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Zhong M, Wang H, Hao X, Liu C, Hao J, Fan S, Han Y. LsFUL-LsSMU2 module positively controls bolting time in leaf lettuce (Lactuca sativa L.) under high temperature. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112195. [PMID: 39002573 DOI: 10.1016/j.plantsci.2024.112195] [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: 02/24/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/15/2024]
Abstract
High temperature (HT) is an environmental factor that considerably affects plant physiology, development, crop yield, and economic value. HT can cause diseases and early bolting of leaf lettuce, thereby reducing the yield and quality of leaf lettuce. Herein, we used two leaf lettuce (Lactuca sativa L.) cultivars (bolting-resistant 'S24' and bolting-sensitive 'S39') to investigate the key factors and molecular mechanism impacting bolting. We found that 14 MADS-box genes implicated in bolting and flowering, LsMADS54 (also referred to as L. sativa FRUITFULL, LsFUL), was significantly up-regulated 1000 times after 5-d HT treatment and that HT-induced up-regulation of LsFUL was higher in bolting-sensitive than in resistant cultivars. The overexpression lines of LsFUL exhibited an earlier bolting time than that in the non-transformed 'S39'(CK). However, the RNA interference, and CRISPR-Cas9-mediated knockout lines of LsFUL exhibited a later bolting time than that in CK. In addition, we found that L. sativa SUPPRESSORS OF MEC-8 AND UNC-52 PROTEIN 2 (LsSMU2) and L. sativa CONSTANS-LIKE PROTEIN 5 (LsCOL5) interact with LsFUL, and these interactions could stimulate or prevent bolting. We observed that elevated temperature stimulated the abundance of LsSMU2 in the stem, which collaborated with LsFUL to accelerate bolting. Conversely, room temperature (RT) condition led to relatively more stable LsCOL5, which worked with LsFUL to postpone bolting. In summary, our findings demonstrate a molecular regulatory module of LsSMU2-LsFUL associated with HT-induced premature bolting, which serves as a reference for understanding HT-induced premature bolting phenomenon in leaf lettuce.
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Affiliation(s)
- Mengjiang Zhong
- Department of Plant Science and Technology, Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing 102206, China.
| | - Huiyu Wang
- Department of Plant Science and Technology, Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing 102206, China.
| | - Xindi Hao
- Department of Plant Science and Technology, Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing 102206, China.
| | - Chaojie Liu
- Department of Plant Science and Technology, Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing 102206, China.
| | - Jinghong Hao
- Department of Plant Science and Technology, Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing 102206, China.
| | - Shuangxi Fan
- Department of Plant Science and Technology, Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing 102206, China.
| | - Yingyan Han
- Department of Plant Science and Technology, Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing 102206, China.
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Berentsen R, Benlloch R, Visser P, Madueño F, Balanzà V. A reduced vernalization requirement is a key component of the early-bolting trait in globe artichoke ( Cynara cardunculus var. scolymus). iScience 2024; 27:110829. [PMID: 39297164 PMCID: PMC11409005 DOI: 10.1016/j.isci.2024.110829] [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: 03/18/2024] [Revised: 06/10/2024] [Accepted: 08/23/2024] [Indexed: 09/21/2024] Open
Abstract
Early bolting is a major breeding objective for globe artichoke (Cynara cardunculus var. scolymus L.). It has been suggested that globe artichoke bolting time is linked to a vernalization requirement, although environmental conditions under which vernalized plants and controls have been grown may not always allow for proper comparison. Here, we defined morphological markers to monitor the vegetative-to-reproductive phase transition at the shoot apex and linked these to expression changes of homologs of key Arabidopsis flowering regulators SOC1, FUL, and AP1. Importantly, we developed an experimental setup where control and vernalized plants grow under comparable conditions. These tools together allowed for comparison of the vegetative-to-reproductive phase transition between early- and late-bolting genotypes and how they respond to vernalization. Our results show that vernalization requirement is significantly lower in early-bolting genotypes, supporting the hypothesis that the early-bolting trait is at least partly underlain by alterations in the network controlling vernalization response.
