1
|
Toora PK, Tuan PA, Nguyen TN, Badea A, Ayele BT. Modulation in the ratio of abscisic acid to gibberellin level determines genetic variation of seed dormancy in barley (Hordeum vulgare L.). JOURNAL OF PLANT PHYSIOLOGY 2024; 301:154301. [PMID: 38968782 DOI: 10.1016/j.jplph.2024.154301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/07/2024]
Abstract
Abscisic acid (ABA) and gibberellin (GA) are major regulators of seed dormancy, an adaptive trait closely associated with preharvest sprouting. This study examined transcriptional regulation of ABA and GA metabolism genes and modulation of ABA and GA levels in seeds of barley genotypes exhibiting a range of dormancy phenotype. We observed a very strong negative correlation between genetic variation in seed germination and embryonic ABA level (r = 0.85), which is regulated by transcriptional modulation of HvNCED1 and/or HvCYP707A genes. A strong positive correlation was evident between variation in seed germination and GA level (r = 0.64), mediated via transcriptional regulation of GA biosynthesis genes, HvGA20ox2 and/or HvGA3oxs, and GA catabolism genes, HvGA2ox3 and/or HvGA3ox6. Modulation of the ABA and GA levels in the genotypes led to the prevalence of ABA to GA level ratio that exhibited a very strong negative correlation (r = 0.84) with seed germination, highlighting the importance of a shift in ABA/GA ratio in determining genetic variation of dormancy in barley seeds. Our results overall show that transcriptional regulation of specific ABA and GA metabolism genes underlies genetic variation in ABA/GA ratio and seed dormancy, reflecting the potential use of these genes as molecular tools for enhancing preharvest sprouting resistance in barley.
Collapse
Affiliation(s)
- Parneet K Toora
- Department of Plant Science, 222 Agriculture Building, University of Manitoba, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Pham Anh Tuan
- Department of Plant Science, 222 Agriculture Building, University of Manitoba, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Tran-Nguyen Nguyen
- Department of Plant Science, 222 Agriculture Building, University of Manitoba, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Ana Badea
- Brandon Research and Development Center, Agriculture and Agri-Food Canada, Brandon, Manitoba, Canada, R7A 5Y3
| | - Belay T Ayele
- Department of Plant Science, 222 Agriculture Building, University of Manitoba, Winnipeg, Manitoba, Canada, R3T 2N2.
| |
Collapse
|
2
|
Li X, Zhang J, Guo X, Qiu L, Chen K, Wang J, Cheng T, Zhang Q, Zheng T. Genome-Wide Analysis of the Gibberellin-Oxidases Family Members in Four Prunus Species and a Functional Analysis of PmGA2ox8 in Plant Height. Int J Mol Sci 2024; 25:8697. [PMID: 39201381 PMCID: PMC11354515 DOI: 10.3390/ijms25168697] [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: 07/04/2024] [Revised: 07/24/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Gibberellins (GAs), enzymes that play a significant role in plant growth and development, and their levels in plants could be regulated by gibberellin-oxidases (GAoxs). As important fruit trees and ornamental plants, the study of the mechanism of plant architecture formation of the Prunus genus is crucial. Here, 85 GAox genes were identified from P. mume, P. armeniaca, P. salicina, and P. persica, and they were classified into six subgroups. Conserved motif and gene structure analysis showed that GAoxs were conserved in the four Prunus species. Collinearity analysis revealed two fragment replication events of PmGAoxs in the P. mume genome. Promoter cis-elements analysis revealed 24 PmGAoxs contained hormone-responsive elements and development regulatory elements. The expression profile indicated that PmGAoxs have tissue expression specificity, and GA levels during the dormancy stage of flower buds were controlled by certain PmGAoxs. After being treated with IAA or GA3, the transcription level of PmGA2ox8 in stems was significantly increased and showed a differential expression level between upright and weeping stems. GUS activity driven by PmGA2ox8 promoter was detected in roots, stems, leaves, and flower organs of Arabidopsis. PmGA2ox8 overexpression in Arabidopsis leads to dwarfing phenotype, increased number of rosette leaves but decreased leaf area, and delayed flowering. Our results showed that GAoxs were conserved in Prunus species, and PmGA2ox8 played an essential role in regulating plant height.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, State Key Laboratory of Efficient Production of Forest Resources, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (X.L.); (J.Z.); (X.G.); (L.Q.); (K.C.); (J.W.); (T.C.); (Q.Z.)
| |
Collapse
|
3
|
Palayam M, Yan L, Nagalakshmi U, Gilio AK, Cornu D, Boyer FD, Dinesh-Kumar SP, Shabek N. Structural insights into strigolactone catabolism by carboxylesterases reveal a conserved conformational regulation. Nat Commun 2024; 15:6500. [PMID: 39090154 PMCID: PMC11294565 DOI: 10.1038/s41467-024-50928-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Phytohormone levels are regulated through specialized enzymes, participating not only in their biosynthesis but also in post-signaling processes for signal inactivation and cue depletion. Arabidopsis thaliana (At) carboxylesterase 15 (CXE15) and carboxylesterase 20 (CXE20) have been shown to deplete strigolactones (SLs) that coordinate various growth and developmental processes and function as signaling molecules in the rhizosphere. Here, we elucidate the X-ray crystal structures of AtCXE15 (both apo and SL intermediate bound) and AtCXE20, revealing insights into the mechanisms of SL binding and catabolism. The N-terminal regions of CXE15 and CXE20 exhibit distinct secondary structures, with CXE15 characterized by an alpha helix and CXE20 by an alpha/beta fold. These structural differences play pivotal roles in regulating variable SL hydrolysis rates. Our findings, both in vitro and in planta, indicate that a transition of the N-terminal helix domain of CXE15 between open and closed forms facilitates robust SL hydrolysis. The results not only illuminate the distinctive process of phytohormone breakdown but also uncover a molecular architecture and mode of plasticity within a specific class of carboxylesterases.
Collapse
Affiliation(s)
- Malathy Palayam
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA, USA
| | - Linyi Yan
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA, USA
| | - Ugrappa Nagalakshmi
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA, USA
| | - Amelia K Gilio
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA, USA
| | - David Cornu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - François-Didier Boyer
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS UPR 2301, Gif-sur-Yvette, France
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA, USA
- The Genome Center, University of California-Davis, Davis, CA, USA
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA, USA.
| |
Collapse
|
4
|
Xu L, Xu Y, Jiang JR, Cheng CX, Yang WW, Deng LL, Mi QL, Zeng WL, Li J, Gao Q, Xiang HY, Li XM. A novel AP2/ERF transcription factor, NtERF10, positively regulates plant height in tobacco. Transgenic Res 2024; 33:195-210. [PMID: 39105946 PMCID: PMC11319389 DOI: 10.1007/s11248-024-00383-z] [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: 05/29/2023] [Accepted: 04/05/2024] [Indexed: 08/07/2024]
Abstract
Ethylene response factors have been shown to be involved in the effects of plant developmental processes and to regulate stress tolerance. The aim of this study was to recognize the regulatory mechanisms of ethylene response factors on tobacco plant height. In this study, a gene-edited mutant (ERF10-KO) and wild type (WT) were utilized as experimental materials. Transcriptome and metabolome analyses were used to investigate the regulatory mechanism of NtERF10 gene editing on plant height in tobacco. Here, through the analysis of differentially expressed genes (DEGs), 2051 genes were upregulated and 1965 genes were downregulated. We characterized the different ERF10-KO and WT plant heights and identified key genes for photosynthesis, the plant hormone signal transduction pathway and the terpene biosynthesis pathway. NtERF10 was found to affect the growth and development of tobacco by regulating the expression levels of the PSAA, PSBA, GLY17 and GGP3 genes. Amino acid metabolism was analyzed by combining analyses of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). In addition, we found that members of the bHLH, NAC, MYB, and WRKY transcription factor families have vital roles in regulating plant height. This study not only provides important insights into the positive regulation of the ethylene response factor NtERF10 on plant height during plant growth and development but also provides new research ideas for tobacco molecular breeding.
Collapse
Affiliation(s)
- Li Xu
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Yong Xu
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Jia-Rui Jiang
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | | | - Wen-Wu Yang
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Le-le Deng
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Qi-Li Mi
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Wan-Li Zeng
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Jing Li
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Qian Gao
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Hai-Ying Xiang
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Xue-Mei Li
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China.
| |
Collapse
|
5
|
Shen Y, Li L. Research Overview and Trends of the Effects of Gibberellins (GAs) on Rice Biological Processes: A Bibliometric Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1548. [PMID: 38891356 PMCID: PMC11174460 DOI: 10.3390/plants13111548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
Rice (Oryza sativa L.) is a vital crop that feeds more than half of the world's population. Gibberellins (GAs), a crucial phytohormone, play a significant role in the growth and development of rice. Since 1985, there has been a notable increase in the number of studies investigating the effects of GA on various biological processes in rice. Nevertheless, conducting scientific and quantitative research on the extensive literature available poses significant challenges, particularly in understanding the development trajectory of the field, examining major contributors, and identifying emerging research trends. The objective of this study is to address these challenges by analyzing global research patterns and trends using bibliometric methods from 1985 to 2024. Through the application of advanced analytical tools, progress in this field is studied in depth and the global research landscape is characterized from multiple dimensions including countries, institutions, authors, and journals. The analysis of 2118 articles extracted and screened from the Web of Science Core dataset shows a steady growth in the number of publications. The research published in China and the USA has significantly advanced the development of the field. In particular, institutions such as the Chinese Academy of Sciences and Nagoya University have shown impressive productivity. Lee In-Jung stands out as the most influential author. The journal Plant Physiology publishes the highest number of articles. The study also provides a thorough examination of current research hotspots, indicating a predominant focus on understanding the role of GAs in the biological processes that regulate diverse rice phenotypes, including plant height, seed dormancy, germination, and stress resistance. By tracing the development characteristics and key points in this area, this study contributes to a quantitative and comprehensive understanding of the impact of GAs on rice.
Collapse
Affiliation(s)
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China;
| |
Collapse
|
6
|
Yang G, Sun M, Brewer L, Tang Z, Nieuwenhuizen N, Cooney J, Xu S, Sheng J, Andre C, Xue C, Rebstock R, Yang B, Chang W, Liu Y, Li J, Wang R, Qin M, Brendolise C, Allan AC, Espley RV, Lin‐Wang K, Wu J. Allelic variation of BBX24 is a dominant determinant controlling red coloration and dwarfism in pear. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1468-1490. [PMID: 38169146 PMCID: PMC11123420 DOI: 10.1111/pbi.14280] [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: 10/09/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Variation in anthocyanin biosynthesis in pear fruit provides genetic germplasm resources for breeding, while dwarfing is an important agronomic trait, which is beneficial to reduce the management costs and allow for the implementation of high-density cultivation. Here, we combined bulked segregant analysis (BSA), quantitative trait loci (QTL), and structural variation (SV) analysis to identify a 14-bp deletion which caused a frame shift mutation and resulted in the premature translation termination of a B-box (BBX) family of zinc transcription factor, PyBBX24, and its allelic variation termed PyBBX24ΔN14. PyBBX24ΔN14 overexpression promotes anthocyanin biosynthesis in pear, strawberry, Arabidopsis, tobacco, and tomato, while that of PyBBX24 did not. PyBBX24ΔN14 directly activates the transcription of PyUFGT and PyMYB10 through interaction with PyHY5. Moreover, stable overexpression of PyBBX24ΔN14 exhibits a dwarfing phenotype in Arabidopsis, tobacco, and tomato plants. PyBBX24ΔN14 can activate the expression of PyGA2ox8 via directly binding to its promoter, thereby deactivating bioactive GAs and reducing the plant height. However, the nuclear localization signal (NLS) and Valine-Proline (VP) motifs in the C-terminus of PyBBX24 reverse these effects. Interestingly, mutations leading to premature termination of PyBBX24 were also identified in red sports of un-related European pear varieties. We conclude that mutations in PyBBX24 gene link both an increase in pigmentation and a decrease in plant height.
