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Li D, Fan L, Shu Q, Guo F. Ectopic expression of OsWOX9A alters leaf anatomy and plant architecture in rice. PLANTA 2024; 260:30. [PMID: 38879830 DOI: 10.1007/s00425-024-04463-6] [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: 03/09/2024] [Accepted: 06/09/2024] [Indexed: 07/03/2024]
Abstract
MAIN CONCLUSION Ectopic expression of OsWOX9A induces narrow adaxially rolled rice leaves with larger bulliform cells and fewer large veins, probably through regulating the expression of auxin-related and expansin genes. The WUSCHEL-related homeobox (WOX) family plays a pivotal role in plant development by regulating genes involved in various aspects of growth and differentiation. OsWOX9A (DWT1) has been linked to tiller growth, uniform plant growth, and flower meristem activity. However, its impact on leaf growth and development in rice has not been studied. In this study, we investigated the biological role of OsWOX9A in rice growth and development using transgenic plants. Overexpression of OsWOX9A conferred narrow adaxially rolled rice leaves and altered plant architecture. These plants exhibited larger bulliform cells and fewer larger veins compared to wild-type plants. OsWOX9A overexpression also reduced plant height, tiller number, and seed-setting rate. Comparative transcriptome analysis revealed several differentially expressed auxin-related and expansin genes in OsWOX9A overexpressing plants, consistent with their roles in leaf and plant development. These results indicate that the ectopic expression of OsWOX9A may have multiple effects on the development and growth of rice, providing a more comprehensive picture of how the WOX9 subfamily contributes to leaf development and plant architecture.
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Affiliation(s)
- Dandan Li
- Hainan Institute, Yazhou Bay Science and Technology City, Zhejiang University, Sanya, 572025, China
| | - Longjiang Fan
- Hainan Institute, Yazhou Bay Science and Technology City, Zhejiang University, Sanya, 572025, China
| | - Qingyao Shu
- Hainan Institute, Yazhou Bay Science and Technology City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fu Guo
- Hainan Institute, Yazhou Bay Science and Technology City, Zhejiang University, Sanya, 572025, China.
- Hainan Seed Industry Laboratory, Yazhou Bay Science and Technology City, Sanya, 572025, China.
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Wang Y, Yang L, Geng W, Cheng R, Zhang H, Zhou H. Genome-wide prediction and functional analysis of WOX genes in blueberry. BMC Genomics 2024; 25:434. [PMID: 38693497 PMCID: PMC11064388 DOI: 10.1186/s12864-024-10356-5] [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: 11/02/2023] [Accepted: 04/26/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND WOX genes are a class of plant-specific transcription factors. The WUSCHEL-related homeobox (WOX) family is a member of the homeobox transcription factor superfamily. Previous studies have shown that WOX members play important roles in plant growth and development. However, studies of the WOX gene family in blueberry plants have not been reported. RESULTS In order to understand the biological function of the WOX gene family in blueberries, bioinformatics were used methods to identify WOX gene family members in the blueberry genome, and analyzed the basic physical and chemical properties, gene structure, gene motifs, promoter cis-acting elements, chromosome location, evolutionary relationships, expression pattern of these family members and predicted their functions. Finally, 12 genes containing the WOX domain were identified and found to be distributed on eight chromosomes. Phylogenetic tree analysis showed that the blueberry WOX gene family had three major branches: ancient branch, middle branch, and WUS branch. Blueberry WOX gene family protein sequences differ in amino acid number, molecular weight, isoelectric point and hydrophobicity. Predictive analysis of promoter cis-acting elements showed that the promoters of the VdWOX genes contained abundant light response, hormone, and stress response elements. The VdWOX genes were induced to express in both stems and leaves in response to salt and drought stress. CONCLUSIONS Our results provided comprehensive characteristics of the WOX gene family and important clues for further exploration of its role in the growth, development and resistance to various stress in blueberry plants.
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Affiliation(s)
- Yanwen Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, 264025, Shandong, China
| | - Lei Yang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, 264025, Shandong, China.
- Bestplant (Shandong) Stem Cell Engineering Co., Ltd, 300 Changjiang Road, Yantai, 264001, Shandong, China.
| | - Wenzhu Geng
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, 264025, Shandong, China
| | - Rui Cheng
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, 264025, Shandong, China
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, 264025, Shandong, China.
- Bestplant (Shandong) Stem Cell Engineering Co., Ltd, 300 Changjiang Road, Yantai, 264001, Shandong, China.
| | - Houjun Zhou
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, 264025, Shandong, China.
- Bestplant (Shandong) Stem Cell Engineering Co., Ltd, 300 Changjiang Road, Yantai, 264001, Shandong, China.
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Kaur H, Manchanda P, Sidhu GS, Chhuneja P. Genome-wide identification and characterization of flowering genes in Citrus sinensis (L.) Osbeck: a comparison among C. Medica L., C. Reticulata Blanco, C. Grandis (L.) Osbeck and C. Clementina. BMC Genom Data 2024; 25:20. [PMID: 38378481 PMCID: PMC10880302 DOI: 10.1186/s12863-024-01201-5] [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: 03/02/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Flowering plays an important role in completing the reproductive cycle of plants and obtaining next generation of plants. In case of citrus, it may take more than a year to achieve progeny. Therefore, in order to fasten the breeding processes, the juvenility period needs to be reduced. The juvenility in plants is regulated by set of various flowering genes. The citrus fruit and leaves possess various medicinal properties and are subjected to intensive breeding programs to produce hybrids with improved quality traits. In order to break juvenility in Citrus, it is important to study the role of flowering genes. The present study involved identification of genes regulating flowering in Citrus sinensis L. Osbeck via homology based approach. The structural and functional characterization of these genes would help in targeting genome editing techniques to induce mutations in these genes for producing desirable results. RESULTS A total of 43 genes were identified which were located on all the 9 chromosomes of citrus. The in-silico analysis was performed to determine the genetic structure, conserved motifs, cis-regulatory elements (CREs) and phylogenetic relationship of the genes. A total of 10 CREs responsible for flowering were detected in 33 genes and 8 conserved motifs were identified in all the genes. The protein structure, protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed to study the functioning of these genes which revealed the involvement of flowering proteins in circadian rhythm pathways. The gene ontology (GO) and gene function analysis was performed to functionally annotate the genes. The structure of the genes and proteins were also compared among other Citrus species to study the evolutionary relationship among them. The expression study revealed the expression of flowering genes in floral buds and ovaries. The qRT-PCR analysis revealed that the flowering genes were highly expressed in bud stage, fully grown flower and early stage of fruit development. CONCLUSIONS The findings suggested that the flowering genes were highly conserved in citrus species. The qRT-PCR analysis revealed the tissue specific expression of flowering genes (CsFT, CsCO, CsSOC, CsAP, CsSEP and CsLFY) which would help in easy detection and targeting of genes through various forward and reverse genetic approaches.