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Affiliation(s)
- Rick Berentsen
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Valencia, Spain
- Nunhems Spain SAU, BASF|Nunhems, La Palma (Cartagena), Spain
| | - Reyes Benlloch
- Departamento de Biología Vegetal, Facultad de Farmacia, Universitat de València, Burjassot, Valencia, Spain
| | - Peter Visser
- Nunhems Spain SAU, BASF|Nunhems, La Palma (Cartagena), Spain
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Valencia, Spain
| | - Vicente Balanzà
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Valencia, Spain
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Zhang G, Yang J, Zhang C, Jiao B, Panero JL, Cai J, Zhang ZR, Gao LM, Gao T, Ma H. Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution. PLANT COMMUNICATIONS 2024; 5:100851. [PMID: 38409784 PMCID: PMC11211554 DOI: 10.1016/j.xplc.2024.100851] [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: 07/29/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups, but it is limited to taxa with available fresh materials. Asteraceae, which are one of the two largest angiosperm families and are important for both ecosystems and human livelihood, show multiple examples of convergent evolution. Nuclear Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes, but many phylogenetic and evolutionary questions regarding subtribes and genera remain, owing to limited sampling. Here, we increased the sampling for Asteraceae phylogenetic reconstruction using transcriptomes and genome-skimming datasets and produced nuclear phylogenetic trees with 706 species representing two-thirds of recognized subtribes. Ancestral character reconstruction supports multiple convergent evolutionary events in Asteraceae, with gains and losses of bilateral floral symmetry correlated with diversification of some subfamilies and smaller groups, respectively. Presence of the calyx-related pappus may have been especially important for the success of some subtribes and genera. Molecular evolutionary analyses support the likely contribution of duplications of MADS-box and TCP floral regulatory genes to innovations in floral morphology, including capitulum inflorescences and bilaterally symmetric flowers, potentially promoting the diversification of Asteraceae. Subsequent divergences and reductions in CYC2 gene expression are related to the gain and loss of zygomorphic flowers. This phylogenomic work with greater taxon sampling through inclusion of genome-skimming datasets reveals the feasibility of expanded evolutionary analyses using DNA samples for understanding convergent evolution.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA; State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Caifei Zhang
- Wuhan Botanical Garden and Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Bohan Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - José L Panero
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Lijiang National Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan 674100, China.
| | - Tiangang Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hong Ma
- Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA.
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Chen L, Qin Y, Fan S. Genome-Wide Identification and Characterization of the GRAS Gene Family in Lettuce Revealed That Silencing LsGRAS13 Delayed Bolting. PLANTS (BASEL, SWITZERLAND) 2024; 13:1360. [PMID: 38794431 PMCID: PMC11124801 DOI: 10.3390/plants13101360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Lettuce is susceptible to high-temperature stress during cultivation, leading to bolting and affecting yield. Plant-specific transcription factors, known as GRAS proteins, play a crucial role in regulating plant growth, development, and abiotic stress responses. In this study, the entire lettuce LsGRAS gene family was identified. The results show that 59 LsGRAS genes are unevenly distributed across the nine chromosomes. Additionally, all LsGRAS proteins showed 100% nuclear localization based on the predicted subcellular localization and were phylogenetically classified into nine conserved subfamilies. To investigate the expression profiles of these genes in lettuce, we analyzed the transcription levels of all 59 LsGRAS genes in the publicly available RNA-seq data under the high-temperature treatment conducted in the presence of exogenous melatonin. The findings indicate that the transcript levels of the LsGRAS13 gene were higher on days 6, 9, 15, 18, and 27 under the high-temperature (35/30 °C) treatment with melatonin than on the same treatment days without melatonin. The functional studies demonstrate that silencing LsGRAS13 accelerated bolting in lettuce. Furthermore, the paraffin sectioning results showed that flower bud differentiation in LsGRAS13-silenced plants occurred significantly faster than in control plants. In this study, the LsGRAS genes were annotated and analyzed, and the expression pattern of the LsGRAS gene following melatonin treatment under high-temperature conditions was explored. This exploration provides valuable information and identifies candidate genes associated with the response mechanism of lettuce plants high-temperature stress.
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Affiliation(s)
- Li Chen
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China; (L.C.); (Y.Q.)
| | - Yong Qin
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China; (L.C.); (Y.Q.)
| | - Shuangxi Fan
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China; (L.C.); (Y.Q.)