Collapse
Affiliation(s)
- Guangyan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Zhongshan Biological Breeding LaboratoryNanjingJiangsuChina
| | - Manyi Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Zhongshan Biological Breeding LaboratoryNanjingJiangsuChina
| | - Lester Brewer
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Zikai Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Niels Nieuwenhuizen
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Janine Cooney
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Shaozhuo Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Jiawen Sheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Christelle Andre
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Cheng Xue
- State Key Laboratory of Crop Biology, College of Horticulture Science and EngineeringShandong Agricultural UniversityTai'anChina
| | - Ria Rebstock
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Bo Yang
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Wenjing Chang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yueyuan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Jiaming Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Zhongshan Biological Breeding LaboratoryNanjingJiangsuChina
| | - Runze Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Mengfan Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Cyril Brendolise
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Andrew C. Allan
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Richard V. Espley
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Kui Lin‐Wang
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Jun Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Zhongshan Biological Breeding LaboratoryNanjingJiangsuChina
| |
Collapse
|
7
|
Hu D, Cui R, Wang K, Yang Y, Wang R, Zhu H, He M, Fan Y, Wang L, Wang L, Chu S, Zhang J, Zhang S, Yang Y, Zhai X, Lü H, Zhang D, Wang J, Kong F, Yu D, Zhang H, Zhang D. The Myb73-GDPD2-GA2ox1 transcriptional regulatory module confers phosphate deficiency tolerance in soybean. THE PLANT CELL 2024; 36:2176-2200. [PMID: 38345432 PMCID: PMC11132883 DOI: 10.1093/plcell/koae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/07/2024] [Indexed: 05/30/2024]
Abstract
Phosphorus is indispensable in agricultural production. An increasing food supply requires more efficient use of phosphate due to limited phosphate resources. However, how crops regulate phosphate efficiency remains largely unknown. Here, we identified a major quantitative trait locus, qPE19, that controls 7 low-phosphate (LP)-related traits in soybean (Glycine max) through linkage mapping and genome-wide association studies. We identified the gene responsible for qPE19 as GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE2 (GmGDPD2), and haplotype 5 represents the optimal allele favoring LP tolerance. Overexpression of GmGDPD2 significantly affects hormone signaling and improves root architecture, phosphate efficiency and yield-related traits; conversely, CRISPR/Cas9-edited plants show decreases in these traits. GmMyb73 negatively regulates GmGDPD2 by directly binding to its promoter; thus, GmMyb73 negatively regulates LP tolerance. GmGDPD2 physically interacts with GA 2-oxidase 1 (GmGA2ox1) in the plasma membrane, and overexpressing GmGA2ox1 enhances LP-associated traits, similar to GmGDPD2 overexpression. Analysis of double mutants for GmGDPD2 and GmGA2ox1 demonstrated that GmGDPD2 regulates LP tolerance likely by influencing auxin and gibberellin dose-associated cell division in the root. These results reveal a regulatory module that plays a major role in regulating LP tolerance in soybeans and is expected to be utilized to develop phosphate-efficient varieties to enhance soybean production, particularly in phosphate-deficient soils.
Collapse
Affiliation(s)
- Dandan Hu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ke Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongqing Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Mengshi He
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yukun Fan
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Le Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Li Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jinyu Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Shanshan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yifei Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuhao Zhai
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Haiyan Lü
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dandan Zhang
- State Key Laboratory of Agricultural Microbiology, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshe Wang
- Zhengzhou National Subcenter for Soybean Improvement, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| |
Collapse
|
8
|
Ahmad S, Lu C, Gao J, Wei Y, Xie Q, Jin J, Zhu G, Yang F. Integrated proteomic, transcriptomic, and metabolomic profiling reveals that the gibberellin-abscisic acid hub runs flower development in the Chinese orchid Cymbidium sinense. HORTICULTURE RESEARCH 2024; 11:uhae073. [PMID: 38738212 PMCID: PMC11088716 DOI: 10.1093/hr/uhae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/01/2024] [Indexed: 05/14/2024]
Abstract
The seasonal flowering Chinese Cymbidium produce an axillary floral meristem and require a dormancy period during cold conditions for flower development. However, the bud activation mechanism remains elusive. This study evaluates the multi-omics across six stages of flower development, along with functional analysis of core genes to decipher the innate mechanism of floral bud initiation and outgrowth in the Chinese orchid Cymbidium sinense. Transcriptome and proteome analyses identified 10 modules with essential roles in floral bud dormancy and activation. Gene clusters in the early stages of flower development were mainly related to flowering time regulation and meristem determination, while the late stages were correlated with hormone signaling pathways. The metabolome identified 69 potential hormones in which gibberellin (GA) and abscisic acid (ABA) were the main regulatory hubs, and GA4 and GA53 exhibited a reciprocal loop. Extraneous GA application caused rapid elongation of flower buds and promoted the expression of flower development genes. Contrarily, exogenous ABA application extended the dormancy process and ABA inhibitors induced dormancy release. Moreover, CsAPETALA1 (CsAP1) was identified as the potential target of ABA for floral bud activation. Transformation of CsAP1 in Arabidopsis and its transient overexpression in C. sinense protoplasts not only affected flowering time and floral organ morphogenesis in Arabidopsis but also orchestrated the expression of flowering and hormone regulatory genes. The presence of ABA response elements in the CsAP1 promoter, rapid downregulation of CsAP1 after exogenous ABA application, and the activation of the floral bud after ABA inhibitor treatment suggest that ABA can control bud outgrowth through CsAP1.
Collapse
Affiliation(s)
- Sagheer Ahmad
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qi Xie
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
| | - Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
| |
Collapse
|
9
|
Andres J, Schmunk LJ, Grau-Enguix F, Braguy J, Samodelov SL, Blomeier T, Ochoa-Fernandez R, Weber W, Al-Babili S, Alabadí D, Blázquez MA, Zurbriggen MD. Ratiometric gibberellin biosensors for the analysis of signaling dynamics and metabolism in plant protoplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:927-939. [PMID: 38525669 DOI: 10.1111/tpj.16725] [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: 07/26/2021] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
Gibberellins (GAs) are major regulators of developmental and growth processes in plants. Using the degradation-based signaling mechanism of GAs, we have built transcriptional regulator (DELLA)-based, genetically encoded ratiometric biosensors as proxies for hormone quantification at high temporal resolution and sensitivity that allow dynamic, rapid and simple analysis in a plant cell system, i.e. Arabidopsis protoplasts. These ratiometric biosensors incorporate a DELLA protein as a degradation target fused to a firefly luciferase connected via a 2A peptide to a renilla luciferase as a co-expressed normalization element. We have implemented these biosensors for all five Arabidopsis DELLA proteins, GA-INSENSITIVE, GAI; REPRESSOR-of-ga1-3, RGA; RGA-like1, RGL1; RGL2 and RGL3, by applying a modular design. The sensors are highly sensitive (in the low pm range), specific and dynamic. As a proof of concept, we have tested the applicability in three domains: the study of substrate specificity and activity of putative GA-oxidases, the characterization of GA transporters, and the use as a discrimination platform coupled to a GA agonists' chemical screening. This work demonstrates the development of a genetically encoded quantitative biosensor complementary to existing tools that allow the visualization of GA in planta.
Collapse
Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Lisa J Schmunk
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Federico Grau-Enguix
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Justine Braguy
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- The BioActives Lab, Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sophia L Samodelov
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Rocio Ochoa-Fernandez
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS and Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Salim Al-Babili
- The BioActives Lab, Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| |
Collapse
|
10
|
Shani E, Hedden P, Sun TP. Highlights in gibberellin research: A tale of the dwarf and the slender. PLANT PHYSIOLOGY 2024; 195:111-134. [PMID: 38290048 PMCID: PMC11060689 DOI: 10.1093/plphys/kiae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 02/01/2024]
Abstract
It has been almost a century since biologically active gibberellin (GA) was isolated. Here, we give a historical overview of the early efforts in establishing the GA biosynthesis and catabolism pathway, characterizing the enzymes for GA metabolism, and elucidating their corresponding genes. We then highlight more recent studies that have identified the GA receptors and early GA signaling components (DELLA repressors and F-box activators), determined the molecular mechanism of DELLA-mediated transcription reprograming, and revealed how DELLAs integrate multiple signaling pathways to regulate plant vegetative and reproductive development in response to internal and external cues. Finally, we discuss the GA transporters and their roles in GA-mediated plant development.
Collapse
Affiliation(s)
- Eilon Shani
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Peter Hedden
- Laboratory of Growth Regulators, Institute of Experimental Botany and Palacky University, 78371 Olomouc, Czech Republic
- Sustainable Soils and Crops, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Tai-ping Sun
- Department of Biology, Duke University, Durham, NC 27708, USA
| |
Collapse
|
11
|
Kaur Y, Das N. Gibberellin 2-Oxidases in Potato (Solanum tuberosum L.): Cloning, Characterization, In Silico Analysis and Molecular Docking. Mol Biotechnol 2024; 66:902-917. [PMID: 37061992 DOI: 10.1007/s12033-023-00745-8] [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: 08/31/2022] [Accepted: 04/02/2023] [Indexed: 04/17/2023]
Abstract
Gibberellins (GAs; tetracyclic di-terpenoid carboxylic acids) are endogenous plant growth regulators responsible for stimulating plant growth and development from seed germination to plant maturity. In potato (Solanum tuberosum L.), GA levels are known to be crucial in the complex process of tuberization. Gibberellin 2-oxidases (GA2oxs) inactivate bioactive GAs during stolon swelling and early stages of tuberization as evident from the predominant expression of a member of this gene family namely GA2ox1. We isolated and characterized a 1105-bp cDNA clone encoding a 340-aa GA2ox1 form, designated St-GA2ox1, using total RNA from growing tuber of a potato (Solanum tuberosum L.) cultivar, Kufri Chipsona-1 (KC-1) based on RT-PCR approach. A total of 26 GA2ox sequences were also retrieved from potato genome database and analysed. Multiple sequence alignment revealed sequence relatedness between the GA2oxs. Crucial protein motifs were identified. Phylogenetic analysis revealed the evolutionary relationships between the GA2oxs. Three-dimensional structure of St-GA2ox1 was predicted by using AlphaFold tool, validated by the predicted local-distance difference test and Ramachandran Plot. Structural analysis and molecular docking were carried out to identify domains, binding sites and affinity for the ligand. The STRING database and hydropathy analysis revealed the presence of a putative interaction site for other enzymes. Expression Atlas database and semi-quantitative RT-PCR revealed the expression patterns of various GA2ox forms in different potato organs. This comprehensive report would be useful in providing new insights into possible underlying mechanisms involved in tuber development, and could facilitate the targeted alteration of genes responsible to combat the stress and enhance tuber production.
Collapse
Affiliation(s)
- Yadveer Kaur
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India
| | - Niranjan Das
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India.
| |
Collapse
|
12
|
Cheng J, Jia Y, Hill C, He T, Wang K, Guo G, Shabala S, Zhou M, Han Y, Li C. Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement. J Adv Res 2024:S2090-1232(23)00408-3. [PMID: 38199453 DOI: 10.1016/j.jare.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
INTRODUCTION Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the "Green Revolution", modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known. OBJECTIVES This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits. METHODS Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8a in barley and RNA-seq was conducted to compare the transcriptome between wild type and mutants. Also, field trials in multiple environments were performed to detect the functional haplotypes. RESULTS There were ten GA2oxs that distinctly expressed in shoot, tiller, inflorescence, grain, embryo and root. Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA4 level. RNA-seq analysis revealed that genes involved in starch and sucrose metabolism were significantly decreased in the inflorescence of ga2ox8a mutants. Furthermore, haplotype analysis revealed one naturally occurring HvGA2ox8a haplotype was associated with decreased plant height, early flowering and wider and heavier seed. CONCLUSION Our results demonstrate the potential of manipulating GA2ox genes to fine tune GA signalling and biofunctions in desired plant tissues and open a promising avenue for minimising the trade-off effects of Green Revolution semi-dwarfing genes on grain size and weight. The knowledge will promote the development of next generation barley cultivars with better adaptation to a changing climate.
Collapse
Affiliation(s)
- Jingye Cheng
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia; Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Jia
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Camilla Hill
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia
| | - Tianhua He
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia
| | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ganggang Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia.
| | - Yong Han
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
| | - Chengdao Li
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
| |
Collapse
|
13
|
Zhou M, Li Y, Cheng Z, Zheng X, Cai C, Wang H, Lu K, Zhu C, Ding Y. Important Factors Controlling Gibberellin Homeostasis in Plant Height Regulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15895-15907. [PMID: 37862148 DOI: 10.1021/acs.jafc.3c03560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Plant height is an important agronomic trait that is closely associated with crop yield and quality. Gibberellins (GAs), a class of highly efficient plant growth regulators, play key roles in regulating plant height. Increasing reports indicate that transcriptional regulation is a major point of regulation of the GA pathways. Although substantial knowledge has been gained regarding GA biosynthetic and signaling pathways, important factors contributing to the regulatory mechanisms homeostatically controlling GA levels remain to be elucidated. Here, we provide an overview of current knowledge regarding the regulatory network involving transcription factors, noncoding RNAs, and histone modifications involved in GA pathways. We also discuss the mechanisms of interaction between GAs and other hormones in plant height development. Finally, future directions for applying knowledge of the GA hormone in crop breeding are described.