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Affiliation(s)
- Harleen Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141001, Punjab, India
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141001, Punjab, India.
| | - Gurupkar S Sidhu
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141001, Punjab, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141001, Punjab, India
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Xu A, Yang J, Wang S, Zheng L, Wang J, Zhang Y, Bi X, Wang H. Characterization and expression profiles of WUSCHEL-related homeobox (WOX) gene family in cultivated alfalfa (Medicago sativa L.). BMC PLANT BIOLOGY 2023; 23:471. [PMID: 37803258 PMCID: PMC10557229 DOI: 10.1186/s12870-023-04476-5] [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: 04/05/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
The WUSCHEL-related homeobox (WOX) family members are plant-specific transcriptional factors, which function in meristem maintenance, embryogenesis, lateral organ development, as well as abiotic stress tolerance. In this study, 14 MsWOX transcription factors were identified and comprehensively analyzed in the cultivated alfalfa cv. Zhongmu No.1. Overall, 14 putative MsWOX members containing conserved structural regions were clustered into three clades according to phylogenetic analysis. Specific expression patterns of MsWOXs in different tissues at different levels indicated that the MsWOX genes play various roles in alfalfa. MsWUS, MsWOX3, MsWOX9, and MsWOX13-1 from the three subclades were localized in the nucleus, among which, MsWUS and MsWOX13-1 exhibited strong self-activations in yeast. In addition, various cis-acting elements related to hormone responses, plant growth, and stress responses were identified in the 3.0 kb promoter regions of MsWOXs. Expression detection of separated shoots and roots under hormones including auxin, cytokinin, GA, and ABA, as well as drought and cold stresses, showed that MsWOX genes respond to different hormones and abiotic stress treatments. Furthermore, transcript abundance of MsWOX3, and MsWOX13-2 were significantly increased after rhizobia inoculation. This study presented comprehensive data on MsWOX transcription factors and provided valuable insights into further studies of their roles in developmental processes and abiotic stress responses in alfalfa.
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Affiliation(s)
- Aijiao Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jiaqi Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Siqi Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lin Zheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Jing Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yunwei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xiaojing Bi
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Hui Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Singh V, Gupta K, Singh S, Jain M, Garg R. Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1156606. [PMID: 37287713 PMCID: PMC10242046 DOI: 10.3389/fpls.2023.1156606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/18/2023] [Indexed: 06/09/2023]
Abstract
Drought stress affects growth and productivity significantly in chickpea. An integrated multi-omics analysis can provide a better molecular-level understanding of drought stress tolerance. In the present study, comparative transcriptome, proteome and metabolome analyses of two chickpea genotypes with contrasting responses to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), was performed to gain insights into the molecular mechanisms underlying drought stress response/tolerance. Pathway enrichment analysis of differentially abundant transcripts and proteins suggested the involvement of glycolysis/gluconeogenesis, galactose metabolism, and starch and sucrose metabolism in the DT genotype. An integrated multi-omics analysis of transcriptome, proteome and metabolome data revealed co-expressed genes, proteins and metabolites involved in phosphatidylinositol signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways, specifically in the DT genotype under drought. These stress-responsive pathways were coordinately regulated by the differentially abundant transcripts, proteins and metabolites to circumvent the drought stress response/tolerance in the DT genotype. The QTL-hotspot associated genes, proteins and transcription factors may further contribute to improved drought tolerance in the DT genotype. Altogether, the multi-omics approach provided an in-depth understanding of stress-responsive pathways and candidate genes involved in drought tolerance in chickpea.
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Affiliation(s)
- Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Khushboo Gupta
- Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Shubhangi Singh
- Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
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Muhammad Tajo S, Pan Z, He S, Chen B, KM Y, Mahmood T, Bello Sadau S, Shahid Iqbal M, Gereziher T, Suleiman Abubakar U, Joseph M, Sammani T, Geng X, Du X. Characterization of WOX genes revealed drought tolerance, callus induction, and tissue regeneration in Gossypium hirsutum. Front Genet 2022; 13:928055. [PMCID: PMC9597092 DOI: 10.3389/fgene.2022.928055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Cotton is an important natural fiber crop; its seeds are the main oil source. Abiotic stresses cause a significant decline in its production. The WUSCHEL-related Homeobox (WOX) genes have been involved in plant growth, development, and stress responses. However, the functions of WOX genes are less known in cotton. This study identified 39, 40, 21, and 20 WOX genes in Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum, and Gossypium raimondii, respectively. All the WOX genes in four cotton species could be classified into three clades, which is consistent with previous research. The gene structure and conserved domain of all WOX genes were analyzed. The expressions of WOX genes in germinating hypocotyls and callus were characterized, and it was found that most genes were up-regulated. One candidate gene Gh_ A01G127500 was selected to perform the virus-induced gene silencing (VIGS) experiment, and it was found that the growth of the silenced plant (pCLCrVA: GhWOX4_A01) was significantly inhibited compared with the wild type. In the silenced plant, there is an increase in antioxidant activities and a decrease in oxidant activities compared with the control plant. In physiological analysis, the relative electrolyte leakage level and the excised leaf water loss of the infected plant were increased. Still, both the relative leaf water content and the chlorophyll content were decreased. This study proved that WOX genes play important roles in drought stress and callus induction, but more work must be performed to address the molecular functions of WOX genes.
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Affiliation(s)
- Sani Muhammad Tajo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Bioresources Development Centre, National Biotechnology Development Agency, Abuja, Nigeria
| | - Zhaoe Pan
- *Correspondence: Xiaoli Geng, ; Xiongming Du,
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Yusuf KM
- Bioresources Development Centre, National Biotechnology Development Agency, Abuja, Nigeria
| | - Tahir Mahmood
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Salisu Bello Sadau
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Shahid Iqbal
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Teame Gereziher
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Umar Suleiman Abubakar
- Bioresources Development Centre, National Biotechnology Development Agency, Abuja, Nigeria
| | - Masha Joseph
- Bioresources Development Centre, National Biotechnology Development Agency, Abuja, Nigeria
| | - Tajo Sammani
- Department of Agricultural Economics, University of Maiduguri, Maiduguri, Nigeria
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- *Correspondence: Xiaoli Geng, ; Xiongming Du,
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- *Correspondence: Xiaoli Geng, ; Xiongming Du,
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Hu Y, Chen X, Shen X. Regulatory network established by transcription factors transmits drought stress signals in plant. STRESS BIOLOGY 2022; 2:26. [PMID: 37676542 PMCID: PMC10442052 DOI: 10.1007/s44154-022-00048-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/20/2022] [Indexed: 09/08/2023]
Abstract
Plants are sessile organisms that evolve with a flexible signal transduction system in order to rapidly respond to environmental changes. Drought, a common abiotic stress, affects multiple plant developmental processes especially growth. In response to drought stress, an intricate hierarchical regulatory network is established in plant to survive from the extreme environment. The transcriptional regulation carried out by transcription factors (TFs) is the most important step for the establishment of the network. In this review, we summarized almost all the TFs that have been reported to participate in drought tolerance (DT) in plant. Totally 466 TFs from 86 plant species that mostly belong to 11 families are collected here. This demonstrates that TFs in these 11 families are the main transcriptional regulators of plant DT. The regulatory network is built by direct protein-protein interaction or mutual regulation of TFs. TFs receive upstream signals possibly via post-transcriptional regulation and output signals to downstream targets via direct binding to their promoters to regulate gene expression.
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Affiliation(s)
- Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, 443002 Hubei China
| | - Xiaoliang Chen
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, 443002 Hubei China
| | - Xiangling Shen
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, 443002 Hubei China
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Zhang Y, Liu Y, Wang X, Wang R, Chen X, Wang S, Wei H, Wei Z. PtrWOX13A Promotes Wood Formation and Bioactive Gibberellins Biosynthesis in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2022; 13:835035. [PMID: 35837467 PMCID: PMC9274204 DOI: 10.3389/fpls.2022.835035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
WUSCHEL-related homeobox (WOX) genes are plant-specific transcription factors (TFs) involved in multiple processes of plant development. However, there have hitherto no studies on the WOX TFs involved in secondary cell wall (SCW) formation been reported. In this study, we identified a Populus trichocarpa WOX gene, PtrWOX13A, which was predominantly expressed in SCW, and then characterized its functions through generating PtrWOX13A overexpression poplar transgenic lines; these lines exhibited not only significantly enhanced growth potential, but also remarkably increased SCW thicknesses, fiber lengths, and lignin and hemicellulose contents. However, no obvious change in cellulose content was observed. We revealed that PtrWOX13A directly activated its target genes through binding to two cis-elements, ATTGATTG and TTAATSS, in their promoter regions. The fact that PtrWOX13A responded to the exogenous GAs implies that it is responsive to GA homeostasis caused by GA inactivation and activation genes (e.g., PtrGA20ox4, PtrGA2ox1, and PtrGA3ox1), which were regulated by PtrWOX13A directly or indirectly. Since the master switch gene of SCW formation, PtrWND6A, and lignin biosynthesis regulator, MYB28, significantly increased in PtrWOX13A transgenic lines, we proposed that PtrWOX13A, as a higher hierarchy TF, participated in SCW formation through controlling the genes that are components of the known hierarchical transcription regulation network of poplar SCW formation, and simultaneously triggering a gibberellin-mediated signaling cascade. The discovery of PtrWOX13A predominantly expressed in SCW and its regulatory functions in the poplar wood formation has important implications for improving the wood quality of trees via genetic engineering.