- Plant Science and Technology College, Beijing Vocational College of Agriculture, Beijing 102442, China
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Liu Y, Guan C, Chen Y, Shi Y, Long O, Lin H, Zhang K, Zhou M. Evolutionary analysis of MADS-box genes in buckwheat species and functional study of FdMADS28 in flavonoid metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108637. [PMID: 38670031 DOI: 10.1016/j.plaphy.2024.108637] [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: 12/22/2023] [Revised: 04/01/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
The MADS-box gene family is a transcription factor family that is widely expressed in plants. It controls secondary metabolic processes in plants and encourages the development of tissues like roots and flowers. However, the phylogenetic analysis and evolutionary model of MADS-box genes in Fagopyrum species has not been reported yet. This study identified the MADS-box genes of three buckwheat species at the whole genome level, and conducted systematic evolution and physicochemical analysis. The results showed that these genes can be divided into four subfamilies, with fragment duplication being the main way for the gene family expansion. During the domestication process from golden buckwheat to tartary buckwheat and the common buckwheat, the Ka/Ks ratio indicated that most members of the family experienced strong purification selection pressure, and with individual gene pairs experiencing positive selection. In addition, we combined the expression profile data of the MADS genes, mGWAS data, and WGCNA data to mine genes FdMADS28/48/50 that may be related to flavonoid metabolism. The results also showed that overexpression of FdMADS28 could increase rutin content by decreasing Kaempferol pathway content in hairy roots, and increase the resistance and growth of hairy roots to PEG and NaCl. This study systematically analyzed the evolutionary relationship of MADS-box genes in the buckwheat species, and elaborated on the expression patterns of MADS genes in different tissues under biotic and abiotic stresses, laying an important theoretical foundation for further elucidating their role in flavonoid metabolism.
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Affiliation(s)
- Yang Liu
- Sanya Nan Fan Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaonan Guan
- Sanya Nan Fan Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanyuan Chen
- College of Agriculture, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Yaliang Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ou Long
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meiliang Zhou
- Sanya Nan Fan Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Qiao Z, Deng F, Zeng H, Li X, Lu L, Lei Y, Li L, Chen Y, Chen J. MADS-Box Family Genes in Lagerstroemia indica and Their Involvement in Flower Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:709. [PMID: 38475555 DOI: 10.3390/plants13050709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/25/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
MADS-box is a key transcription factor regulating the transition to flowering and flower development. Lagerstroemia indica 'Xiang Yun' is a new cultivar of crape myrtle characterized by its non-fruiting nature. To study the molecular mechanism underlying the non-fruiting characteristics of 'Xiang Yun', 82 MADS-box genes were identified from the genome of L. indica. The physicochemical properties of these genes were examined using bioinformatics methods, and their expression as well as endogenous hormone levels at various stages of flower development were analyzed. The results showed that LiMADS genes were primarily classified into two types: type I and type II, with the majority being type II that contained an abundance of cis-acting elements in their promoters. By screening nine core proteins by predicted protein interactions and performing qRT-PCR analysis as well as in combination with transcriptome data, we found that the expression levels of most MADS genes involved in flower development were significantly lower in 'Xiang Yun' than in the wild type 'Hong Ye'. Hormonal analysis indicated that 'Xiang Yun' had higher levels of iP, IPR, TZR, and zeatin during its early stages of flower development than 'Hong Ye', whereas the MeJA content was substantially lower at the late stage of flower development of 'Hong Ye'. Finally, correlation analysis showed that JA, IAA, SA, and TZR were positively correlated with the expression levels of most type II genes. Based on these analyses, a working model for the non-fruiting 'Xiang Yun' was proposed. During the course of flower development, plant hormone response pathways may affect the expression of MADS genes, resulting in their low expression in flower development, which led to the abnormal development of the stamen and embryo sac and ultimately affected the fruiting process of 'Xiang Yun'.