Collapse
Affiliation(s)
- Mei Zhou
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yakun Li
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhuowei Cheng
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xinyu Zheng
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Chong Cai
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Huizhen Wang
- Huangshan Institute of Product Quality Inspection, Huangshan 242700, China
| | - Kaixing Lu
- Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Ningbo 315000, China
| | - Cheng Zhu
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yanfei Ding
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| |
Collapse
|
14
|
Fukazawa J, Mori K, Ando H, Mori R, Kanno Y, Seo M, Takahashi Y. Jasmonate inhibits plant growth and reduces gibberellin levels via microRNA5998 and transcription factor MYC2. PLANT PHYSIOLOGY 2023; 193:2197-2214. [PMID: 37562026 DOI: 10.1093/plphys/kiad453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 08/12/2023]
Abstract
Jasmonate (JA) and gibberellins (GAs) exert antagonistic effects on plant growth and development in response to environmental and endogenous stimuli. Although the crosstalk between JA and GA has been elucidated, the role of JA in GA biosynthesis remains unclear. Therefore, in this study, we investigated the mechanism underlying JA-mediated regulation of endogenous GA levels in Arabidopsis (Arabidopsis thaliana). Transient and electrophoretic mobility shift assays showed that transcription factor MYC2 regulates GA inactivation genes. Using transgenic plants, we further evaluated the contribution of MYC2 in regulating GA inactivation genes. JA treatment increased DELLA accumulation but did not inhibit DELLA protein degradation. Additionally, JA treatment decreased bioactive GA content, including GA4, significantly decreased the expression of GA biosynthesis genes, including ent-kaurene synthase (AtKS), GA 3β-hydroxylase (AtGA3ox1), and AtGA3ox2, and increased the expression of GA inactivation genes, including GA 2 oxidase (AtGA2ox4), AtGA2ox7, and AtGA2ox9. Conversely, JA treatment did not significantly affect gene expression in the myc2 myc3 myc4 triple mutant, demonstrating the MYC2-4-dependent effects of JA in GA biosynthesis. Additionally, JA post-transcriptionally regulated AtGA3ox1 expression. We identified microRNA miR5998 as an AtGA3ox1-associated miRNA; its overexpression inhibited plant growth by suppressing AtGA3ox1 expression. Overall, our findings indicate that JA treatment inhibits endogenous GA levels and plant growth by decreasing the expression of GA biosynthesis genes and increasing the expression of GA inactivation genes via miR5998 and MYC2 activities.
Collapse
Affiliation(s)
- Jutarou Fukazawa
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Kazuya Mori
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Hiroki Ando
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Ryota Mori
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Yuri Kanno
- RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Yohsuke Takahashi
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| |
Collapse
|
15
|
Chan YO, Biová J, Mahmood A, Dietz N, Bilyeu K, Škrabišová M, Joshi T. Genomic Variations Explorer (GenVarX): a toolset for annotating promoter and CNV regions using genotypic and phenotypic differences. Front Genet 2023; 14:1251382. [PMID: 37928239 PMCID: PMC10623549 DOI: 10.3389/fgene.2023.1251382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/27/2023] [Indexed: 11/07/2023] Open
Abstract
The rapid growth of sequencing technology and its increasing popularity in biology-related research over the years has made whole genome re-sequencing (WGRS) data become widely available. A large amount of WGRS data can unlock the knowledge gap between genomics and phenomics through gaining an understanding of the genomic variations that can lead to phenotype changes. These genomic variations are usually comprised of allele and structural changes in DNA, and these changes can affect the regulatory mechanisms causing changes in gene expression and altering the phenotypes of organisms. In this research work, we created the GenVarX toolset, that is backed by transcription factor binding sequence data in promoter regions, the copy number variations data, SNPs and Indels data, and phenotypes data which can potentially provide insights about phenotypic differences and solve compelling questions in plant research. Analytics-wise, we have developed strategies to better utilize the WGRS data and mine the data using efficient data processing scripts, libraries, tools, and frameworks to create the interactive and visualization-enhanced GenVarX toolset that encompasses both promoter regions and copy number variation analysis components. The main capabilities of the GenVarX toolset are to provide easy-to-use interfaces for users to perform queries, visualize data, and interact with the data. Based on different input windows on the user interface, users can provide inputs corresponding to each field and submit the information as a query. The data returned on the results page is usually displayed in a tabular fashion. In addition, interactive figures are also included in the toolset to facilitate the visualization of statistical results or tool outputs. Currently, the GenVarX toolset supports soybean, rice, and Arabidopsis. The researchers can access the soybean GenVarX toolset from SoyKB via https://soykb.org/SoybeanGenVarX/, rice GenVarX toolset, and Arabidopsis GenVarX toolset from KBCommons web portal with links https://kbcommons.org/system/tools/GenVarX/Osativa and https://kbcommons.org/system/tools/GenVarX/Athaliana, respectively.
Collapse
Affiliation(s)
- Yen On Chan
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
| | - Jana Biová
- Department of Biochemistry, Faculty of Science, Palacky University in Olomouc, Olomouc, Czechia
| | - Anser Mahmood
- Division of Plant Science and Technology, University of Missouri-Columbia, Columbia, MO, United States
| | - Nicholas Dietz
- Division of Plant Science and Technology, University of Missouri-Columbia, Columbia, MO, United States
| | - Kristin Bilyeu
- Division of Plant Science and Technology, University of Missouri-Columbia, Columbia, MO, United States
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Columbia, MO, United States
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacky University in Olomouc, Olomouc, Czechia
| | - Trupti Joshi
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
- Department of Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri-Columbia, Columbia, MO, United States
| |
Collapse
|
16
|
Rashid D, Devani RS, Rodriguez-Granados NY, Abou-Choucha F, Troadec C, Morin H, Tan FQ, Marcel F, Huang HY, Hanique M, Zhang S, Verdenaud M, Pichot C, Rittener V, Huang Y, Benhamed M, Dogimont C, Boualem A, Bendahmane A. Ethylene produced in carpel primordia controls CmHB40 expression to inhibit stamen development. NATURE PLANTS 2023; 9:1675-1687. [PMID: 37653338 DOI: 10.1038/s41477-023-01511-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
Sex determination evolved to control the development of unisexual flowers. In agriculture, it conditions how plants are cultivated and bred. We investigated how female flowers develop in monoecious cucurbits. We discovered in melon, Cucumis melo, a mechanism in which ethylene produced in the carpel is perceived in the stamen primordia through spatially differentially expressed ethylene receptors. Subsequently, the CmEIN3/CmEIL1 ethylene signalling module, in stamen primordia, activates the expression of CmHB40, a transcription factor that downregulates genes required for stamen development and upregulates genes associated with organ senescence. Investigation of melon genetic biodiversity revealed a haplotype, originating in Africa, altered in EIN3/EIL1 binding to CmHB40 promoter and associated with bisexual flower development. In contrast to other bisexual mutants in cucurbits, CmHB40 mutations do not alter fruit shape. By disentangling fruit shape and sex-determination pathways, our work opens up new avenues in plant breeding.
Collapse
Affiliation(s)
- Dali Rashid
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Ravi Sureshbhai Devani
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Natalia Yaneth Rodriguez-Granados
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Fadi Abou-Choucha
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Christelle Troadec
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Halima Morin
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Feng-Quan Tan
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Fabien Marcel
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Hsin-Ya Huang
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Melissa Hanique
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Siqi Zhang
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Marion Verdenaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Clement Pichot
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Vincent Rittener
- Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE, Montfavet, France
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Catherine Dogimont
- Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE, Montfavet, France
| | - Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France.
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France.
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France.
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France.
| |
Collapse
|
17
|
Liu X, Wickland DP, Lin Z, Liu Q, Dos Santos LB, Hudson KA, Hudson ME. Promoter deletion in the soybean Compact mutant leads to overexpression of a gene with homology to the C20-gibberellin 2-oxidase family. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5153-5165. [PMID: 37551820 DOI: 10.1093/jxb/erad267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Height is a critical component of plant architecture, significantly affecting crop yield. The genetic basis of this trait in soybean remains unclear. In this study, we report the characterization of the Compact mutant of soybean, which has short internodes. The candidate gene was mapped to chromosome 17, and the interval containing the causative mutation was further delineated using biparental mapping. Whole-genome sequencing of the mutant revealed an 8.7 kb deletion in the promoter of the Glyma.17g145200 gene, which encodes a member of the class III gibberellin (GA) 2-oxidases. The mutation has a dominant effect, likely via increased expression of the GA 2-oxidase transcript observed in green tissue, as a result of the deletion in the promoter of Glyma.17g145200. We further demonstrate that levels of GA precursors are altered in the Compact mutant, supporting a role in GA metabolism, and that the mutant phenotype can be rescued with exogenous GA3. We also determined that overexpression of Glyma.17g145200 in Arabidopsis results in dwarfed plants. Thus, gain of promoter activity in the Compact mutant leads to a short internode phenotype in soybean through altered metabolism of gibberellin precursors. These results provide an example of how structural variation can control an important crop trait and a role for Glyma.17g145200 in soybean architecture, with potential implications for increasing crop yield.
Collapse
Affiliation(s)
- Xing Liu
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
- Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Daniel P Wickland
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Zhicong Lin
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
- Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Quilin Liu
- Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Karen A Hudson
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, USA
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois, Urbana, IL, USA
| |
Collapse
|
18
|
Wang T, Li J, Jiang Y, Zhang J, Ni Y, Zhang P, Yao Z, Jiao Z, Li H, Li L, Niu Y, Li Q, Yin G, Niu J. Wheat gibberellin oxidase genes and their functions in regulating tillering. PeerJ 2023; 11:e15924. [PMID: 37671358 PMCID: PMC10476609 DOI: 10.7717/peerj.15924] [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: 12/28/2022] [Accepted: 07/30/2023] [Indexed: 09/07/2023] Open
Abstract
Multiple genetic factors control tillering, a key agronomy trait for wheat (Triticum aestivum L.) yield. Previously, we reported a dwarf-monoculm mutant (dmc) derived from wheat cultivar Guomai 301, and found that the contents of gibberellic acid 3 (GA3) in the tiller primordia of dmc were significantly higher. Transcriptome analysis indicated that some wheat gibberellin oxidase (TaGAox) genes TaGA20ox-A2, TaGA20ox-B2, TaGA3ox-A2, TaGA20ox-A4, TaGA2ox-A10 and TaGA2ox-B10 were differentially expressed in dmc. Therefore, this study systematically analyzed the roles of gibberellin oxidase genes during wheat tillering. A total of 63 TaGAox genes were identified by whole genome analysis. The TaGAoxs were clustered to four subfamilies, GA20oxs, GA2oxs, GA3oxs and GA7oxs, including seven subgroups based on their protein structures. The promoter regions of TaGAox genes contain a large number of cis-acting elements closely related to hormone, plant growth and development, light, and abiotic stress responses. Segmental duplication events played a major role in TaGAoxs expansion. Compared to Arabidopsis, the gene collinearity degrees of the GAoxs were significantly higher among wheat, rice and maize. TaGAox genes showed tissue-specific expression patterns. The expressions of TaGAox genes (TaGA20ox-B2, TaGA7ox-A1, TaGA2ox10 and TaGA3ox-A2) were significantly affected by exogenous GA3 applications, which also significantly promoted tillering of Guomai 301, but didn't promote dmc. TaGA7ox-A1 overexpression transgenic wheat lines were obtained by Agrobacterium mediated transformation. Genomic PCR and first-generation sequencing demonstrated that the gene was integrated into the wheat genome. Association analysis of TaGA7ox-A1 expression level and tiller number per plant demonstrated that the tillering capacities of some TaGA7ox-A1 transgenic lines were increased. These data demonstrated that some TaGAoxs as well as GA signaling were involved in regulating wheat tillering, but the GA signaling pathway was disturbed in dmc. This study provided valuable clues for functional characterization of GAox genes in wheat.