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Affiliation(s)
- Yang Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xueying Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xuebing Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shuang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States
| | - Zhigang Wei
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
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9
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Yang T, Gao T, Wang C, Wang X, Chen C, Tian M, Yang W. In silico genome wide identification and expression analysis of the WUSCHEL-related homeobox gene family in Medicago sativa. Genomics Inform 2022; 20:e19. [PMID: 35794699 PMCID: PMC9299560 DOI: 10.5808/gi.22013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/28/2022] [Indexed: 11/20/2022] Open
Abstract
Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.
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Affiliation(s)
- Tianhui Yang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Ting Gao
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Chuang Wang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Xiaochun Wang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Caijin Chen
- Branch Institute of Guyuan, Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 756000, China
| | - Mei Tian
- Institute of Horticultural Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Weidi Yang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
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10
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Mishra M, Rathore RS, Joshi R, Pareek A, Singla-Pareek SL. DTH8 overexpression induces early flowering, boosts yield, and improves stress recovery in rice cv IR64. PHYSIOLOGIA PLANTARUM 2022; 174:e13691. [PMID: 35575899 DOI: 10.1111/ppl.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/17/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Rice yield and heading date are the two discrete traits controlled by quantitative trait loci (QTLs). Both traits are influenced by the genetic make-up of the plant as well as the environmental factors where it thrives. Drought and salinity adversely affect crop productivity in many parts of the world. Tolerance to these stresses is multigenic and complex in nature. In this study, we have characterized a QTL, DTH8 (days to heading) from Oryza sativa L. cv IR64 that encodes a putative HAP3/NF-YB/CBF subunit of CCAAT-box binding protein (HAP complex). We demonstrate DTH8 to be positively influencing the yield, heading date, and stress tolerance in IR64. DTH8 up-regulates the transcription of RFT1, Hd3a, GHD7, MOC1, and RCN1 in IR64 at the pre-flowering stage and plays a role in early flowering, increased number of tillers, enhanced panicle branching, and improved tolerance towards drought and salinity stress at the reproductive stage. The presence of DTH8 binding elements (CCAAT) in the promoter regions of all of these genes, predicted by in silico analysis of the promoter region, indicates the regulation of their expression by DTH8. In addition, DTH8 overexpressing transgenic lines showed favorable physiological parameters causing less yield penalty under stress than the WT plants. Taken together, DTH8 is a positive regulator of the network of genes related to early flowering/heading, higher yield, as well as salinity and drought stress tolerance, thus, enabling the crops to adapt to a wide range of climatic conditions.
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Affiliation(s)
- Manjari Mishra
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ray Singh Rathore
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rohit Joshi
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
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Yan T, Mei C, Song H, Shan D, Sun Y, Hu Z, Wang L, Zhang T, Wang J, Kong J. Potential roles of melatonin and ABA on apple dwarfing in semi-arid area of Xinjiang China. PeerJ 2022; 10:e13008. [PMID: 35382008 PMCID: PMC8977067 DOI: 10.7717/peerj.13008] [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: 09/30/2021] [Accepted: 02/04/2022] [Indexed: 01/11/2023] Open
Abstract
Dwarfing is a typic breeding trait for mechanical strengthening and relatively high yield in modern apple orchards. Clarification of the mechanisms associated with dwarfing is important for use of molecular technology to breed apple. Herein, we identified four dwarfing apple germplasms in semi-arid area of Xinjiang, China. The internodal distance of these four germplasms were significantly shorter than non-dwarfing control. Their high melatonin (MT) contents are negatively associated with their malondialdehyde (MDA) levels and oxidative damage. In addition, among the detected hormones including auxin (IAA), gibberellin (GA), brassinolide (BR), zeatin-riboside (ZR), and abscisic acid (ABA), only ABA and ZR levels were in good correlation with the dwarfing phenotype. The qPCR results showed that the expression of melatonin synthetic enzyme genes MdASMT1 and MdSNAT5, ABA synthetic enzyme gene MdAAO3 and degradative gene MdCYP707A, ZR synthetic enzyme gene MdIPT5 all correlated well with the enhanced levels of MT, ABA and the reduced level of of ZR in the dwarfing germplasms. Furthermore, the significantly higher expression of ABA marker genes (MdRD22 and MdRD29) and the lower expression of ZR marker genes (MdRR1 and MdRR2) in all the four dwarf germplasms were consistent with the ABA and ZR levels. Considering the yearly long-term drought occurring in Xinjiang, China, it seems that dwarfing with high contents of MT and ABA may be a good strategy for these germplasms to survive against drought stress. This trait of dwarfing may also benefit apple production and breeding in this semi-arid area.
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Affiliation(s)
- Tianci Yan
- College of Horticulture, China Agricultural University, Beijing, China,Sanya Institute of China Agricultural University, Sanya, Hainan, China
| | - Chuang Mei
- Scientific Observing and Experimental Station of Pomology (Xinjiang), Ministry of Agriculture, Urumqi, Xinjiang Uygur Autonomous Region, China,Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Handong Song
- College of Horticulture, China Agricultural University, Beijing, China
| | - Dongqian Shan
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yanzhao Sun
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zehui Hu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Lin Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Tong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jixun Wang
- Scientific Observing and Experimental Station of Pomology (Xinjiang), Ministry of Agriculture, Urumqi, Xinjiang Uygur Autonomous Region, China,Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Jin Kong
- College of Horticulture, China Agricultural University, Beijing, China,Sanya Institute of China Agricultural University, Sanya, Hainan, China
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12
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Expression profiling of TaARGOS homoeologous drought responsive genes in bread wheat. Sci Rep 2022; 12:3595. [PMID: 35246579 PMCID: PMC8897478 DOI: 10.1038/s41598-022-07637-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Drought tolerant germplasm is needed to increase crop production, since water scarcity is a critical bottleneck in crop productivity worldwide. Auxin Regulated Gene involved in Organ Size (ARGOS) is a large protein family of transcription factors that plays a vital role in organ size, plant growth, development, and abiotic stress responses in plants. Although, the ARGOS gene family has been discovered and functionalized in a variety of crop plants, but a comprehensive and systematic investigation of ARGOS genes in locally used commercial wheat cultivars is still yet to be reported. The relative expression of three highly conserved TaARGOS homoeologous genes (TaARGOS-A, TaARGOS-B, TaARGOS-D) was studied in three drought-tolerant (Pakistan-2013, NARC-2009 and NR-499) and three sensitive (Borlaug-2016, NR-514 and NR-516) wheat genotypes under osmotic stress, induced by PEG-6000 at 0 (exogenous control), 2, 4, 6, and 12 h. The normalization of target genes was done using β-actin as endogenous control, whereas DREB3, as a marker gene was also transcribed, reinforcing the prevalence of dehydration in all stress treatments. Real-time quantitative PCR revealed that osmotic stress induced expression of the three TaARGOS transcripts in different wheat seedlings at distinct timepoints. Overall, all genes exhibited significantly higher expression in the drought-tolerant genotypes as compared to the sensitive ones. For instance, the expression profile of TaARGOS-A and TaARGOS-D showed more than threefold increase at 2 h and six to sevenfold increase after 4 h of osmotic stress. However, after 6 h of osmotic stress these genes started to downregulate, and the lowest gene expression was noticed after 12 h of osmotic stress. Among all the homoeologous genes, TaARGOS-D, in particular, had a more significant influence on controlling plant growth and drought tolerance as it showed the highest expression. Altogether, TaARGOSs are involved in seedling establishment and overall plant growth. In addition, the tolerant group of genotypes had a much greater relative fold expression than the sensitive genotypes. Ultimately, Pakistan-2013 showed the highest relative expression of the studied genes than other genotypes which shows its proficiency to mitigate osmotic stress. Therefore, it could be cultivated in arid and semi-arid regions under moisture-deficient regimes. These findings advocated the molecular mechanism and regulatory roles of TaARGOS genes in plant growth and osmotic stress tolerance in contrasting groups of wheat genotypes, accompanied by the genetic nature of identified genotypes in terms of their potential for drought tolerance.