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Affiliation(s)
- Zhongquan Qiao
- Hunan Provincial Key Laboratory of Forest Clonal Breeding, Hunan Academy of Forestry, Changsha 410004, China
| | - Fuyuan Deng
- Hunan Provincial Key Laboratory of Forest Clonal Breeding, Hunan Academy of Forestry, Changsha 410004, China
| | - Huijie Zeng
- Hunan Provincial Key Laboratory of Forest Clonal Breeding, Hunan Academy of Forestry, Changsha 410004, China
| | - Xuelu Li
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Liushu Lu
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yuxing Lei
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Lu Li
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yi Chen
- Hunan Provincial Key Laboratory of Forest Clonal Breeding, Hunan Academy of Forestry, Changsha 410004, China
| | - Jianjun Chen
- Mid-Florida Research and Education Center, Environmental Horticulture Department, University of Florida, 2725 S. Binion Road, Apopka, FL 32703, USA
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Gui FF, Jiang GG, Bin Dong, Zhong SW, Xiao Z, Qiu Fang, Wang YG, Yang LY, Zhao H. Genome-wide identification and analysis of MIKC-type MADS-box genes expression in Chimonanthus salicifolius. Genes Genomics 2023; 45:1127-1141. [PMID: 37438657 DOI: 10.1007/s13258-023-01420-7] [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: 02/13/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND MIKC type MADS-box transcription factors are one of the largest gene families and play a pivotal role in flowering time and flower development. Chimonanthus salicifolius belongs to the family Calycanthaceae and has a unique flowering time and flowering morphology compared to other Chimonanthus species, but the research on MIKC type MADS-box gene family of C. salicifolius has not been reported. OBJECTIVE Identification, comprehensive bioinformatic analysis, the expression pattern of MIKC-type MADS-box gene family from different tissues of C. salicifolius. METHODS Genome-wide investigation and expression pattern under different tissues of the MIKC-type MADS-box gene family in C. salicifolius, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, promoter cis-acting element were performed. RESULTS A total of 29 MIKC-type MADS-box genes were identified from the whole genome sequencing. Interspecies synteny analysis revealed more significant collinearity between C. salicifolius and the magnoliids species compared to eudicots and monocots. MIKC-type MADS-box genes from the same subfamily share similar distribution patterns, gene structure, and expression patterns. Compared with Arabidopsis thaliana, Nymphaea colorata, and Chimonanthus praecox, the FLC genes were absent in C. salicifolius, while the AGL6 subfamily was expanded in C. salicifolius. The selectively expanded promoter (AGL6) and lack of repressor (FLC) genes may explain the earlier flowering in C. salicifolius. The loss of the AP3 homologous gene in C. salicifolius is probably the primary cause of the morphological distinction between C. salicifolius and C. praecox. The csAGL6a gene is specifically expressed in the flowering process and indicates the potential function of promoting flowering. CONCLUSION This study offers a genome-wide identification and expression profiling of the MIKC-types MADS-box genes in the C. salicifolius, and establishes the foundation for screening flowering development genes and understanding the potential function of the MIKC-types MADS-box genes in the C. salicifolius.
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Affiliation(s)
- Fang-Fang Gui
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Ge-Ge Jiang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Bin Dong
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Shi-Wei Zhong
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Zheng Xiao
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Qiu Fang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Yi-Guang Wang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Li-Yuan Yang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China.
| | - Hongbo Zhao
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China.
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Hu J, Chen Q, Idrees A, Bi W, Lai Z, Sun Y. Structural and Functional Analysis of the MADS-Box Genes Reveals Their Functions in Cold Stress Responses and Flower Development in Tea Plant ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2023; 12:2929. [PMID: 37631141 PMCID: PMC10458798 DOI: 10.3390/plants12162929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
MADS-box genes comprise a large family of transcription factors that play crucial roles in all aspects of plant growth and development. However, no detailed information on the evolutionary relationship and functional characterization of MADS-box genes is currently available for some representative lineages, such as the Camellia plant. In this study, 136 MADS-box genes were detected from a reference genome of the tea plant (Camellia sinensis) by employing a 569 bp HMM (Hidden Markov Model) developed using nucleotide sequencing including 73 type I and 63 type II genes. An additional twenty-seven genes were identified, with five MIKC-type genes. Truncated and/or inaccurate gene models were manually verified and curated to improve their functional characterization. Subsequently, phylogenetic relationships, chromosome locations, conserved motifs, gene structures, and gene expression profiles were systematically investigated. Tea plant MIKC genes were divided into all 14 major eudicot subfamilies, and no gene was found in Mβ. The expansion of MADS-box genes in the tea plant was mainly contributed by WGD/fragment and tandem duplications. The expression profiles of tea plant MADS-box genes in different tissues and seasons were analyzed, revealing widespread evolutionary conservation and genetic redundancy. The expression profiles linked to cold stress treatments suggested the wide involvement of MADS-box genes from the tea plant in response to low temperatures. Moreover, a floral 'ABCE' model was proposed in the tea plant and proved to be both conserved and ancient. Our analyses offer a detailed overview of MADS-box genes in the tea plant, allowing us to hypothesize the potential functions of unknown genes and providing a foundation for further functional characterizations.