Collapse
Affiliation(s)
- Ting Wang
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Junchang Li
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yumei Jiang
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jing Zhang
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yongjing Ni
- Henan Engineering Research Center of Wheat Spring Freeze Injury Identification, Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu, Henan, China, Shangqiu, China
| | - Peipei Zhang
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ziping Yao
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhixin Jiao
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Huijuan Li
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Lei Li
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yufan Niu
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Qiaoyun Li
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Guihong Yin
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jishan Niu
- Henan Technology Innovation Centre of Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan, China
| |
Collapse
|
19
|
Zhu W, Qi J, Chen J, Ma S, Liu K, Su H, Chai M, Huang Y, Xi X, Cao Z, Qin Y, Cai H. Identification of GA2ox Family Genes and Expression Analysis under Gibberellin Treatment in Pineapple ( Ananas comosus (L.) Merr.). PLANTS (BASEL, SWITZERLAND) 2023; 12:2673. [PMID: 37514287 PMCID: PMC10383957 DOI: 10.3390/plants12142673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
Gibberellin (GAs) plays an important regulatory role in the development and growth of pineapple (Ananas comosus (L.) Merr.). Bioinformatics was used to confirm the differential expression of GA2 gibberellin oxidase gene AcGA2oxs in the pineapple genome, which laid the foundation for exploring its role in pineapple. In this study, 42 GA2ox genes (AcGA2oxs) were identified in the pineapple genome, named from AcGA2ox1 to AcGA2ox42, and divided into four groups according to phylogenetic analysis. We also analyzed the gene structure, conserved motifs and chromosome localization of AcGA2oxs. AcGA2oxs within the same group had similar gene structure and motifs composition. Collinear analysis and cis-element analysis provided the basis for understanding the evolution and function of GA2ox genes in pineapple. In addition, we selected different tissue parts to analyze the expression profile of AcGA2oxs, and the results show that 41 genes were expressed, except for AcGA2ox18. AcGA2ox18 may not be expressed in these sites or may be pseudogenes. qRT-PCR (real-time fluorescence quantitative PCR) was used to detect the relative expression levels of the GA2ox gene family under different concentrations of GA3 treatment, and it was found that AcGA2ox gene expression was upregulated in different degrees under GA3 treatment. These results provide useful information for further study on the evolution and function of the GA2ox family in pineapple.
Collapse
Affiliation(s)
- Wenhui Zhu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingang Qi
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingdong Chen
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Suzhuo Ma
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kaichuang Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Han Su
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengnan Chai
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youmei Huang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinpeng Xi
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuangyuan Cao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Qin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hanyang Cai
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
20
|
Riekötter J, Oklestkova J, Muth J, Twyman RM, Epping J. Transcriptomic analysis of Chinese yam ( Dioscorea polystachya Turcz.) variants indicates brassinosteroid involvement in tuber development. Front Nutr 2023; 10:1112793. [PMID: 37215221 PMCID: PMC10196131 DOI: 10.3389/fnut.2023.1112793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Dioscorea is an important but underutilized genus of flowering plants that grows predominantly in tropical and subtropical regions. Several species, known as yam, develop large underground tubers and aerial bulbils that are used as food. The Chinese yam (D. polystachya Turcz.) is one of the few Dioscorea species that grows well in temperate regions and has been proposed as a climate-resilient crop to enhance food security in Europe. However, the fragile, club-like tubers are unsuitable for mechanical harvesting, which is facilitated by shorter and thicker storage organs. Brassinosteroids (BRs) play a key role in plant cell division, cell elongation and proliferation, as well as in the gravitropic response. We collected RNA-Seq data from the head, middle and tip of two tuber shape variants: F60 (long, thin) and F2000 (short, thick). Comparative transcriptome analysis of F60 vs. F2000 revealed 30,229 differentially expressed genes (DEGs), 1,393 of which were differentially expressed in the growing tip. Several DEGs are involved in steroid/BR biosynthesis or signaling, or may be regulated by BRs. The quantification of endogenous BRs revealed higher levels of castasterone (CS), 28-norCS, 28-homoCS and brassinolide in F2000 compared to F60 tubers. The highest BR levels were detected in the growing tip, and CS was the most abundant (439.6 ± 196.41 pmol/g in F2000 and 365.6 ± 112.78 pmol/g in F60). Exogenous 24-epi-brassinolide (epi-BL) treatment (20 nM) in an aeroponic system significantly increased the width-to-length ratio (0.045 ± 0.002) compared to the mock-treated plants (0.03 ± 0.002) after 7 weeks, indicating that exogenous epi-BL produces shorter and thicker tubers. In this study we demonstrate the role of BRs in D. polystachya tuber shape, providing insight into the role of plant hormones in yam storage organ development. We found that BRs can influence tuber shape in Chinese yam by regulating the expression of genes involved cell expansion. Our data can help to improve the efficiency of Chinese yam cultivation, which could provide an alternative food source and thus contribute to future food security in Europe.
Collapse
Affiliation(s)
- Jenny Riekötter
- Department of Biology, Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Jana Oklestkova
- Laboratory of Growth Regulators, The Czech Academy of Science, Institute of Experimental Botany and Palacký University, Faculty of Science, Olomouc, Czechia
| | - Jost Muth
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | | | - Janina Epping
- Department of Biology, Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| |
Collapse
|
21
|
Li Q, Liu N, Wu C. Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization. PLANTA 2023; 257:94. [PMID: 37031436 DOI: 10.1007/s00425-023-04126-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.
Collapse
Affiliation(s)
- Qinglin Li
- Crop Genesis and Novel Agronomy Center, Yangling, 712100, Shaanxi, China.
| | - Ning Liu
- Shandong ZhongnongTiantai Seed Co., Ltd, Pingyi, 273300, Shandong, China
| | - Chenglai Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| |
Collapse
|
22
|
Kaur H, Manchanda P, Kumar P, Dhall RK, Chhuneja P, Weng Y. Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.). Sci Rep 2023; 13:2403. [PMID: 36765113 PMCID: PMC9918540 DOI: 10.1038/s41598-023-29660-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertilization which can be either natural or induced. So far, a limited number of genes regulating parthenocarpic fruit set have been reported in several fruit or vegetable crops, most of which are involved in hormone biosynthesis or signalling. Although parthenocarpic cucumber has been widely used in commercial production for a long time; its genetic basis is not well understood. In this study, we retrieved thirty five parthenocarpy fruit-set related genes (PRGs) from bibliomic data in various plants. Thirty-five PRG homologs were identified in the cucumber genome via homology-based search. An in silico analysis was performed on phylogenetic tree, exon-intron structure, cis-regulatory elements in the promoter region, and conserved domains of their deduced proteins, which provided insights into the genetic make-up of parthenocarpy-related genes in cucumber. Simple sequence repeat (SSR) sequences were mined in these PRGs, and 31 SSR markers were designed. SSR genotyping identified three SSRs in two polymorphic genes. Quantitative real-time PCR of selected genes was conducted in five cucumber lines with varying degrees of parthenocarpic fruit set capacities, which revealed possible association of their expression with parthenocarpy. The results revealed that homologs CsWD40 and CsPIN-4 could be considered potential genes for determination of parthenocarpy as these genes showed parental polymorphism and differential gene expression in case of parthenocarpic and non-parthenocarpic parents.
Collapse
Affiliation(s)
- Harleen Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Pankaj Kumar
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Rajinder Kumar Dhall
- Department of Vegetable Science, College of Horticulture and Forestry, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
| |
Collapse
|
23
|
Gu Q, Wei Q, Hu Y, Chen M, Chen Z, Zheng S, Ma Q, Luo Z. Physiological and Full-Length Transcriptome Analyses Reveal the Dwarfing Regulation in Trifoliate Orange ( Poncirus trifoliata L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:271. [PMID: 36678984 PMCID: PMC9860739 DOI: 10.3390/plants12020271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Dwarfing rootstocks are capable of high-density planting and are therefore urgently needed in the modern citrus cultivation system. However, little is known about the physiological relevance and molecular basis underlying citrus height. This study aimed to comprehensively analyze phytohormone, carbohydrate, and associated transcriptome changes in the stem of two weak growth rootstocks ('TO' and 'FD') relative to the vigorous 'CC' rootstock. The phenotypic observation revealed that the plant height, plant weight, and internode length were reduced in dwarfing rootstocks. Moreover, the contents of indole-3-acetic acid (IAA), trans-zeatin (tZ), and abscisic acid (ABA), were higher in TO and FD rootstocks, whereas the gibberellin 3 (GA3) content was higher in the CC rootstocks. The carbohydrate contents, including sucrose, fructose, glucose, starch, and lignin significantly decreased in both the TO and FD rootstocks. The full-length transcriptome analysis revealed a potential mechanism regulating dwarfing phenotype that was mainly related to the phytohormone signaling transduction, sugar and starch degradation, lignin synthesis, and cellulose and hemicellulose degradation processes. In addition, many transcription factors (TFs), long non-coding RNAs (lncRNAs), and alternative splicing (AS) events were identified, which might act as important contributors to control the stem elongation and development in the weak growth rootstocks. These findings might deepen the understanding of the complex mechanisms of the stem development responsible for citrus dwarfing and provide a series of candidate genes for the application in breeding new rootstocks with intensive dwarfing.
Collapse
Affiliation(s)
- Qingqing Gu
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qingjiang Wei
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yongwei Hu
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Mengru Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ziwen Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shuang Zheng
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qiaoli Ma
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
24
|
Kong L, Wang Y, Chen L, Fang R, Li Y, Fang C, Dong L, Yuan X, Kong F, Liu B, Cheng Q, Lu S. Candidate loci for breeding compact plant-type soybean varieties. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:6. [PMID: 37312867 PMCID: PMC10248646 DOI: 10.1007/s11032-022-01352-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/24/2022] [Indexed: 06/15/2023]
Abstract
Plant height and node number are important agronomic traits that influence yield in soybean (Glycine max L.). Here, to better understand the genetic basis of the traits, we used two recombinant inbred line (RIL) populations to detect quantitative trait loci (QTLs) associated with plant height and node number in different environments. This analysis detected 9 and 21 QTLs that control plant height and node number, respectively. Among them, we identified two genomic regions that overlap with Determinate stem 1 (Dt1) and Dt2, which are known to influence both plant height and node number. Furthermore, different combinations of Dt1 and Dt2 alleles were enriched in distinct latitudes. In addition, we determined that the QTLs qPH-13-SE and qPH-13-DW in the two RIL populations overlap with genomic intervals associated with plant height and the QTL qNN-04-DW overlaps with an interval associated with node number. Combining the dwarf allele of qPH-13-SE/qPH-13-DW and the multiple-node allele of qNN-04-DW produced plants with ideal plant architecture, i.e., shorter main stems with more nodes. This plant type may help increase yield at high planting density. This study thus provides candidate loci for breeding elite soybean cultivars for plant height and node number. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01352-2.
Collapse
Affiliation(s)
- Lingping Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanping Wang
- Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Liyu Chen
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Ran Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yaru Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lidong Dong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaohui Yuan
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qun Cheng
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| |
Collapse
|
25
|
Zhang T, Wang J, Luo R, Man J, Long Q, Xu N. OsHLS1 regulates plant height and development by controlling active gibberellin accumulation in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111508. [PMID: 36283578 DOI: 10.1016/j.plantsci.2022.111508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
In this study, we identified a gene related to plant height, leaf, and premature senescence in rice, and named it OsHLS1. Through bioinformatics analysis, it was found that this gene belongs to a new gene family-HLS family, and this gene family exists widely in higher plants. Expression of OsHLS1 was significantly brought about by gibberellin (GA). Subcellular localization showed that OsHLS1 was located in the nucleus. oshls1-3 displayed a GA-deficient phenotype, with dwarf plants. In addition, oshls1-3 also showed premature senescence, shorter and narrower leaves, and pollen abortion. Exogenous GA3 can restore the plant height of oshls1-3. Histomorphological analysis showed that the gene affected the progress of internode cells in the first and third nodes under the rice panicle. Through the verification of the homologous gene AT4G25690 in Arabidopsis, it was found that the mutant at4g25690 lines also showed plant dwarfing, premature senescence, and shortening and narrowing of leaves and pollen abortion. OsHLS1 affected the expression levels of genes involved in the GA metabolic pathway and affected the content of active GA, thereby regulating plant height development in rice. In conclusion, we suggest that OsHLS1 regulates plant height and development by controlling the accumulation of active gibberellins in rice.
Collapse
Affiliation(s)
- Tonghua Zhang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Jiafu Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Rui Luo
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Jianmin Man
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Qing Long
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Ning Xu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China.
| |
Collapse
|
26
|
Qin L, Li C, Guo C, Wei L, Tian D, Li B, Wei D, Zhou W, Long S, He Z, Huang S, Wei S. Integrated metabolomic and transcriptomic analyses of regulatory mechanisms associated with uniconazole-induced dwarfism in banana. BMC PLANT BIOLOGY 2022; 22:614. [PMID: 36575388 PMCID: PMC9795754 DOI: 10.1186/s12870-022-04005-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Uniconazole is an effective plant growth regulator that can be used in banana cultivation to promote dwarfing and enhance lodging resistance. However, the mechanisms underlying banana dwarfing induced by uniconazole are unknown. In uniconazole-treated bananas, gibberellin (GA) was downregulated compared to the control groups. An integrative analysis of transcriptomes and metabolomes was performed on dwarf bananas induced by uniconazole and control groups. The key pathways involved in uniconazole-induced dwarfism in banana were determined according to the overlap of KEGG annotation of differentially expressed genes and (DEGs) differential abundant metabolites (DAMs). RESULTS Compared with the control groups, the levels of some flavonoids, tannins, and alkaloids increased, and those of most lipids, amino acids and derivatives, organic acids, nucleotides and derivatives, and terpenoids decreased in uniconazole-treated bananas. Metabolome analysis revealed the significant changes of flavonoids in uniconazole-treated bananas compared to control samples at both 15 days and 25 days post treatment. Transcriptome analysis shows that the DEGs between the treatment and control groups were related to a series of metabolic pathways, including lignin biosynthesis, phenylpropanoid metabolism, and peroxidase activity. Comprehensive analysis of the key pathways of co-enrichment of DEGs and DAMs from 15 d to 25 d after uniconazole treatment shows that flavonoid biosynthesis was upregulated. CONCLUSIONS In addition to the decrease in GA, the increase in tannin procyanidin B1 may contribute to dwarfing of banana plants by inhibiting the activity of GA. The increased of flavonoid biosynthesis and the change of lignin biosynthesis may lead to dwarfing phenotype of banana plants. This study expands our understanding of the mechanisms underlying uniconazole-induced banana dwarfing.