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13
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Fang C, Wang Z, Wang P, Song Y, Ahmad A, Dong F, Hong D, Yang G. Heterosis Derived From Nonadditive Effects of the BnFLC Homologs Coordinates Early Flowering and High Yield in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 12:798371. [PMID: 35251061 PMCID: PMC8893081 DOI: 10.3389/fpls.2021.798371] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/22/2021] [Indexed: 05/31/2023]
Abstract
Early flowering facilitates crops to adapt multiple cropping systems or growing regions with a short frost-free season; however, it usually brings an obvious yield loss. In this study, we identified that the three genes, namely, BnFLC.A2, BnFLC.C2, and BnFLC.A3b, are the major determinants for the flowering time (FT) variation of two elite rapeseed (Brassica napus L.) accessions, i.e., 616A and R11. The early-flowering alleles (i.e., Bnflc.a2 and Bnflc.c2) and late-flowering allele (i.e., BnFLC.A3b) from R11 were introgressed into the recipient parent 616A through a breeding strategy of marker-assisted backcross, giving rise to eight homozygous near-isogenic lines (NILs) associated with these three loci and 19 NIL hybrids produced by the mutual crossing of these NILs. Phenotypic investigations showed that NILs displayed significant variations in both FT and plant yield (PY). Notably, genetic analysis indicated that BnFLC.A2, BnFLC.C2, and BnFLC.A3b have additive effects of 1.446, 1.365, and 1.361 g on PY, respectively, while their dominant effects reached 3.504, 2.991, and 3.284 g, respectively, indicating that the yield loss caused by early flowering can be successfully compensated by exploring the heterosis of FT genes in the hybrid NILs. Moreover, we further validated that the heterosis of FT genes in PY was also effective in non-NIL hybrids. The results demonstrate that the exploration of the potential heterosis underlying the FT genes can coordinate early flowering (maturation) and high yield in rapeseed (B. napus L.), providing an effective strategy for early flowering breeding in crops.
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Affiliation(s)
- Caochuang Fang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhaoyang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yixian Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ali Ahmad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Faming Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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14
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Zheng Y, Wang N, Zhang Z, Liu W, Xie W. Identification of Flowering Regulatory Networks and Hub Genes Expressed in the Leaves of Elymus sibiricus L. Using Comparative Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:877908. [PMID: 35651764 PMCID: PMC9150504 DOI: 10.3389/fpls.2022.877908] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/19/2022] [Indexed: 05/10/2023]
Abstract
Flowering is a significant stage from vegetative growth to reproductive growth in higher plants, which impacts the biomass and seed yield. To reveal the flowering time variations and identify the flowering regulatory networks and hub genes in Elymus sibiricus, we measured the booting, heading, and flowering times of 66 E. sibiricus accessions. The booting, heading, and flowering times varied from 136 to 188, 142 to 194, and 148 to 201 days, respectively. The difference in flowering time between the earliest- and the last-flowering accessions was 53 days. Furthermore, transcriptome analyses were performed at the three developmental stages of six accessions with contrasting flowering times. A total of 3,526 differentially expressed genes (DEGs) were predicted and 72 candidate genes were identified, including transcription factors, known flowering genes, and plant hormone-related genes. Among them, four candidate genes (LATE, GA2OX6, FAR3, and MFT1) were significantly upregulated in late-flowering accessions. LIMYB, PEX19, GWD3, BOR7, PMEI28, LRR, and AIRP2 were identified as hub genes in the turquoise and blue modules which were related to the development time of flowering by weighted gene co-expression network analysis (WGCNA). A single-nucleotide polymorphism (SNP) of LIMYB found by multiple sequence alignment may cause late flowering. The expression pattern of flowering candidate genes was verified in eight flowering promoters (CRY, COL, FPF1, Hd3, GID1, FLK, VIN3, and FPA) and four flowering suppressors (CCA1, ELF3, Ghd7, and COL4) under drought and salt stress by qRT-PCR. The results suggested that drought and salt stress activated the flowering regulation pathways to some extent. The findings of the present study lay a foundation for the functional verification of flowering genes and breeding of new varieties of early- and late-flowering E. sibiricus.
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Affiliation(s)
- Yuying Zheng
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Na Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zongyu Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, China
| | - Wengang Xie
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- *Correspondence: Wengang Xie
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15
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Jung WJ, Lee YJ, Kang CS, Seo YW. Identification of genetic loci associated with major agronomic traits of wheat (Triticum aestivum L.) based on genome-wide association analysis. BMC PLANT BIOLOGY 2021; 21:418. [PMID: 34517837 PMCID: PMC8436466 DOI: 10.1186/s12870-021-03180-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Bread wheat (Triticum aestivum L.) is one of the most widely consumed cereal crops, but its complex genome makes it difficult to investigate the genetic effect on important agronomic traits. Genome-wide association (GWA) analysis is a useful method to identify genetic loci controlling complex phenotypic traits. With the RNA-sequencing based gene expression analysis, putative candidate genes governing important agronomic trait can be suggested and also molecular markers can be developed. RESULTS We observed major quantitative agronomic traits of wheat; the winter survival rate (WSR), days to heading (DTH), days to maturity (DTM), stem length (SL), spike length (SPL), awn length (AL), liter weight (LW), thousand kernel weight (TKW), and the number of seeds per spike (SPS), of 287 wheat accessions from diverse country origins. A significant correlation was observed between the observed traits, and the wheat genotypes were divided into three subpopulations according to the population structure analysis. The best linear unbiased prediction (BLUP) values of the genotypic effect for each trait under different environments were predicted, and these were used for GWA analysis based on a mixed linear model (MLM). A total of 254 highly significant marker-trait associations (MTAs) were identified, and 28 candidate genes closely located to the significant markers were predicted by searching the wheat reference genome and RNAseq data. Further, it was shown that the phenotypic traits were significantly affected by the accumulation of favorable or unfavorable alleles. CONCLUSIONS From this study, newly identified MTA and putative agronomically useful genes will help to study molecular mechanism of each phenotypic trait. Further, the agronomically favorable alleles found in this study can be used to develop wheats with superior agronomic traits.
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Affiliation(s)
- Woo Joo Jung
- Department of Plant Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Yong Jin Lee
- Department of Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Chon-Sik Kang
- National Institute of Crop Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul, 02841, South Korea.
- Department of Biotechnology, Korea University, Seoul, 02841, South Korea.
