics analyses. The 126 BnLBDs were phylogenetically classified into two groups and nine subgroups. Evolutionary analysis indicated that whole genome duplication (WGD) and segmental duplication played important roles in the expansion of the BnLBD gene family. On the basis of the RNA-seq analyses, we identified BnLBD genes with tissue or developmental specific expression patterns. Through cis-acting element analysis and hormone treatment, we identified 19 BnLBD genes with putative functions in plant response to abscisic acid (ABA) treatment. This study provides a comprehensive understanding on the origin and evolutionary history of LBDs in B. napus, and will be helpful in further functional characterisation of BnLBDs.
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Affiliation(s)
- Tao Xie
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (L.Z.); (X.C.); (H.R.); (J.W.); (Y.W.)
| | - Lei Zeng
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (L.Z.); (X.C.); (H.R.); (J.W.); (Y.W.)
| | - Xin Chen
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (L.Z.); (X.C.); (H.R.); (J.W.); (Y.W.)
| | - Hao Rong
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (L.Z.); (X.C.); (H.R.); (J.W.); (Y.W.)
| | - Jingjing Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (L.Z.); (X.C.); (H.R.); (J.W.); (Y.W.)
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia;
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (L.Z.); (X.C.); (H.R.); (J.W.); (Y.W.)
- Correspondence: ; Tel.: +86-514-87997303
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (L.Z.); (X.C.); (H.R.); (J.W.); (Y.W.)
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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: 2] [Impact Index Per Article: 0.5] [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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Zhang L, Sun X, Wilson IW, Shao F, Qiu D. Identification of the Genes Involved in Anthocyanin Biosynthesis and Accumulation in Taxus chinensis. Genes (Basel) 2019; 10:E982. [PMID: 31795268 PMCID: PMC6947853 DOI: 10.3390/genes10120982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 01/04/2023] Open
Abstract
Taxus chinensis is a precious woody species with significant economic value. Anthocyanin as flavonoid derivatives plays a crucial role in plant biology and human health. However, the genes involved in anthocyanin biosynthesis have not been identified in T. chinensis. In this study, twenty-five genes involved in anthocyanin biosynthesis were identified, including chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, anthocyanidin synthase, flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase, dihydroflavonol 4-reductase, anthocyanidin reductase, and leucoanthocyanidin reductase. The conserved domains and phylogenetic relationships of these genes were characterized. The expression levels of these genes in different tissues and different ages of xylem were investigated. Additionally, the anthocyanin accumulation in xylem of different ages of T. chinensis was measured. The results showed the anthocyanin accumulation was correlated with the expression levels of dihydroflavonol 4-reductase, anthocyanidin synthase, flavonoid 3'-hydroxylase, and flavonoid 3',5'-hydroxylase. Our results provide a basis for studying the regulation of the biosynthetic pathway for anthocyanins and wood color formation in T. chinensis.
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Affiliation(s)
- Lisha Zhang
- State Key Laboratory of Tree Genetics and Breeding &Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (L.Z.); (X.S.); (D.Q.)
| | - Xiaomei Sun
- State Key Laboratory of Tree Genetics and Breeding &Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (L.Z.); (X.S.); (D.Q.)
| | - Iain W. Wilson
- CSIRO Agriculture and Food, P.O. Box 1600, Canberra, ACT 2601, Australia;
| | - Fenjuan Shao
- State Key Laboratory of Tree Genetics and Breeding &Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (L.Z.); (X.S.); (D.Q.)
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding &Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (L.Z.); (X.S.); (D.Q.)
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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: 18] [Impact Index Per Article: 3.6] [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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Yue H, Chang X, Zhi Y, Wang L, Xing G, Song W, Nie X. Evolution and Identification of the WRKY Gene Family in Quinoa ( Chenopodium quinoa). Genes (Basel) 2019; 10:genes10020131. [PMID: 30754717 PMCID: PMC6409747 DOI: 10.3390/genes10020131] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/26/2019] [Accepted: 01/28/2019] [Indexed: 12/02/2022] Open
Abstract
The WRKY gene family plays a unique role in plant stress tolerance. Quinoa is a cultivated crop worldwide that is known for its high stress tolerance. The WRKY gene family in quinoa has not yet been studied. Using a genome-wide search method, we identified 1226 WRKY genes in 15 plant species, seven animal species, and seven fungi species. WRKY proteins were not found in animal species and five fungi species, but were, however, widespread in land plants. A total of 92 CqWRKY genes were identified in quinoa. Based on the phylogenetic analysis, these CqWRKY genes were classified into three groups. The CqWRKY proteins have a highly conserved heptapeptide WRKYGQK with 15 conserved elements. Furthermore, a total of 25 CqWRKY genes were involved in the co-expression pathway of organ development and osmotic stress. The expression level of more than half of these CqWRKY genes showed significant variation under salt or drought stress. This study reports, for the first time, the findings of the CqWRKY gene family in quinoa at the genome-wide level. This information will be beneficial for our understanding of the molecular mechanisms of stress tolerance in crops, such as quinoa.
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Affiliation(s)
- Hong Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
- College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xi Chang
- Xizang Agriculture and Animal Husbandry College, Linzhi 860000, Xizang, China.
| | - Yongqiang Zhi
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Guangwei Xing
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Shao F, Zhang L, Wilson IW, Qiu D. Transcriptomic Analysis of Betula halophila in Response to Salt Stress. Int J Mol Sci 2018; 19:ijms19113412. [PMID: 30384437 PMCID: PMC6274945 DOI: 10.3390/ijms19113412] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 01/30/2023] Open
Abstract
Soil salinization is a matter of concern worldwide. It can eventually lead to the desertification of land and severely damage local agricultural production and the ecological environment. Betula halophila is a tree with high salt tolerance, so it is of importance to understand and discover the salt responsive genes of B. halophila for breeding salinity resistant varieties of trees. However, there is no report on the transcriptome in response to salt stress in B. halophila. Using Illumina sequencing platform, approximately 460 M raw reads were generated and assembled into 117,091 unigenes. Among these unigenes, 64,551 unigenes (55.12%) were annotated with gene descriptions, while the other 44.88% were unknown. 168 up-regulated genes and 351 down-regulated genes were identified, respectively. These Differentially Expressed Genes (DEGs) involved in multiple pathways including the Salt Overly Sensitive (SOS) pathway, ion transport and uptake, antioxidant enzyme, ABA signal pathway and so on. The gene ontology (GO) enrichments suggested that the DEGs were mainly involved in a plant-type cell wall organization biological process, cell wall cellular component, and structural constituent of cell wall molecular function. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment showed that the top-four enriched pathways were 'Fatty acid elongation', 'Ribosome', 'Sphingolipid metabolism' and 'Flavonoid biosynthesis'. The expression patterns of sixteen DEGs were analyzed by qRT-PCR to verify the RNA-seq data. Among them, the transcription factor AT-Hook Motif Nuclear Localized gene and dehydrins might play an important role in response to salt stress in B. halophila. Our results provide an important gene resource to breed salt tolerant plants and useful information for further elucidation of the molecular mechanism of salt tolerance in B. halophila.
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Affiliation(s)
- Fenjuan Shao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Lisha Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Iain W Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
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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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