Collapse
Affiliation(s)
- Liuyan Qin
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China
| | - Chaosheng Li
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China.
| | - Chenglin Guo
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Liping Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China
| | - Dandan Tian
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China
| | - Baoshen Li
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China
| | - Wei Zhou
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China
| | - Shengfeng Long
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China
| | - Zhangfei He
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China
| | - Sumei Huang
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China
| | - Shaolong Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences/National Local Joint Engineering Research Center for Genetic Improvement and Cultivation Techniques of Banana Varieties/National Tropical Fruit Variety improvement Center Guangxi Banana Branch Center, Nanning, 530007, China.
| |
Collapse
|
27
|
Botton A, Girardi F, Ruperti B, Brilli M, Tijero V, Eccher G, Populin F, Schievano E, Riello T, Munné-Bosch S, Canton M, Rasori A, Cardillo V, Meggio F. Grape Berry Responses to Sequential Flooding and Heatwave Events: A Physiological, Transcriptional, and Metabolic Overview. PLANTS (BASEL, SWITZERLAND) 2022; 11:3574. [PMID: 36559686 PMCID: PMC9788187 DOI: 10.3390/plants11243574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Grapevine cultivation, such as the whole horticulture, is currently challenged by several factors, among which the extreme weather events occurring under the climate change scenario are the most relevant. Within this context, the present study aims at characterizing at the berry level the physiological response of Vitis vinifera cv. Sauvignon Blanc to sequential stresses simulated under a semi-controlled environment: flooding at bud-break followed by multiple summer stress (drought plus heatwave) occurring at pre-vèraison. Transcriptomic and metabolomic assessments were performed through RNASeq and NMR, respectively. A comprehensive hormone profiling was also carried out. Results pointed out a different response to the heatwave in the two situations. Flooding caused a developmental advance, determining a different physiological background in the berry, thus affecting its response to the summer stress at both transcriptional levels, with the upregulation of genes involved in oxidative stress responses, and metabolic level, with the increase in osmoprotectants, such as proline and other amino acids. In conclusion, sequential stress, including a flooding event at bud-break followed by a summer heatwave, may impact phenological development and berry ripening, with possible consequences on berry and wine quality. A berry physiological model is presented that may support the development of sustainable vineyard management solutions to improve the water use efficiency and adaptation capacity of actual viticultural systems to future scenarios.
Collapse
Affiliation(s)
- Alessandro Botton
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
- Interdepartmental Research Centre for Viticulture and Enology—CIRVE, University of Padova, Via XXVIII Aprile 14, Conegliano, 31015 Treviso, Italy
| | - Francesco Girardi
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Benedetto Ruperti
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
- Interdepartmental Research Centre for Viticulture and Enology—CIRVE, University of Padova, Via XXVIII Aprile 14, Conegliano, 31015 Treviso, Italy
| | - Matteo Brilli
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Veronica Tijero
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Giulia Eccher
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Francesca Populin
- Unit of Fruit Crop Genetics and Breeding, Research and Innovation Centre—CRI, Edmund Mach Foundation—FEM, Via E. Mach 1, San Michele all’Adige, 38098 Trento, Italy
| | - Elisabetta Schievano
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Tobia Riello
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Diagonal 643, 08017 Barcelona, Spain
| | - Monica Canton
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Angela Rasori
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Valerio Cardillo
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Franco Meggio
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
- Interdepartmental Research Centre for Viticulture and Enology—CIRVE, University of Padova, Via XXVIII Aprile 14, Conegliano, 31015 Treviso, Italy
| |
Collapse
|
28
|
Manipulating GA-Related Genes for Cereal Crop Improvement. Int J Mol Sci 2022; 23:ijms232214046. [PMID: 36430524 PMCID: PMC9696284 DOI: 10.3390/ijms232214046] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
The global population is projected to experience a rapid increase in the future, which poses a challenge to global food sustainability. The "Green Revolution" beginning in the 1960s allowed grain yield to reach two billion tons in 2000 due to the introduction of semi-dwarfing genes in cereal crops. Semi-dwarfing genes reduce the gibberellin (GA) signal, leading to short plant stature, which improves the lodging resistance and harvest index under modern fertilization practices. Here, we reviewed the literature on the function of GA in plant growth and development, and the role of GA-related genes in controlling key agronomic traits that contribute to grain yield in cereal crops. We showed that: (1) GA is a significant phytohormone in regulating plant development and reproduction; (2) GA metabolism and GA signalling pathways are two key components in GA-regulated plant growth; (3) GA interacts with other phytohormones manipulating plant development and reproduction; and (4) targeting GA signalling pathways is an effective genetic solution to improve agronomic traits in cereal crops. We suggest that the modification of GA-related genes and the identification of novel alleles without a negative impact on yield and adaptation are significant in cereal crop breeding for plant architecture improvement. We observed that an increasing number of GA-related genes and their mutants have been functionally validated, but only a limited number of GA-related genes have been genetically modified through conventional breeding tools and are widely used in crop breeding successfully. New genome editing technologies, such as the CRISPR/Cas9 system, hold the promise of validating the effectiveness of GA-related genes in crop development and opening a new venue for efficient and accelerated crop breeding.
Collapse
|
29
|
Ma Z, Jin YM, Wu T, Hu L, Zhang Y, Jiang W, Du X. OsDREB2B, an AP2/ERF transcription factor, negatively regulates plant height by conferring GA metabolism in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1007811. [PMID: 36388558 PMCID: PMC9650310 DOI: 10.3389/fpls.2022.1007811] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/05/2022] [Indexed: 05/31/2023]
Abstract
The AP2/ERF family is a large group of plant-specific transcription factors that play an important role in many biological processes, such as growth, development, and abiotic stress responses. OsDREB2B, a dehydration responsive factor (DRE/CRT) in the DREB subgroup of the AP2/ERF family, is associated with abiotic stress responses, such as cold, drought, salt, and heat stress, in Arabidopsis or rice. However, its role in regulating plant growth and development in rice is unclear. In this study, we reported a new function of OsDREB2B, which negatively regulates plant height in rice. Compared with wild type (WT), OsDREB2B-overexpressing (OE) rice exhibited dwarf phenotypes, such as reduction in plant height, internode length, and seed length, as well as grain yield, while the knockout mutants developed by CRISPR/Cas9 technology exhibited similar phenotypes. Spatial expression analysis revealed that OsDREB2B was highly expressed in the leaf sheaths. Under exogenous GA3 application, OsDREB2B expression was induced, and the length of the second leaf sheath of the OsDREB2B-OE lines recovered to that of the WT. OsDREB2B localized to the nucleus of the rice protoplast acted as a transcription activator and upregulated OsAP2-39 by directly binding to its promoter. OsDREB2B-OE lines reduced endogenous bioactive GA levels by downregulating seven GA biosynthesis genes and upregulating eight GA deactivation genes but not GA signaling genes. The yeast two-hybrid assay and bimolecular fluorescence complementation assay showed that OsDREB2B interacted with OsWRKY21. In summary, our study suggests that OsDREB2B plays a negative role in rice growth and development by regulating GA metabolic gene expression, which is mediated by OsAP2-39 and OsWRKY21, thereby reducing GA content and rice plant height.
Collapse
Affiliation(s)
- Ziming Ma
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Yong-Mei Jin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Tao Wu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Lanjuan Hu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Ying Zhang
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wenzhu Jiang
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Xinglin Du
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| |
Collapse
|
30
|
Li L, Wang J, Chen J, Wang Z, Qaseem MF, Li H, Wu A. Physiological and Transcriptomic Responses of Growth in Neolamarckia cadamba Stimulated by Exogenous Gibberellins. Int J Mol Sci 2022; 23:ijms231911842. [PMID: 36233144 PMCID: PMC9569647 DOI: 10.3390/ijms231911842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 01/09/2023] Open
Abstract
(1) The phytohormones gibberellins (GAs) play a crucial role in plant growth and development, such as seed germination, flowering, fruiting, and stem elongation. Although many biological roles of GAs have been studied intensively, the molecular mechanisms of GAs in woody plants are still unclear. (2) In this study, we investigated the effects of exogenous application of GAs on Neolamarckia cadamba. (3) The height and biomass of N. cadamba increased after 7 days of GA treatment, especially on the second internode. Transcriptome analysis showed that although the majority of genes involved in the GA signaling pathway were up-regulated, the expression of GA20 oxidase (GA20ox) and GA3 oxidase (GA3ox) was down-regulated in the 3 days GA-treated group compared to the CK group. The expression of the cell elongation-related basic helix-loop-helix genes bHLH74 and bHLH49 was up-regulated in the GA-treated group compared with the CK group. Transcriptional expression levels of transcription factors involved in hormone signaling were changed, mainly including bHLH, ethylene response factor (ERF), and WRKY families. In addition, the transcriptional expression level of the key enzymes engaged in the phenylalanine pathway was downregulated after GA treatment. (4) In brief, our findings reveal the physiological and molecular mechanisms of exogenous GA treatment stimulation in N. cadamba.
Collapse
Affiliation(s)
- Lu Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Jiaqi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Jiajun Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Zhihua Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Mirza Faisal Qaseem
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Huiling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (H.L.); (A.W.)
| | - Aimin Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (H.L.); (A.W.)
| |
Collapse
|
31
|
Zhao L, Li M, Ma X, Luo D, Zhou Q, Liu W, Liu Z. Transcriptome analysis and identification of abscisic acid and gibberellin-related genes during seed development of alfalfa (Medicago sativa L.). BMC Genomics 2022; 23:651. [PMID: 36100883 PMCID: PMC9472388 DOI: 10.1186/s12864-022-08875-0] [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: 02/13/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alfalfa (Medicago sativa) is a widely cultivated plant. Unlike many crops, the main goal of breeding alfalfa is to increase its aboveground biomass rather than the biomass of its seeds. However, the low yield of alfalfa seeds limits alfalfa production. Many studies have explored the factors affecting seed development, in which phytohormones, especially ABA and GAs, play an important role in seed development. RESULTS Here, we performed a transcriptome analysis of alfalfa seeds at five development stages. A total of 16,899 differentially expressed genes (DEGs) were identified and classified into 10 clusters, and the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined. The contents of ABA, GA1, GA3, GA4 and GA7 in alfalfa seeds at five development stages were determined. In addition, 14 ABA-related DEGs and 20 GA-related DEGs were identified and analysed. These DEGs are involved in plant hormone pathways and play an important role in seed development. Moreover, morphological and physiological analyses revealed the dynamic changes during the development of alfalfa seeds. CONCLUSION Overall, our study is the first to analyse the transcriptome across various stages of seed development in alfalfa. The results of our study could be used to improve alfalfa seed yield. The key ABA and GA related-genes are potential targets for improving alfalfa seed yield via genetic engineering in the future.
Collapse
Affiliation(s)
- Lu Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Mingyu Li
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Xiaomei Ma
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Dong Luo
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Qiang Zhou
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
| |
Collapse
|
32
|
Li C, Dong S, Beckles DM, Miao H, Sun J, Liu X, Wang W, Zhang S, Gu X. The qLTG1.1 candidate gene CsGAI regulates low temperature seed germination in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2593-2607. [PMID: 35764690 DOI: 10.1007/s00122-022-04097-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
The CsGAI gene, identified by map-based, was involved in regulating seed germination in low temperature via the GA and ABA signaling pathways. Low temperature reduces the percentage of seeds germinating and delays seed germinating time, thus posing a threat to cucumber production. However, the molecular mechanism regulating low temperature germination in cucumber is unknown. We here dissected a major quantitative trait locus qLTG1.1 that controls seed germination at low temperature in cucumber. First, we fine-mapped qLTG1.1 to a 46.3-kb interval, containing three candidate genes. Sequence alignment and gene expression analysis identified Csa1G408720 as the gene of interest that was highly expressed in seeds, and encoded a highly conserved, low temperature-regulated DELLA family protein CsGAI. GUS expression analysis indicated that higher promoter activity underscored higher transcriptional expression of the CsGAI gene. Consistent with the known roles of GAI in ABA and GA signaling during germination, genes involved in the GA (CsGA2ox, CsGA3ox) and ABA biosynthetic pathways (CsABA1, CsABA2, CsAAO3 and CsNCED) were found to be differently regulated in the tolerant and sensitive genotypes under low temperatures, and this was reflected in differences in their ratio of GA-to-ABA. Based on these data, we proposed a working model explaining how CsGAI integrates the GA and ABA signaling pathways, to regulate cucumber seed germination at low temperature, thus providing new insights into this mechanism.