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16
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Hussain Q, Asim M, Zhang R, Khan R, Farooq S, Wu J. Transcription Factors Interact with ABA through Gene Expression and Signaling Pathways to Mitigate Drought and Salinity Stress. Biomolecules 2021; 11:1159. [PMID: 34439825 PMCID: PMC8393639 DOI: 10.3390/biom11081159] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 12/18/2022] Open
Abstract
Among abiotic stressors, drought and salinity seriously affect crop growth worldwide. In plants, research has aimed to increase stress-responsive protein synthesis upstream or downstream of the various transcription factors (TFs) that alleviate drought and salinity stress. TFs play diverse roles in controlling gene expression in plants, which is necessary to regulate biological processes, such as development and environmental stress responses. In general, plant responses to different stress conditions may be either abscisic acid (ABA)-dependent or ABA-independent. A detailed understanding of how TF pathways and ABA interact to cause stress responses is essential to improve tolerance to drought and salinity stress. Despite previous progress, more active approaches based on TFs are the current focus. Therefore, the present review emphasizes the recent advancements in complex cascades of gene expression during drought and salinity responses, especially identifying the specificity and crosstalk in ABA-dependent and -independent signaling pathways. This review also highlights the transcriptional regulation of gene expression governed by various key TF pathways, including AP2/ERF, bHLH, bZIP, DREB, GATA, HD-Zip, Homeo-box, MADS-box, MYB, NAC, Tri-helix, WHIRLY, WOX, WRKY, YABBY, and zinc finger, operating in ABA-dependent and -independent signaling pathways.
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Affiliation(s)
- Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China; (Q.H.); (R.Z.)
| | - Muhammad Asim
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Qingdao 266101, China; (M.A.); (R.K.)
| | - Rui Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China; (Q.H.); (R.Z.)
| | - Rayyan Khan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Qingdao 266101, China; (M.A.); (R.K.)
| | - Saqib Farooq
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, Agricultural College of Guangxi University, Nanning 530004, China;
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China; (Q.H.); (R.Z.)
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17
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Shafique Khan F, Zeng RF, Gan ZM, Zhang JZ, Hu CG. Genome-Wide Identification and Expression Profiling of the WOX Gene Family in Citrus sinensis and Functional Analysis of a CsWUS Member. Int J Mol Sci 2021; 22:4919. [PMID: 34066408 PMCID: PMC8124563 DOI: 10.3390/ijms22094919] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/23/2023] Open
Abstract
WUSCHEL-related homeobox (WOX) transcription factors (TFs) are well known for their role in plant development but are rarely studied in citrus. In this study, we identified 11 putative genes from the sweet orange genome and divided the citrus WOX genes into three clades (modern/WUSCHEL(WUS), intermediate, and ancient). Subsequently, we performed syntenic relationship, intron-exon organization, motif composition, and cis-element analysis. Co-expression analysis based on RNA-seq and tissue-specific expression patterns revealed that CsWOX gene expression has multiple intrinsic functions. CsWUS homolog of AtWUS functions as a transcriptional activator and binds to specific DNA. Overexpression of CsWUS in tobacco revealed dramatic phenotypic changes, including malformed leaves and reduced gynoecia with no seed development. Silencing of CsWUS in lemon using the virus-induced gene silencing (VIGS) system implied the involvement of CsWUS in cells of the plant stem. In addition, CsWUS was found to interact with CsCYCD3, an ortholog in Arabidopsis (AtCYCD3,1). Yeast one-hybrid screening and dual luciferase activity revealed that two TFs (CsRAP2.12 and CsHB22) bind to the promoter of CsWUS and regulate its expression. Altogether, these results extend our knowledge of the WOX gene family along with CsWUS function and provide valuable findings for future study on development regulation and comprehensive data of WOX members in citrus.
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Affiliation(s)
| | | | | | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (F.S.K.); (R.-F.Z.); (Z.-M.G.)
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (F.S.K.); (R.-F.Z.); (Z.-M.G.)
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18
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Zhou S, Zhu S, Cui S, Hou H, Wu H, Hao B, Cai L, Xu Z, Liu L, Jiang L, Wang H, Wan J. Transcriptional and post-transcriptional regulation of heading date in rice. THE NEW PHYTOLOGIST 2021; 230:943-956. [PMID: 33341945 PMCID: PMC8048436 DOI: 10.1111/nph.17158] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/15/2020] [Indexed: 05/04/2023]
Abstract
Rice is a facultative short day (SD) plant. In addition to serving as a model plant for molecular genetic studies of monocots, rice is a staple crop for about half of the world's population. Heading date is a critical agronomic trait, and many genes controlling heading date have been cloned over the last 2 decades. The mechanism of flowering in rice from recognition of day length by leaves to floral activation in the shoot apical meristem has been extensively studied. In this review, we summarise current progress on transcriptional and post-transcriptional regulation of heading date in rice, with emphasis on post-translational modifications of key regulators, including Heading date 1 (Hd1), Early heading date 1 (Ehd1), Grain number, plant height, and heading date7 (Ghd7). The contribution of heading date genes to heterosis and the expansion of rice cultivation areas from low-latitude to high-latitude regions are also discussed. To overcome the limitations of diverse genetic backgrounds used in heading date studies and to gain a clearer understanding of flowering in rice, we propose a systematic collection of genetic resources in a common genetic background. Strategies in breeding adapted cultivars by rational design are also discussed.
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Affiliation(s)
- Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Song Cui
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haigang Hou
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haoqin Wu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Benyuan Hao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Liang Cai
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Zhuang Xu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Linglong Liu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
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19
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Han N, Tang R, Chen X, Xu Z, Ren Z, Wang L. Genome-wide identification and characterization of WOX genes in Cucumis sativus. Genome 2021; 64:761-776. [PMID: 33493082 DOI: 10.1139/gen-2020-0029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
WUSCHEL-related homeobox (WOX) proteins are plant-specific transcription factors that are profoundly involved in regulation of plant development and stress responses. In this study, we totally identified 11 WOX transcription factor family members in cucumber (Cucumis sativus, CsWOX) genome and classified them into three clades with nine subclades based on phylogenetic analysis results. Alignment of amino acid sequences revealed that all WOX members in cucumber contained the typical homeodomain, which consists of 60-66 amino acids and is folded into a helix-turn-helix structure. Gene duplication event analysis indicated that CsWOX1a and CsWOX1b were a segment duplication pair, which might affect the number of WOX members in cucumber genome. The expression profiles of CsWOX genes in different tissues demonstrated that the members sorted into the ancient clade (CsWOX13a and CsWOX13b) were constitutively expressed at higher levels in comparison to the others. Cis-element analysis in promoter regions suggested that the expression of CsWOX genes was associated with phytohormone pathways and stress responses, which was further supported by RNA-seq data. Taken together, our results provide new insights into the evolution of cucumber WOX genes and improve our understanding about the biological functions of the CsWOX gene family.
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Affiliation(s)
- Ni Han
- State Key Laboratory of Crop Biology, Tai'an, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China.,Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai'an, China.,College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Rui Tang
- State Key Laboratory of Crop Biology, Tai'an, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China.,Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai'an, China.,College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xueqian Chen
- State Key Laboratory of Crop Biology, Tai'an, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China.,Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai'an, China.,College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Zhixuan Xu
- State Key Laboratory of Crop Biology, Tai'an, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China.,Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai'an, China.,College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Zhonghai Ren
- State Key Laboratory of Crop Biology, Tai'an, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China.,Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai'an, China.,College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Lina Wang
- State Key Laboratory of Crop Biology, Tai'an, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China.,Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai'an, China.,College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
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20
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Kim JS, Chae S, Jun KM, Lee GS, Jeon JS, Kim KD, Kim YK. Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice. PLANTA 2021; 253:40. [PMID: 33475863 PMCID: PMC7819943 DOI: 10.1007/s00425-021-03572-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/08/2021] [Indexed: 05/20/2023]
Abstract
The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5' upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.