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Affiliation(s)
- Juan Hu
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.H.); (W.B.)
| | - Qianqian Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Atif Idrees
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs, Institute of Entomology, Guizhou University, Guiyang 550025, China;
| | - Wanjun Bi
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.H.); (W.B.)
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yun Sun
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.H.); (W.B.)
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Lin Y, Qi X, Wan Y, Chen Z, Fang H, Liang C. Genome-wide analysis of the MADS-box gene family in Lonicera japonica and a proposed floral organ identity model. BMC Genomics 2023; 24:447. [PMID: 37553575 PMCID: PMC10408238 DOI: 10.1186/s12864-023-09509-9] [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: 12/01/2022] [Accepted: 07/08/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Lonicera japonica Thunb. is widely used in traditional Chinese medicine. Medicinal L. japonica mainly consists of dried flower buds and partially opened flowers, thus flowers are an important quality indicator. MADS-box genes encode transcription factors that regulate flower development. However, little is known about these genes in L. japonica. RESULTS In this study, 48 MADS-box genes were identified in L. japonica, including 20 Type-I genes (8 Mα, 2 Mβ, and 10 Mγ) and 28 Type-II genes (26 MIKCc and 2 MIKC*). The Type-I and Type-II genes differed significantly in gene structure, conserved domains, protein structure, chromosomal distribution, phylogenesis, and expression pattern. Type-I genes had a simpler gene structure, lacked the K domain, had low protein structure conservation, were tandemly distributed on the chromosomes, had more frequent lineage-specific duplications, and were expressed at low levels. In contrast, Type-II genes had a more complex gene structure; contained conserved M, I, K, and C domains; had highly conserved protein structure; and were expressed at high levels throughout the flowering period. Eleven floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in L. japonica. By integrating expression pattern and protein interaction data for these genes, we developed a possible model for floral organ identity determination. CONCLUSION This study genome-widely identified and characterized the MADS-box gene family in L. japonica. Eleven floral homeotic MADS-box genes were identified and a possible model for floral organ identity determination was also developed. This study contributes to our understanding of the MADS-box gene family and its possible involvement in floral organ development in L. japonica.
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Affiliation(s)
- Yi Lin
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiwu Qi
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yan Wan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zequn Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Hailing Fang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Chengyuan Liang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China.
- Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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Chen J, Yang Y, Li C, Chen Q, Liu S, Qin B. Genome-Wide Identification of MADS-Box Genes in Taraxacum kok-saghyz and Taraxacum mongolicum: Evolutionary Mechanisms, Conserved Functions and New Functions Related to Natural Rubber Yield Formation. Int J Mol Sci 2023; 24:10997. [PMID: 37446175 DOI: 10.3390/ijms241310997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
MADS-box transcription regulators play important roles in plant growth and development. However, very few MADS-box genes have been isolated in the genus Taraxacum, which consists of more than 3000 species. To explore their functions in the promising natural rubber (NR)-producing plant Taraxacum kok-saghyz (TKS), MADS-box genes were identified in the genome of TKS and the related species Taraxacum mongolicum (TM; non-NR-producing) via genome-wide screening. In total, 66 TkMADSs and 59 TmMADSs were identified in the TKS and TM genomes, respectively. From diploid TKS to triploid TM, the total number of MADS-box genes did not increase, but expansion occurred in specific subfamilies. Between the two genomes, a total of 11 duplications, which promoted the expansion of MADS-box genes, were identified in the two species. TkMADS and TmMADS were highly conserved, and showed good collinearity. Furthermore, most TkMADS genes exhibiting tissue-specific expression patterns, especially genes associated with the ABCDE model, were preferentially expressed in the flowers, suggesting their conserved and dominant functions in flower development in TKS. Moreover, by comparing the transcriptomes of different TKS lines, we identified 25 TkMADSs related to biomass formation and 4 TkMADSs related to NR content, which represented new targets for improving the NR yield of TKS.