Collapse
Affiliation(s)
- Caixia Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shaoyun Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Diane M Beckles
- Department of Plant Sciences, University of California, One Shield Avenue, Dav is Davis, CA, 95616, USA
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaqiang Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoping Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
33
|
Huang S, Gao Y, Xue M, Xu J, Liao R, Shang S, Yang X, Zhao Y, Li C, Liu Z, Feng H. BrKAO2 mutations disrupt leafy head formation in Chinese cabbage (Brassica rapa L. ssp. pekinensis). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2453-2468. [PMID: 35726066 DOI: 10.1007/s00122-022-04126-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
The role of BrKAO2 in leafy head formation was confirmed by using two allelic Chinese cabbage mutants. Chinese cabbage yield and quality are determined by leafy head formation. Cloning and characterising the key genes regulating leafy head formation are essential for its varietal improvement. We used an EMS-mutagenised population of the heading type 'FT' Chinese cabbage line and identified two allelic non-heading mutants, i.e. nhm3-1 and nhm3-2. Genetic analysis showed that the mutant trait was controlled by a single recessive gene. MutMap and Kompetitive Allele Specific PCR genotyping revealed that BraA05g012440.3C was the candidate gene, which encodes ent-kaurenoic acid oxidase 2 in gibberellin (GA) biosynthetic pathway. It was named BrKAO2. Two non-synonymous mutations in the second BrKAO2 exon, respectively, accounted for the mutant phenotypes of nhm3-1 and nhm3-2. BrKAO2 was expressed during all leaf development stages, and there were no significant differences between the wild type and mutants in terms of BrKAO2 expression. The mutant phenotypes were restored to the wild type via exogenous GA3 application. RNA-Seq was performed on wild-type 'FT', nhm3-1, and nhm3-1 + GA3 rosette leaves, and several key genes involved in GA biosynthesis, signal transduction, and leafy head development were identified. These findings indicate that BrKAO2 is responsible for the leafy head formation in nhm3 mutants.
Collapse
Affiliation(s)
- Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Yue Gao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Meihui Xue
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Junjie Xu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Ruiqi Liao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Shayu Shang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Xiaofei Yang
- Integrated Department, Wafangdian Agriculture Technology and Popularization Center, Dalian, 116300, China
| | - Yonghui Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Chengyu Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China.
| |
Collapse
|
34
|
Ptošková K, Szecówka M, Jaworek P, Tarkowská D, Petřík I, Pavlović I, Novák O, Thomas SG, Phillips AL, Hedden P. Changes in the concentrations and transcripts for gibberellins and other hormones in a growing leaf and roots of wheat seedlings in response to water restriction. BMC PLANT BIOLOGY 2022; 22:284. [PMID: 35676624 PMCID: PMC9178827 DOI: 10.1186/s12870-022-03667-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Bread wheat (Triticum aestivum) is a major source of nutrition globally, but yields can be seriously compromised by water limitation. Redistribution of growth between shoots and roots is a common response to drought, promoting plant survival, but reducing yield. Gibberellins (GAs) are necessary for shoot and root elongation, but roots maintain growth at lower GA concentrations compared with shoots, making GA a suitable hormone for mediating this growth redistribution. In this study, the effect of progressive drought on GA content was determined in the base of the 4th leaf and root tips of wheat seedlings, containing the growing regions, as well as in the remaining leaf and root tissues. In addition, the contents of other selected hormones known to be involved in stress responses were determined. Transcriptome analysis was performed on equivalent tissues and drought-associated differential expression was determined for hormone-related genes. RESULTS After 5 days of applying progressive drought to 10-day old seedlings, the length of leaf 4 was reduced by 31% compared with watered seedlings and this was associated with significant decreases in the concentrations of bioactive GA1 and GA4 in the leaf base, as well as of their catabolites and precursors. Root length was unaffected by drought, while GA concentrations were slightly, but significantly higher in the tips of droughted roots compared with watered plants. Transcripts for the GA-inactivating gene TaGA2ox4 were elevated in the droughted leaf, while those for several GA-biosynthesis genes were reduced by drought, but mainly in the non-growing region. In response to drought the concentrations of abscisic acid, cis-zeatin and its riboside increased in all tissues, indole-acetic acid was unchanged, while trans-zeatin and riboside, jasmonate and salicylic acid concentrations were reduced. CONCLUSIONS Reduced leaf elongation and maintained root growth in wheat seedlings subjected to progressive drought were associated with attenuated and increased GA content, respectively, in the growing regions. Despite increased TaGA2ox4 expression, lower GA levels in the leaf base of droughted plants were due to reduced biosynthesis rather than increased catabolism. In contrast to GA, the other hormones analysed responded to drought similarly in the leaf and roots, indicating organ-specific differential regulation of GA metabolism in response to drought.
Collapse
Affiliation(s)
- Klára Ptošková
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Marek Szecówka
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Pavel Jaworek
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Ivan Petřík
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Iva Pavlović
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Stephen G Thomas
- Department of Plant Science, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Andrew L Phillips
- Department of Plant Science, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Peter Hedden
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic.
- Department of Plant Science, Rothamsted Research, Harpenden, AL5 2JQ, UK.
| |
Collapse
|
35
|
Interactions of Gibberellins with Phytohormones and Their Role in Stress Responses. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, the current knowledge on gibberellins’ homeostasis and modes of action is outlined. Besides this, the complex interrelations between gibberellins and other plant growth regulators are also described, providing an intricate network of interactions that ultimately drives towards precise and specific gene expression. Thus, genes and proteins identified as being involved in gibberellin responses in model and non-model species are highlighted. Furthermore, the molecular mechanisms governing the gibberellins’ relation to stress responses are also depicted. This review aims to provide a comprehensive picture of the state-of-the-art of the current perceptions of the interactions of gibberellins with other phytohormones, and their responses to plant stresses, thus allowing for the identification of the specific mechanisms involved. This knowledge will help us to improve our understanding of gibberellins’ biology, and might help increase the biotechnological toolbox needed to refine plant resilience, particularly under a climate change scenario.
Collapse
|
36
|
Basnet P, Um T, Roy NS, Cho WS, Park SC, Park KC, Choi IY. Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean. Front Genet 2022; 13:805347. [PMID: 35281824 PMCID: PMC8907156 DOI: 10.3389/fgene.2022.805347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
In cultivated plants, shoot morphology is an important factor that influences crop economic value. However, the effects of gene expression patterns on shoot morphology are not clearly understood. In this study, the molecular mechanism behind shoot morphology (including leaf, stem, and node) was analyzed using RNA sequencing to compare weedy (creeper) and cultivar (stand) growth types obtained in F7 derived from a cross of wild and cultivated soybeans. A total of 12,513 (in leaves), 14,255 (in stems), and 11,850 (in nodes) differentially expressed genes were identified among weedy and cultivar soybeans. Comparative transcriptome and expression analyses revealed 22 phytohormone-responsive genes. We found that GIBBERELLIN 2-OXIDASE 8 (GA2ox), SPINDLY (SPY), FERONIA (FER), AUXIN RESPONSE FACTOR 8 (ARF8), CYTOKININ DEHYDROGENASE-1 (CKX1), and ARABIDOPSIS HISTIDINE KINASE-3 (AHK3), which are crucial phytohormone response genes, were mainly regulated in the shoot of weedy and cultivar types. These results indicate that interactions between phytohormone signaling genes regulate shoot morphology in weedy and cultivar growth type plants. Our study provides insights that are useful for breeding and improving crops to generate high-yield soybean varieties.
Collapse
Affiliation(s)
- Prakash Basnet
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Taeyoung Um
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Neha Samir Roy
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Woo Suk Cho
- Department of Agricultural Biotechnology/National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Soo Chul Park
- Department of Agricultural Biotechnology/National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Kyong-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
- *Correspondence: Ik-Young Choi,
| |
Collapse
|
37
|
Dong S, Tarkowska D, Sedaghatmehr M, Welsch M, Gupta S, Mueller-Roeber B, Balazadeh S. The HB40-JUB1 transcriptional regulatory network controls gibberellin homeostasis in Arabidopsis. MOLECULAR PLANT 2022; 15:322-339. [PMID: 34728415 DOI: 10.1016/j.molp.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 10/11/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
The gibberellins (GAs) are phytohormones that play fundamental roles in almost every aspect of plant growth and development. Although GA biosynthetic and signaling pathways are well understood, the mechanisms that control GA homeostasis remain largely unclear in plants. Here, we demonstrate that the homeobox transcription factor (TF) HB40 of the HD-Zip family regulates GA content at two additive control levels in Arabidopsis thaliana. We show that HB40 expression is induced by GA and in turn reduces the levels of endogenous bioactive GAs by simultaneously reducing GA biosynthesis and increasing GA deactivation. Consistently, HB40 overexpression leads to typical GA-deficiency traits, such as small rosettes, reduced plant height, delayed flowering, and male sterility. By contrast, a loss-of-function hb40 mutation enhances GA-controlled growth. Genome-wide RNA sequencing combined with molecular-genetic analyses revealed that HB40 directly activates the transcription of JUNGBRUNNEN1 (JUB1), a key TF that represses growth by suppressing GA biosynthesis and signaling. HB40 also activates genes encoding GA 2-oxidases (GA2oxs), which are major GA-catabolic enzymes. The effect of HB40 on plant growth is ultimately mediated through the induction of nuclear growth-repressing DELLA proteins. Collectively, our results reveal the important role of the HB40-JUB1 regulatory network in controlling GA homeostasis during plant growth.
Collapse
Affiliation(s)
- Shuchao Dong
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Danuse Tarkowska
- Laboratory of Growth Regulators, Czech Academy of Sciences, Institute of Experimental Botany & Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Mastoureh Sedaghatmehr
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Maryna Welsch
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
| | - Saurabh Gupta
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
| | - Salma Balazadeh
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| |
Collapse
|
38
|
Gómez-Soto D, Allona I, Perales M. FLOWERING LOCUS T2 Promotes Shoot Apex Development and Restricts Internode Elongation via the 13-Hydroxylation Gibberellin Biosynthesis Pathway in Poplar. FRONTIERS IN PLANT SCIENCE 2022; 12:814195. [PMID: 35185961 PMCID: PMC8853612 DOI: 10.3389/fpls.2021.814195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/22/2021] [Indexed: 06/11/2023]
Abstract
The adaptation and survival of boreal and temperate perennials relies on the precise demarcation of the growing season. Seasonal growth and development are defined by day length and temperature signals. Under long-day conditions in spring, poplar FLOWERING LOCUS T2 (FT2) systemically induces shoot growth. In contrast, FT2 downregulation induced by autumnal short days triggers growth cessation and bud set. However, the molecular role of FT2 in local and long-range signaling is not entirely understood. In this study, the CRISPR/Cas9 editing tool was used to generate FT2 loss of function lines of hybrid poplar. Results indicate that FT2 is essential to promote shoot apex development and restrict internode elongation under conditions of long days. The application of bioactive gibberellins (GAs) to apical buds in FT2 loss of function lines was able to rescue bud set. Expression analysis of GA sensing and metabolic genes and hormone quantification revealed that FT2 boosts the 13-hydroxylation branch of the GA biosynthesis pathway in the shoot apex. Paclobutrazol treatment of WT leaves led to limited internode growth in the stem elongation zone. In mature leaves, FT2 was found to control the GA 13-hydroxylation pathway by increasing GA2ox1 and reducing GA3ox2 expression, causing reduced GA1 levels. We here show that in poplar, the FT2 signal promotes shoot apex development and restricts internode elongation through the GA 13-hydroxylation pathway.