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Affiliation(s)
- Joung Sug Kim
- Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea
| | - SongHwa Chae
- Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea
| | - Kyong Mi Jun
- Genomics Genetics Institute, GreenGene BioTech Inc., 16-4 Dongbaekjungang-ro 16beon-gil, Giheung-gu, Yongin, Gyeonggi-do, 17015, Republic of Korea
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, 54875, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Republic of Korea
| | - Kyung Do Kim
- Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea
| | - Yeon-Ki Kim
- Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea.
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21
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Sajjad M, Wei X, Liu L, Li F, Ge X. Transcriptome Analysis Revealed GhWOX4 Intercedes Myriad Regulatory Pathways to Modulate Drought Tolerance and Vascular Growth in Cotton. Int J Mol Sci 2021; 22:ijms22020898. [PMID: 33477464 PMCID: PMC7829754 DOI: 10.3390/ijms22020898] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 11/17/2022] Open
Abstract
Cotton is a paramount cash crop around the globe. Among all abiotic stresses, drought is a leading cause of cotton growth and yield loss. However, the molecular link between drought stress and vascular growth and development is relatively uncharted. Here, we validated a crucial role of GhWOX4, a transcription factor, modulating drought stress with that of vasculature growth in cotton. Knock-down of GhWOX4 decreased the stem width and severely compromised vascular growth and drought tolerance. Conversely, ectopic expression of GhWOX4 in Arabidopsis enhanced the tolerance to drought stress. Comparative RNAseq analysis revealed auxin responsive protein (AUX/IAA), abscisic acid (ABA), and ethylene were significantly induced. Additionally, MYC-bHLH, WRKY, MYB, homeodomain, and heat-shock transcription factors (HSF) were differentially expressed in control plants as compared to GhWOX4-silenced plants. The promotor zone of GhWOX4 was found congested with plant growth, light, and stress response related cis-elements. differentially expressed genes (DEGs) related to stress, water deprivation, and desiccation response were repressed in drought treated GhWOX4-virus-induced gene silencing (VIGS) plants as compared to control. Gene ontology (GO) functions related to cell proliferation, light response, fluid transport, and flavonoid biosynthesis were over-induced in TRV: 156-0 h/TRV: 156-1 h (control) in comparison to TRV: VIGS-0 h/TRV: VIGS-1 h (GhWOX4-silenced) plants. This study improves our context for elucidating the pivotal role of GhWOX4 transcription factors (TF), which mediates drought tolerance, plays a decisive role in plant growth and development, and is likely involved in different regulatory pathways in cotton.
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Affiliation(s)
- Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.S.); (L.L.)
| | - Xi Wei
- Institute of Cotton Research, Henan Normal University Research Base of State Key Laboratory of Cotton Biology, Xinxiang 453000, China;
| | - Lisen Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.S.); (L.L.)
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.S.); (L.L.)
- Institute of Cotton Research, Henan Normal University Research Base of State Key Laboratory of Cotton Biology, Xinxiang 453000, China;
- Correspondence: (F.L.); (X.G.)
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.S.); (L.L.)
- Institute of Cotton Research, Henan Normal University Research Base of State Key Laboratory of Cotton Biology, Xinxiang 453000, China;
- Correspondence: (F.L.); (X.G.)
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22
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Tang Y, Li H, Guan Y, Li S, Xun C, Dong Y, Huo R, Guo Y, Bao X, Pei E, Shen Q, Zhou H, Liao J. Genome-Wide Identification of the Physic Nut WUSCHEL-Related Homeobox Gene Family and Functional Analysis of the Abiotic Stress Responsive Gene JcWOX5. Front Genet 2020; 11:670. [PMID: 32655627 PMCID: PMC7325900 DOI: 10.3389/fgene.2020.00670] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/02/2020] [Indexed: 11/29/2022] Open
Abstract
Plant-specific WOX transcription factors have important regulatory functions in plant development and response to abiotic stress. However, the identification and functional analysis of members of the WOX family have rarely been reported in the physic nut plant until now. Our research identified 12 WOX genes (JcWOXs) in physic nut, and these genes were divided into three groups corresponding to the ancient clade, WUS clade, and intermediate clade. Expression analysis based on RNA-seq and qRT-PCR showed that most of the JcWOX genes were expressed in at least one of the tissues tested, whereas five genes were identified as being highly responsive to drought and salt stresses. Subcellular localization analysis in Arabidopsis protoplast cells showed that JcWOX5 encoded a nuclear-localized protein. JcWOX5-overexpression plants increased sensitivity to drought stress, and transgenic plants suggested a lower proline content and CAT activity, higher relative electrolyte leakage, higher MDA content, and higher rate of water loss under drought conditions. Expression of some stress-related genes was obviously lower in the transformed rice lines as compared to their expression in wild-type rice lines under drought stress. Further data on JcWOX5-overexpressing plants reducing drought tolerance verified the potential role of JcWOX genes in responsive to abiotic stress. Collectively, the study provides a foundation for further functional analysis of JcWOX genes and the improvement of physic nut crops.
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Affiliation(s)
- Yuehui Tang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Zhoukou, China
| | - Han Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Yaxin Guan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Shen Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Chunfei Xun
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Yanyang Dong
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Rui Huo
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Yuxi Guo
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Xinxin Bao
- School of Journalism and Communication, Zhoukou Normal University, Zhoukou, China
| | - Enqing Pei
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Qianmiao Shen
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - He Zhou
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Jingjing Liao
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
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Ma X, Su Z, Ma H. Molecular genetic analyses of abiotic stress responses during plant reproductive development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2870-2885. [PMID: 32072177 PMCID: PMC7260722 DOI: 10.1093/jxb/eraa089] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/12/2020] [Indexed: 05/20/2023]
Abstract
Plant responses to abiotic stresses during vegetative growth have been extensively studied for many years. Daily environmental fluctuations can have dramatic effects on plant vegetative growth at multiple levels, resulting in molecular, cellular, physiological, and morphological changes. Plants are even more sensitive to environmental changes during reproductive stages. However, much less is known about how plants respond to abiotic stresses during reproduction. Fortunately, recent advances in this field have begun to provide clues about these important processes, which promise further understanding and a potential contribution to maximize crop yield under adverse environments. Here we summarize information from several plants, focusing on the possible mechanisms that plants use to cope with different types of abiotic stresses during reproductive development, and present a tentative molecular portrait of plant acclimation during reproductive stages. Additionally, we discuss strategies that plants use to balance between survival and productivity, with some comparison among different plants that have adapted to distinct environments.
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Affiliation(s)
- Xinwei Ma
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Zhao Su
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Correspondence:
| | - Hong Ma
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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Xu P, Yang J, Ma Z, Yu D, Zhou J, Tao D, Li Z. Identification and Validation of Aerobic Adaptation QTLs in Upland Rice. Life (Basel) 2020; 10:life10050065. [PMID: 32423169 PMCID: PMC7281610 DOI: 10.3390/life10050065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 12/23/2022] Open
Abstract
The aerobic adaptation of upland rice is considered as the key genetic difference between upland rice and lowland rice. Genetic dissection of the aerobic adaptation is important as the basis for improving drought tolerance and terrestrial adaptation by using the upland rice. We raised BC1-BC3 introgression lines (ILs) in lowland rice Minghui 63 (MH63) background. The QTLs of yield and yield-related traits were detected based on ILs under the aerobic and lowland environments, and then the yield-related QTLs were identified in a backcrossed inbred population of BC4F5 under aerobic condition. We further verified phenotypes of QTL near-isogenic lines. Finally, three QTLs responsible for increasing yield in aerobic environment were detected by multiple locations and generations, which were designated as qAER1, qAER3, and qAER9 (QTL of aerobic adaptation). The qAER1 and qAER9 were fine-mapped. We found that qAER1 and qAER9 controlled plant height and heading date, respectively; while both of them increased yields simultaneously by suitable plant height and heading date without delay in the aerobic environment. The phenotypic differences between lowland rice and upland rice in the aerobic environment further supported the above results. We pyramided the two QTLs as corresponding molecular modules in the irrigated lowland rice MH63 background, and successfully developed a new upland rice variety named as Zhongkexilu 2. This study will lay the foundation for using aerobic adaptation QTLs in rice breeding programs and for further cloning the key genes involved in aerobic adaptation.
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Affiliation(s)
- Peng Xu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Jun Yang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
| | - Zhenbing Ma
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
| | - Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
- Correspondence: (D.T.); (Z.L.); Tel.: +86-871-6589-3754 (D.T.); +86-10-6273-1414 (Z.L.)
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
- Correspondence: (D.T.); (Z.L.); Tel.: +86-871-6589-3754 (D.T.); +86-10-6273-1414 (Z.L.)
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25
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Demmings EM, Williams BR, Lee CR, Barba P, Yang S, Hwang CF, Reisch BI, Chitwood DH, Londo JP. Quantitative Trait Locus Analysis of Leaf Morphology Indicates Conserved Shape Loci in Grapevine. FRONTIERS IN PLANT SCIENCE 2019; 10:1373. [PMID: 31803199 PMCID: PMC6873345 DOI: 10.3389/fpls.2019.01373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/04/2019] [Indexed: 05/02/2023]
Abstract
Leaf shape in plants plays important roles in water use, canopy structure, and physiological tolerances to abiotic stresses; all important traits for the future development and sustainability of grapevine cultivation. Historically, researchers have used ampelography, the study of leaf shape in grapevines, to differentiate Vitis species and cultivars based on finite leaf attributes. However, ampelographic measurements have limitations and new methods for quantifying shape are now available. We paired an analysis of finite trait attributes with a 17-point landmark survey and generalized Procrustes analysis (GPA) to reconstruct grapevine leaves digitally from five interspecific hybrid mapping families. Using the reconstructed leaves, we performed three types of quantitative trait loci (QTL) analyses to determine the genetic architecture that defines leaf shape. In the first analysis, we compared several important ampelographic measurements as finite trait QTL. In the second and third analyses, we identified significant shape variation via principal components analysis (PCA) and using a multivariate least squares interval mapping (MLSIM) approach. In total, we identified 271 significant QTL across the three measures of leaf shape and identified specific QTL hotspots in the grape genome which appear to drive major aspects of grapevine leaf shape.
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Affiliation(s)
- Elizabeth M. Demmings
- Department of Food Science, Cornell University, Geneva, NY, United States
- Horticulture Section, School of Integrative Plant Science, Cornell Agritech at the New York State Agricultural Experiment Station, Geneva, NY, United States
| | - Brigette R. Williams
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Mountain Grove, MO, United States
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology and Institute of Plant Biology, National Taiwan University, Taipei City, Taiwan
| | - Paola Barba
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile
| | - Shanshan Yang
- Bioinformatics Core, Knowledge Enterprise Development, Arizona State University, Tempe, AZ, United States
| | - Chin-Feng Hwang
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Mountain Grove, MO, United States
| | - Bruce I. Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell Agritech at the New York State Agricultural Experiment Station, Geneva, NY, United States
| | - Daniel H. Chitwood
- Department of Horticulture, Michigan State University, Lansing, MI, United States
- Department of Computational Mathematics, Science and Engineering, Michigan State University, Lansing, MI, United States
| | - Jason P. Londo
- Horticulture Section, School of Integrative Plant Science, Cornell Agritech at the New York State Agricultural Experiment Station, Geneva, NY, United States
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY, United States
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26
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Liu T, Luo X, Li ZH, Wu JC, Luo SZ, Xu MY. Zinc-α2-glycoprotein 1 attenuates non-alcoholic fatty liver disease by negatively regulating tumour necrosis factor-α. World J Gastroenterol 2019; 25:5451-5468. [PMID: 31576092 PMCID: PMC6767980 DOI: 10.3748/wjg.v25.i36.5451] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/26/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Zinc-α2-glycoprotein 1 (AZGP1) plays important roles in metabolism-related diseases. The underlying molecular mechanisms and therapeutic effects of AZGP1 remain unknown in non-alcoholic fatty liver disease (NAFLD).
AIM To explore the effects and potential mechanism of AZGP1 on NAFLD in vivo and in vitro.
METHODS The expression of AZGP1 and its effects on hepatocytes were examined in NAFLD patients, CCl4-treated mice fed a high fat diet (HFD), and human LO2 cells.
RESULTS AZGP1 levels were significantly decreased in liver tissues of NAFLD patients and mice. AZGP1 knockdown was found to activate inflammation; enhance steatogenesis, including promoting lipogenesis [sterol regulatory element-binding protein (SREBP)-1c, liver X receptor (LXR), fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), and stearoyl CoA desaturase 1 (SCD)-1], increasing lipid transport and accumulation [fatty acid transport protein (FATP), carnitine palmitoyl transferase (CPT)-1A, and adiponectin], and reducing fatty acid β-oxidation [farnesoid X receptor (FXR) and peroxisome proliferator-activated receptor (PPAR)-α]; accelerate proliferation; and reverse apoptosis in LO2 cells. AZGP1 overexpression (OV-AZGP1) had the opposite effects. Furthermore, AZGP1 alleviated NAFLD by blocking TNF-α-mediated inflammation and intracellular lipid deposition, promoting proliferation, and inhibiting apoptosis in LO2 cells. Finally, treatment with OV-AZGP1 plasmid dramatically improved liver injury and eliminated liver fat in NAFLD mice.
CONCLUSION AZGP1 attenuates NAFLD with regard to ameliorating inflammation, accelerating lipolysis, promoting proliferation, and reducing apoptosis by negatively regulating TNF-α. AZGP1 is suggested to be a novel promising therapeutic target for NAFLD.
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Affiliation(s)
- Ting Liu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei Province, China
- Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Xin Luo
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Zheng-Hong Li
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Jun-Cheng Wu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Sheng-Zheng Luo
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Ming-Yi Xu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
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To HTM, Nguyen HT, Dang NTM, Nguyen NH, Bui TX, Lavarenne J, Phung NTP, Gantet P, Lebrun M, Bellafiore S, Champion A. Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study. RICE (NEW YORK, N.Y.) 2019; 12:69. [PMID: 31485824 PMCID: PMC6726733 DOI: 10.1186/s12284-019-0327-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/22/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Due to their sessile life style, plant survival is dependent on the ability to build up fast and highly adapted responses to environmental stresses by modulating defense response and organ growth. The phytohormone jasmonate plays an essential role in regulating these plant responses to stress. RESULTS To assess variation of plant growth responses and identify genetic determinants associated to JA treatment, we conducted a genome-wide association study (GWAS) using an original panel of Vietnamese rice accessions. The phenotyping results showed a high natural genetic variability of the 155 tested rice accessions in response to JA for shoot and root growth. The level of growth inhibition by JA is different according to the rice varieties tested. We conducted genome-wide association study and identified 28 significant associations for root length (RTL), shoot length (SHL), root weight (RTW), shoot weight (SHW) and total weight (TTW) in response to JA treatment. Three common QTLs were found for RTL, RTW and SHL. Among a list of 560 candidate genes found to co-locate with the QTLs, a transcriptome analysis from public database for the JA response allows us to identify 232 regulated genes including several JA-responsive transcription factors known to play a role in stress response. CONCLUSION Our genome-wide association study shows that common and specific genetic elements are associated with inhibition of shoot and root growth under JA treatment suggesting the involvement of a complex JA-dependent genetic control of rice growth inhibition at the whole plant level. Besides, numerous candidate genes associated to stress and JA response are co-located with the association loci, providing useful information for future studies on genetics and breeding to optimize the growth-defense trade-off in rice.