Collapse
Affiliation(s)
- Daniela Gómez-Soto
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria, CNINIA (CSIC), Madrid, Spain
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria, CNINIA (CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria, CNINIA (CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| |
Collapse
|
39
|
Kawai K, Takehara S, Kashio T, Morii M, Sugihara A, Yoshimura H, Ito A, Hattori M, Toda Y, Kojima M, Takebayashi Y, Furuumi H, Nonomura KI, Mikami B, Akagi T, Sakakibara H, Kitano H, Matsuoka M, Ueguchi-Tanaka M. Evolutionary alterations in gene expression and enzymatic activities of gibberellin 3-oxidase 1 in Oryza. Commun Biol 2022; 5:67. [PMID: 35046494 PMCID: PMC8770518 DOI: 10.1038/s42003-022-03008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 12/23/2021] [Indexed: 11/15/2022] Open
Abstract
Proper anther and pollen development are important for plant reproduction. The plant hormone gibberellin is important for anther development in rice, but its gametophytic functions remain largely unknown. Here, we report the functional and evolutionary analyses of rice gibberellin 3-oxidase 1 (OsGA3ox1), a gibberellin synthetic enzyme specifically expressed in the late developmental stages of anthers. Enzymatic and X-ray crystallography analyses reveal that OsGA3ox1 has a higher GA7 synthesis ratio than OsGA3ox2. In addition, we generate an osga3ox1 knockout mutant by genome editing and demonstrate the bioactive gibberellic acid synthesis by the OsGA3ox1 action during starch accumulation in pollen via invertase regulation. Furthermore, we analyze the evolution of Oryza GA3ox1s and reveal that their enzyme activity and gene expression have evolved in a way that is characteristic of the Oryza genus and contribute to their male reproduction ability. The authors solve the crystal structure of OsGA3ox2 and predict that of OsGA3ox1. These enzymes catalyze the final step in the biosynthesis of gibberellin, one of the plant hormones. Evolutionary analysis combined with the new structure reveal important aspects of the OsGA3ox1’s function in plant male reproduction.
Collapse
|
40
|
Koga H, Kojima M, Takebayashi Y, Sakakibara H, Tsukaya H. Identification of the unique molecular framework of heterophylly in the amphibious plant Callitriche palustris L. THE PLANT CELL 2021; 33:3272-3292. [PMID: 34312675 PMCID: PMC8505872 DOI: 10.1093/plcell/koab192] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/19/2021] [Indexed: 05/19/2023]
Abstract
Heterophylly is the development of different leaf forms in a single plant depending on the environmental conditions. It is often observed in amphibious aquatic plants that can grow under both aerial and submerged conditions. Although heterophylly is well recognized in aquatic plants, the associated developmental mechanisms and the molecular basis remain unclear. To clarify these underlying developmental and molecular mechanisms, we analyzed heterophyllous leaf formation in an aquatic plant, Callitriche palustris. Morphological analyses revealed extensive cell elongation and the rearrangement of cortical microtubules in the elongated submerged leaves of C. palustris. Our observations also suggested that gibberellin, ethylene, and abscisic acid all regulate the formation of submerged leaves. However, the perturbation of one or more of the hormones was insufficient to induce the formation of submerged leaves under aerial conditions. Finally, we analyzed gene expression changes during aerial and submerged leaf development and narrowed down the candidate genes controlling heterophylly via transcriptomic comparisons, including a comparison with a closely related terrestrial species. We discovered that the molecular mechanism regulating heterophylly in C. palustris is associated with hormonal changes and diverse transcription factor gene expression profiles, suggesting differences from the corresponding mechanisms in previously investigated amphibious plants.
Collapse
Affiliation(s)
- Hiroyuki Koga
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Author for correspondence:
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
41
|
Fukazawa J, Miyamoto C, Ando H, Mori K, Takahashi Y. DELLA-GAF1 complex is involved in tissue-specific expression and gibberellin feedback regulation of GA20ox1 in Arabidopsis. PLANT MOLECULAR BIOLOGY 2021; 107:147-158. [PMID: 34562198 DOI: 10.1007/s11103-021-01195-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
The GAF1 transcription factor is shown to bind to the promoter of the Arabidopsis GA-biosynthetic enzyme GA20ox1 and, in association with DELLA protein, promotes GA20ox1 expression, thereby contributing to its feedback regulation and tissue specificity. Gibberellins (GAs) are phytohormones that promote plant growth and development, including germination, elongation, flowering, and floral development. Homeostasis of endogenous GA levels is controlled by GA feedback regulation. DELLAs are negative regulators of GA signaling that are rapidly degraded in the presence of GAs. DELLAs regulate several target genes, including AtGA20ox2 and AtGA3ox1, encoding the GA-biosynthetic enzymes GA 20-oxidase and GA 3-oxidase, respectively. Previous studies have identified GAI-ASSOCIATED FACTOR 1 (GAF1) as a DELLA interactor, with which DELLAs act as transcriptional coactivators; furthermore, AtGA20ox2, AtGA3ox1, and AtGID1b were identified as target genes of the DELLA-GAF1 complex. Among the five Arabidopsis GA20ox genes, AtGA20ox1 is the most highly expressed gene during vegetative growth; its expression is controlled by GA feedback regulation. Here, we investigated whether AtGA20ox1 is regulated by the DELLA-GAF1 complex. The electrophoretic mobility shift and transactivation assays showed that three GAF1-binding sites exist in the AtGA20ox1 promoter. Using transgenic plants, we further evaluated the contribution of the DELLA-GAF1 complex to GA feedback regulation and tissue-specific expression. Mutations in two GAF1-binding sites obliterated the negative feedback regulation and tissue-specific expression of AtGA20ox1 in transgenic plants. Thus, our results showed that GAF1-binding sites are involved in GA feedback regulation and tissue-specific expression of AtGA20ox1 in Arabidopsis, suggesting that the DELLA-GAF1 complex is involved in both processes.
Collapse
Affiliation(s)
- Jutarou Fukazawa
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Chika Miyamoto
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Hiroki Ando
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Kazuya Mori
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Yohsuke Takahashi
- Program of Basic Biology, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| |
Collapse
|
42
|
Gao X, Yuan Y, Liu Z, Liu C, Xin H, Zhang Y, Gai S. Chilling and gibberellin acids hyperinduce β-1,3-glucanases to reopen transport corridor and break endodormancy in tree peony (Paeonia suffruticosa). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:771-784. [PMID: 34530322 DOI: 10.1016/j.plaphy.2021.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 05/21/2023]
Abstract
Bud endodormancy is accompanied by transport channel apertures blockage through callose deposition, and its resume to growth requires evoking β-1,3-glucanases (BGs) to unchoke the conduit. To understand out its working manner, the statuses of the transport channels were evaluated and candidate BGs were identified during chilling and gibberellin acids (GA) induced dormancy release in tree peony. Calcein reflects plasmodesmata permeability, and no calcein was observed in the bud together with density aniline blue fluorescent around the stem phloem at 0 d chilling. With the increase of chilling accumulation, the contents of glucan declined and the activities of gulcanase increased gradually in buds, and the calcein reached the top of flower primordia at 21 d chilled bud. Both GA3 and GA4 feedings promoted bud sprouting and growth along with rapidly unchoking the transport channels, and GA3 was more effective. Several candidate β-1,3-glucanase genes were detected, combining transcriptional profiling and quantitative PCR analysis. PsBG1, PsBG3, PsBG6, PsBG8 and PsBG9 were inducible by chilling accumulation and presented laminarin hydrolyzing activities after prokaryotically expression, while PsBG1, PsBG3, PsBG8 and PsBG9 responded to GAs application. Subcellular localizations revealed that PsBG6 and PsBG9 were plasmodesmata residents. It was concluded that PsBG6 played a vital role in chilling accumulation response and PsBG9 was central in GAs-induced dormancy release, and they could be used as marker genes for dormancy release in tree peony. These results were of great value to understand the mechanism of dormancy regulation and as an important fundamental for forcing culture technology in tree peony.
Collapse
Affiliation(s)
- Xuekai Gao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China; University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China.
| | - Yanchao Yuan
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China; University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China.
| | - Ziqi Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China; University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China.
| | - Chunying Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China; University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China.
| | - Hua Xin
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China; University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China.
| | - Yuxi Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China; University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China.
| | - Shupeng Gai
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China; University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China.
| |
Collapse
|
43
|
Gao K, Zha WL, Zhu JX, Zheng C, Zi JC. A review: biosynthesis of plant-derived labdane-related diterpenoids. Chin J Nat Med 2021; 19:666-674. [PMID: 34561077 DOI: 10.1016/s1875-5364(21)60100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Indexed: 11/16/2022]
Abstract
Plant-derived labdane-related diterpenoids (LRDs) represent a large group of terpenoids. LRDs possess either a labdane-type bicyclic core structure or more complex ring systems derived from labdane-type skeletons, such as abietane, pimarane, kaurane, etc. Due to their various pharmaceutical activities and unique properties, many of LRDs have been widely used in pharmaceutical, food and perfume industries. Biosynthesis of various LRDs has been extensively studied, leading to characterization of a large number of new biosynthetic enzymes. The biosynthetic pathways of important LRDs and the relevant enzymes (especially diterpene synthases and cytochrome P450 enzymes) were summarized in this review.
Collapse
Affiliation(s)
- Ke Gao
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Wen-Long Zha
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jian-Xun Zhu
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Cheng Zheng
- Zhejiang Institute for Food and Drug Control, NMPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine, Hangzhou 310052, China.
| | - Jia-Chen Zi
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
| |
Collapse
|
44
|
Li Y, Shan X, Jiang Z, Zhao L, Jin F. Genome-wide identification and expression analysis of the GA2ox gene family in maize (Zea mays L.) under various abiotic stress conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:621-633. [PMID: 34192648 DOI: 10.1016/j.plaphy.2021.06.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
GA 2-oxidases (GA2oxs) are a class of enzymes that inhibit the biosynthesis of bioactive GAs in plants. Although GA2oxs have clear roles in the development and defence responses in Arabidopsis, rice, and wheat, their potential effects on maize remain unclear. This study identified thirteen ZmGA2ox genes in maize and further characterized them using phylogenetic, gene structure, genomic locus, expression pattern analyses and GA content determination. Phylogenetic relationship analysis clearly divided the ZmGA2ox family into three groups-seven in C19-GA2ox class I, three in C19-GA2ox class II, and three in C20-GA2ox class. Evolutionary analysis suggested that ZmGA2ox1;1 and ZmGA2ox1;2, ZmGA2ox3;1 and ZmGA2ox3;2, and ZmGA2ox7;1 and ZmGA2ox7;2 are three pairs of segmental duplicated genes. Prediction of cis-regulatory elements in promoters suggested that ZmGA2ox genes were mainly associated with growth, development, hormones, and biotic/abiotic stress. Therefore, their spatial and temporal expression patterns and responses to various stress treatments were analysed on the basis of published RNA-seq data. Moreover, the changes of ZmGA2ox expression in leaves and roots of maize seedlings was detected under salt, alkali, dehydration, and cold stresses by qRT-PCR. The ZmGA2oxs exhibited obvious expression tendencies or characteristics in various organs under different abiotic stresses. The variations in the expression of three ZmGA2ox genes in the C20-GA2ox class in maize seedling roots showed significant regularity and a clear negative correlation with bioactive GA contents under cold and drought conditions, indicating that these three genes might exert key effects on the regulation of GA synthesis and the response to drought and cold stress. Taken together, this study is useful for further dissection of the effect of ZmGA2oxs on abiotic stress responses and might provide potential targets for the genetic improvement of maize.
Collapse
Affiliation(s)
- Yidan Li
- Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Xiaohui Shan
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Zhilei Jiang
- Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Lei Zhao
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Fengxue Jin
- Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| |
Collapse
|
45
|
Wang X, Li MW, Wong FL, Luk CY, Chung CYL, Yung WS, Wang Z, Xie M, Song S, Chung G, Chan TF, Lam HM. Increased copy number of gibberellin 2-oxidase 8 genes reduced trailing growth and shoot length during soybean domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1739-1755. [PMID: 34245624 DOI: 10.1111/tpj.15414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/28/2021] [Accepted: 07/06/2021] [Indexed: 05/27/2023]
Abstract
Copy number variations (CNVs) play important roles in crop domestication. However, there is only very limited information on the involvement of CNVs in soybean domestication. Trailing growth and long shoots are soybean adaptations for natural habitats but cause lodging that hampers yield in cultivation. Previous studies have focused on Dt1/2 affecting the indeterminate/determinate growth habit, whereas the possible role of the gibberellin pathway remained unclear. In the present study, quantitative trait locus (QTL) mapping of a recombinant inbred population of 460 lines revealed a trailing-growth-and-shoot-length QTL. A CNV region within this QTL was identified, featuring the apical bud-expressed gibberellin 2-oxidase 8A/B, the copy numbers of which were positively correlated with expression levels and negatively with trailing growth and shoot length, and their effects were demonstrated by transgenic soybean and Arabidopsis thaliana. Based on the fixation index, this CNV region underwent intense selection during the initial domestication process.
Collapse
Affiliation(s)
- Xin Wang
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Man-Wah Li
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Fuk-Ling Wong
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ching-Yee Luk
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Claire Yik-Lok Chung
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Wai-Shing Yung
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Zhili Wang
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Min Xie
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Shikui Song
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Ting-Fung Chan
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Hon-Ming Lam
- School of Life Sciences and the Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China
| |
Collapse
|
46
|
Gibberellins Inhibit Flavonoid Biosynthesis and Promote Nitrogen Metabolism in Medicago truncatula. Int J Mol Sci 2021; 22:ijms22179291. [PMID: 34502200 PMCID: PMC8431309 DOI: 10.3390/ijms22179291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 01/21/2023] Open
Abstract
Bioactive gibberellic acids (GAs) are diterpenoid plant hormones that are biosynthesized through complex pathways and control various aspects of growth and development. Although GA biosynthesis has been intensively studied, the downstream metabolic pathways regulated by GAs have remained largely unexplored. We investigated Tnt1 retrotransposon insertion mutant lines of Medicago truncatula with a dwarf phenotype by forward and reverse genetics screening and phylogenetic, molecular, biochemical, proteomic and metabolomic analyses. Three Tnt1 retrotransposon insertion mutant lines of the gibberellin 3-beta-dioxygenase 1 gene (GA3ox1) with a dwarf phenotype were identified, in which the synthesis of GAs (GA3 and GA4) was inhibited. Phenotypic analysis revealed that plant height, root and petiole length of ga3ox1 mutants were shorter than those of the wild type (Medicago truncatula ecotype R108). Leaf size was also much smaller in ga3ox1 mutants than that in wild-type R108, which is probably due to cell-size diminution instead of a decrease in cell number. Proteomic and metabolomic analyses of ga3ox1/R108 leaves revealed that in the ga3ox1 mutant, flavonoid isoflavonoid biosynthesis was significantly up-regulated, while nitrogen metabolism was down-regulated. Additionally, we further demonstrated that flavonoid and isoflavonoid biosynthesis was induced by prohexadione calcium, an inhibitor of GA3ox enzyme, and inhibited by exogenous GA3. In contrast, nitrogen metabolism was promoted by exogenous GA3 but inhibited by prohexadione calcium. The results of this study further demonstrated that GAs play critical roles in positively regulating nitrogen metabolism and transport and negatively regulating flavonoid biosynthesis through GA-mediated signaling pathways in leaves.
Collapse
|
47
|
Pu X, Tang Y, Zhang M, Li T, Qiu X, Zhang J, Wang J, Li L, Yang Z, Su Y, Zhang H, Liang J, Yu M, Tang Y, Deng G, Long H. Identification and candidate gene mining of HvSS1, a novel qualitative locus on chromosome 6H, regulating the uppermost internode elongation in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2481-2494. [PMID: 33942136 DOI: 10.1007/s00122-021-03837-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/13/2021] [Indexed: 05/27/2023]
Abstract
A novel qualitative locus regulating the uppermost internode elongation of barley was identified and mapped on 6H, and the candidate gene mining was performed by employing various barley genomic resources. The stem of grass crops, such as barley and wheat, is composed of several interconnected internodes. The extent of elongation of these internodes determines stem height, and hence lodging, canopy architecture, and grain yield. The uppermost internode (UI) is the last internode to elongate. Its elongation contributes largely to stem height and facilitates spike exsertion, which is crucial for final grain yield. Despite the molecular mechanism underlying regulation of UI elongation was extensively investigated in rice, little is known in barley. In this study, we characterized a barley spontaneous mutant, Sheathed Spike 1 (SS1), showing significantly shortened UI and sheathed spike (SS). The extension of UI parenchyma cell in SS1 was significantly suppressed. Exogenous hormone treatments and RNA-seq analysis indicated that the suppression of UI elongation is possibly related to insufficient content of endogenous bioactive gibberellin. Genetic analysis showed that SS1 is possibly controlled by a qualitative dominant nuclear factor. Bulked segregant analysis and further molecular marker mapping identified a novel major locus, HvSS1, in a recombination cold spot expanding 173.44-396.33 Mb on chromosome 6H. The candidate gene mining was further conducted by analyzing sequence differences, spatiotemporal expression patterns, and variant distributions of genes in the candidate interval by employing various barley genomic resources of worldwide collections of barley accessions. This study made insight into genetic control of UI elongation in barley and laid a solid foundation for further gene cloning and functional characterization. The results obtained here also provided valuable information for similar research in wheat.
Collapse
Affiliation(s)
- Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Meihao Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xvebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Juanyu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Lilan Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yan Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yawei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, People's Republic of China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China.
| |
Collapse
|
48
|
Hsieh KT, Chen YT, Hu TJ, Lin SM, Hsieh CH, Liu SH, Shiue SY, Lo SF, Wang IW, Tseng CS, Chen LJ. Comparisons within the Rice GA 2-Oxidase Gene Family Revealed Three Dominant Paralogs and a Functional Attenuated Gene that Led to the Identification of Four Amino Acid Variants Associated with GA Deactivation Capability. RICE (NEW YORK, N.Y.) 2021; 14:70. [PMID: 34322729 PMCID: PMC8319247 DOI: 10.1186/s12284-021-00499-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/03/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND GA 2-oxidases (GA2oxs) are involved in regulating GA homeostasis in plants by inactivating bioactive GAs through 2β-hydroxylation. Rice GA2oxs are encoded by a family of 10 genes; some of them have been characterized, but no comprehensive comparisons for all these genes have been conducted. RESULTS Rice plants with nine functional GA2oxs were demonstrated in the present study, and these genes not only were differentially expressed but also revealed various capabilities for GA deactivation based on their height-reducing effects in transgenic plants. Compared to that of wild-type plants, the relative plant height (RPH) of transgenic plants was scored to estimate their reducing effects, and 8.3% to 59.5% RPH was observed. Phylogenetic analysis of class I GA2ox genes revealed two functionally distinct clades in the Poaceae. The OsGA2ox3, 4, and 8 genes belonging to clade A showed the most severe effect (8.3% to 8.7% RPH) on plant height reduction, whereas the OsGA2ox7 gene belonging to clade B showed the least severe effect (59.5% RPH). The clade A OsGA2ox3 gene contained two conserved C186/C194 amino acids that were crucial for enzymatic activity. In the present study, these amino acids were replaced with OsGA2ox7-conserved arginine (C186R) and proline (C194P), respectively, or simultaneously (C186R/C194P) to demonstrate their importance in planta. Another two amino acids, Q220 and Y274, conserved in OsGA2ox3 were substituted with glutamic acid (E) and phenylalanine (F), respectively, or simultaneously to show their significance in planta. In addition, through sequence divergence, RNA expression profile and GA deactivation capability analyses, we proposed that OsGA2ox1, OsGA2ox3 and OsGA2ox6 function as the predominant paralogs in each of their respective classes. CONCLUSIONS This study demonstrates rice has nine functional GA2oxs and the class I GA2ox genes are divided into two functionally distinct clades. Among them, the OsGA2ox7 of clade B is a functional attenuated gene and the OsGA2ox1, OsGA2ox3 and OsGA2ox6 are the three predominant paralogs in the family.
Collapse
Affiliation(s)
- Kun-Ting Hsieh
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Yi-Ting Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Ting-Jen Hu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Shih-Min Lin
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chih-Hung Hsieh
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Su-Hui Liu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Shiau-Yu Shiue
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Shuen-Fang Lo
- Biotechnology Center, National Chung Hsing University, Taichung, 40227, Taiwan
| | - I-Wen Wang
- Division of Biotechnology, Taiwan Agriculture Research Institute, Taichung, 41362, Taiwan
| | - Ching-Shan Tseng
- Division of Biotechnology, Taiwan Agriculture Research Institute, Taichung, 41362, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan.
- Biotechnology Center, National Chung Hsing University, Taichung, 40227, Taiwan.
| |
Collapse
|
49
|
Tuan PA, Nguyen TN, Jordan MC, Ayele BT. A shift in abscisic acid/gibberellin balance underlies retention of dormancy induced by seed development temperature. PLANT, CELL & ENVIRONMENT 2021; 44:2230-2244. [PMID: 33249604 DOI: 10.1111/pce.13963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 05/06/2023]
Abstract
Through a combination of physiological, pharmacological, molecular and targeted metabolomics approaches, we showed that retention of wheat (Triticum aestivum L.) seed dormancy levels induced by low and high seed development temperatures during post-desiccation phases is associated with modulation of gibberellin (GA) level and seed responsiveness to abscisic acid (ABA) and GA via expression of TaABI5 and TaGAMYB, respectively. Dormancy retention during imbibition, however, is associated with modulations of both ABA level and responsiveness via expression of specific ABA metabolism (TaNCED2 and TaCYP707A1) and signalling (TaPYL2, TaSnRK2, TaABI3, TaABI4 and TaABI5) genes, and alterations of GA levels and responsiveness through expression of specific GA biosynthesis (TaGA20ox1, TaGA20ox2 and TaGA3ox2) and signalling (TaGID1 and TaGID2) genes, respectively. Expression patterns of GA signalling genes, TaRHT1 and TaGAMYB, lacked positive correlation with that of GA regulated genes and dormancy level observed in seeds developed at the two temperatures, implying their regulation at post-transcriptional level. Our results overall implicate that a shift in ABA/GA balance underlies retention of dormancy levels induced by seed development temperature during post-desiccation and imbibition phases. Consistently, genes regulated by ABA and GA during imbibition overlapped with those differentially expressed between imbibed seeds developed at the two temperatures and mediate different biological functions.
Collapse
Affiliation(s)
- Pham A Tuan
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tran-Nguyen Nguyen
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mark C Jordan
- Morden Research and Development Center, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - Belay T Ayele
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
50
|
Bolortuya B, Kawabata S, Yamagami A, Davaapurev BO, Takahashi F, Inoue K, Kanatani A, Mochida K, Kumazawa M, Ifuku K, Jigjidsuren S, Battogtokh T, Udval G, Shinozaki K, Asami T, Batkhuu J, Nakano T. Transcriptome Analysis of Chloris virgata, Which Shows the Fastest Germination and Growth in the Major Mongolian Grassland Plant. FRONTIERS IN PLANT SCIENCE 2021; 12:684987. [PMID: 34262584 PMCID: PMC8275185 DOI: 10.3389/fpls.2021.684987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/26/2021] [Indexed: 06/13/2023]
Abstract
Plants in Mongolian grasslands are exposed to short, dry summers and long, cold winters. These plants should be prepared for fast germination and growth activity in response to the limited summer rainfall. The wild plant species adapted to the Mongolian grassland environment may allow us to explore useful genes, as a source of unique genetic codes for crop improvement. Here, we identified the Chloris virgata Dornogovi accession as the fastest germinating plant in major Mongolian grassland plants. It germinated just 5 h after treatment for germination initiation and showed rapid growth, especially in its early and young development stages. This indicates its high growth potential compared to grass crops such as rice and wheat. By assessing growth recovery after animal bite treatment (mimicked by cutting the leaves with scissors), we found that C. virgata could rapidly regenerate leaves after being damaged, suggesting high regeneration potential against grazing. To analyze the regulatory mechanism involved in the high growth potential of C. virgata, we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. Through de novo transcriptome assembly with the RNA-seq reads from whole organ samples of C. virgata at the germination stage (2 days after germination, DAG), early young development stage (8 DAG), young development stage (17 DAG), and adult development stage (28 DAG), we identified 21,589 unified transcripts (contigs) and found that 19,346 and 18,156 protein-coding transcripts were homologous to those in rice and Arabidopsis, respectively. The best-aligned sequences were annotated with gene ontology groups. When comparing the transcriptomes across developmental stages, we found an over-representation of genes involved in growth regulation in the early development stage in C. virgata. Plant development is tightly regulated by phytohormones such as brassinosteroids, gibberellic acid, abscisic acid, and strigolactones. Moreover, our transcriptome map demonstrated the expression profiles of orthologs involved in the biosynthesis of these phytohormones and their signaling networks. We discuss the possibility that C. virgata phytohormone signaling and biosynthesis genes regulate early germination and growth advantages. Comprehensive transcriptome information will provide a useful resource for gene discovery and facilitate a deeper understanding of the diversity of the regulatory systems that have evolved in C. virgata while adapting to severe environmental conditions.
Collapse
Affiliation(s)
- Byambajav Bolortuya
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | | | - Ayumi Yamagami
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Bekh-Ochir Davaapurev
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Asaka Kanatani
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Minoru Kumazawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kentaro Ifuku
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Sodnomdarjaa Jigjidsuren
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Tugsjargal Battogtokh
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Gombosuren Udval
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
| | - Javzan Batkhuu
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Takeshi Nakano
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| |
Collapse
|