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Affiliation(s)
- Huong Thi Mai To
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), LMI-RICE2, 18 Hoang Quoc Viet, Cau Giay district, Hanoi, Vietnam.
| | - Hieu Trang Nguyen
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), LMI-RICE2, 18 Hoang Quoc Viet, Cau Giay district, Hanoi, Vietnam
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, UMR DIADE, UMR IPME, UMR LSTM, Montpellier, France
| | - Nguyet Thi Minh Dang
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), LMI-RICE2, 18 Hoang Quoc Viet, Cau Giay district, Hanoi, Vietnam
| | - Ngan Huyen Nguyen
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), LMI-RICE2, 18 Hoang Quoc Viet, Cau Giay district, Hanoi, Vietnam
| | - Thai Xuan Bui
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), LMI-RICE2, 18 Hoang Quoc Viet, Cau Giay district, Hanoi, Vietnam
| | - Jérémy Lavarenne
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, UMR DIADE, UMR IPME, UMR LSTM, Montpellier, France
| | | | - Pascal Gantet
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, UMR DIADE, UMR IPME, UMR LSTM, Montpellier, France
| | - Michel Lebrun
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), LMI-RICE2, 18 Hoang Quoc Viet, Cau Giay district, Hanoi, Vietnam
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, UMR DIADE, UMR IPME, UMR LSTM, Montpellier, France
| | - Stephane Bellafiore
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, UMR DIADE, UMR IPME, UMR LSTM, Montpellier, France
| | - Antony Champion
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, UMR DIADE, UMR IPME, UMR LSTM, Montpellier, France.
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28
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Lv Y, Xu L, Dossa K, Zhou K, Zhu M, Xie H, Tang S, Yu Y, Guo X, Zhou B. Identification of putative drought-responsive genes in rice using gene co-expression analysis. Bioinformation 2019; 15:480-489. [PMID: 31485134 PMCID: PMC6704332 DOI: 10.6026/97320630015480] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/17/2022] Open
Abstract
Drought is one of the major abiotic stresses causing yield losses and restricted growing area for several major crops. Rice being a major staple food crop and sensitive to water-deficit conditions bears heavy yield losses due to drought stress. To breed drought tolerant rice cultivars, it is of interest to understand the mechanisms of drought tolerance. In this regard, large amount of publicly available transcriptome datasets could be utilized. In this study, we used different transcriptome datasets obtained under drought stress in comparison to normal conditions (control) to identify novel drought responsive genes and their underlying molecular mechanisms. We found 517 core drought responsive differentially expressed genes (DEGs) and different modules using gene co-expression analysis to specifically predict their biological roles in drought tolerance. Gene ontology and KEGG analyses showed key biological processes and metabolic pathways involved in drought tolerance. Further, network analysis pinpointed important hub DEGs and major transcription factors regulating the expression of drought responsive genes in each module. These identified novel DEGs and transcription factors could be functionally characterized using systems biology approaches, which can significantly enhance our knowledge about the molecular mechanisms of drought tolerance in rice.
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Affiliation(s)
- Yanmei Lv
- Hunan Rice Research Institute, Changsha, 410125, China
| | - Lei Xu
- College of Pharmacy, Hubei University of Chinese Medicine, China
| | - Komivi Dossa
- Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China
| | - Kun Zhou
- Hunan Rice Research Institute, Changsha, 410125, China
| | - Mingdong Zhu
- Hunan Rice Research Institute, Changsha, 410125, China
| | - Hongjun Xie
- Hunan Rice Research Institute, Changsha, 410125, China
| | - Shanjun Tang
- Hunan Rice Research Institute, Changsha, 410125, China
| | - Yaying Yu
- Hunan Rice Research Institute, Changsha, 410125, China
| | - Xiayu Guo
- State key laboratory of hybrid rice, Changsha, 410125, China
| | - Bin Zhou
- Hunan Rice Research Institute, Changsha, 410125, China
- Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture,Changsha, 410125, China
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29
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Lu Y, Liu Z, Lyu M, Yuan Y, Wu B. Characterization of JsWOX1 and JsWOX4 during Callus and Root Induction in the Shrub Species Jasminum sambac. PLANTS 2019; 8:plants8040079. [PMID: 30934867 PMCID: PMC6526479 DOI: 10.3390/plants8040079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/22/2019] [Accepted: 03/27/2019] [Indexed: 11/16/2022]
Abstract
Plant regeneration in vitro and the underlying molecular regulatory network are of great interest to developmental biology, and have potential applications in agriculture and biotechnology. Cell growth and re-differentiation during de novo organogenesis require the activation and reprogramming of stem cells within the stem cell niche of the tissues. The WUSCHEL-related homeobox (WOX) factors play important roles in the maintenance and regulation of plant stem cells and are involved in many developmental processes. However, in woody species such as the Jasminum sambac, little is known about the involvement of WOX genes in de novo organogenesis. Here we show that two WOXs, JsWOX4 and JsWOX1, are implicated in callus proliferation and root regeneration, respectively. The expression of both, together with another member JsWOX13, are upregulated during later stage of callus formation. The JsWOX4 is associated with callus proliferation, or cell division during the redifferentiation. The overexpression of this gene results in up-regulation of JsWOX13 and another homeobox gene. The JsWOX1 plays a role in root primordium initiation, as its overexpression leads to more rooty calli and more roots per callus. JsWOX1 also possibly acts upstream of JsWOX4 and JsWOX13 transcriptionally. Our results provide further evidence regarding the functions of WOX genes in organogenesis in a woody plant.
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Affiliation(s)
- Ying Lu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Horticulture, Fujian A & F University, Fuzhou 350002, China.
| | - Zhuoyi Liu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Horticulture, Fujian A & F University, Fuzhou 350002, China.
| | - Meiling Lyu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Horticulture, Fujian A & F University, Fuzhou 350002, China.
| | - Yuan Yuan
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Horticulture, Fujian A & F University, Fuzhou 350002, China.
| | - Binghua Wu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Horticulture, Fujian A & F University, Fuzhou 350002, China.
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30
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Zhang ZH, Zhu YJ, Wang SL, Fan YY, Zhuang JY. Importance of the Interaction between Heading Date Genes Hd1 and Ghd7 for Controlling Yield Traits in Rice. Int J Mol Sci 2019; 20:ijms20030516. [PMID: 30691093 PMCID: PMC6387254 DOI: 10.3390/ijms20030516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/20/2019] [Accepted: 01/23/2019] [Indexed: 12/29/2022] Open
Abstract
Appropriate flowering time is crucial for successful grain production, which relies on not only the action of individual heading date genes, but also the gene-by-gene interactions. In this study, influences of interaction between Hd1 and Ghd7 on flowering time and yield traits were analyzed using near isogenic lines derived from a cross between indica rice cultivars ZS97 and MY46. In the non-functional ghd7ZS97 background, the functional Hd1ZS97 allele promoted flowering under both the natural short-day (NSD) conditions and natural long-day (NLD) conditions. In the functional Ghd7MY46 background, Hd1ZS97 remained to promote flowering under NSD conditions, but repressed flowering under NLD conditions. For Ghd7, the functional Ghd7MY46 allele repressed flowering under both conditions, which was enhanced in the functional Hd1ZS97 background under NLD conditions. With delayed flowering, spikelet number and grain weight increased under both conditions, but spikelet fertility and panicle number fluctuated. Rice lines carrying non-functional hd1MY46 and functional Ghd7MY46 alleles had the highest grain yield under both conditions. These results indicate that longer growth duration for a larger use of available temperature and light does not always result in higher grain production. An optimum heading date gene combination needs to be carefully selected for maximizing grain yield in rice.
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Affiliation(s)
- Zhen-Hua Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Shi-Lin Wang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
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