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Affiliation(s)
- Jiaqi Chen
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Institute of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yushuang Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Chuang Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Institute of Tropical Crops, Hainan University, Haikou 570228, China
| | - Qiuhui Chen
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Shizhong Liu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bi Qin
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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Chai S, Li K, Deng X, Wang L, Jiang Y, Liao J, Yang R, Zhang L. Genome-Wide Analysis of the MADS-box Gene Family and Expression Analysis during Anther Development in Salvia miltiorrhiza. Int J Mol Sci 2023; 24:10937. [PMID: 37446115 DOI: 10.3390/ijms241310937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
MADS-box genes constitute a large family of transcription factors that play important roles in plant growth and development. However, our understanding of MADS-box genes involved in anther development and male sterility in Salvia miltiorrhiza is still limited. In this study, 63 MADS-box genes were identified from the genome of the male sterility ecotype Sichuan S. miltiorrhiza (S. miltiorrhiza_SC) unevenly distributed among eight chromosomes. Phylogenetic analysis classified them into two types and 17 subfamilies. They contained 1 to 12 exons and 10 conserved motifs. Evolution analysis showed that segmental duplication was the main force for the expansion of the SmMADS gene family, and duplication gene pairs were under purifying selection. Cis-acting elements analysis demonstrated that the promoter of SmMADS genes contain numerous elements associated with plant growth and development, plant hormones, and stress response. RNA-seq showed that the expression levels of B-class and C-class SmMADS genes were highly expressed during anther development, with SmMADS11 likely playing an important role in regulating anther development and male fertility in S. miltiorrhiza_SC. Overall, this study provides a comprehensive analysis of the MADS-box gene family in S. miltiorrhiza, shedding light on their potential role in anther development and male sterility.
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Affiliation(s)
- Songyue Chai
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Kexin Li
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Xuexue Deng
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Long Wang
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Yuanyuan Jiang
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Jinqiu Liao
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625014, China
| | - Ruiwu Yang
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625014, China
| | - Li Zhang
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
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12
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Xiong W, Risse J, Berke L, Zhao T, van de Geest H, Oplaat C, Busscher M, Ferreira de Carvalho J, van der Meer IM, Verhoeven KJF, Schranz ME, Vijverberg K. Phylogenomic analysis provides insights into MADS-box and TCP gene diversification and floral development of the Asteraceae, supported by de novo genome and transcriptome sequences from dandelion ( Taraxacum officinale). FRONTIERS IN PLANT SCIENCE 2023; 14:1198909. [PMCID: PMC10338227 DOI: 10.3389/fpls.2023.1198909] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/26/2023] [Indexed: 07/15/2023]
Abstract
The Asteraceae is the largest angiosperm family with more than 25,000 species. Individual studies have shown that MADS-box and TCP transcription factors are regulators of the development and symmetry of flowers, contributing to their iconic flower-head (capitulum) and floret. However, a systematic study of MADS-box and TCP genes across the Asteraceae is lacking. We performed a comparative analysis of genome sequences of 33 angiosperm species including our de novo assembly of diploid sexual dandelion (Taraxacum officinale) and 11 other Asteraceae to investigate the lineage-specific evolution of MADS-box and TCP genes in the Asteraceae. We compared the phylogenomic results of MADS-box and TCP genes with their expression in T. officinale floral tissues at different developmental stages to demonstrate the regulation of genes with Asteraceae-specific attributes. Here, we show that MADS-box MIKCc and TCP-CYCLOIDEA (CYC) genes have expanded in the Asteraceae. The phylogenomic analysis identified AGAMOUS-like (AG-like: SEEDSTICK [STK]-like), SEPALATA-like (SEP3-like), and TCP-PROLIFERATING CELL FACTOR (PCF)-like copies with lineage-specific genomic contexts in the Asteraceae, Cichorioideae, or dandelion. Different expression patterns of some of these gene copies suggest functional divergence. We also confirm the presence and revisit the evolutionary history of previously named “Asteraceae-Specific MADS-box genes (AS-MADS).” Specifically, we identify non-Asteraceae homologs, indicating a more ancient origin of this gene clade. Syntenic relationships support that AS-MADS is paralogous to FLOWERING LOCUS C (FLC) as demonstrated by the shared ancient duplication of FLC and SEP3.
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Affiliation(s)
- Wei Xiong
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Judith Risse
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Lidija Berke
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Tao Zhao
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | | | - Carla Oplaat
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Marco Busscher
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
- Bioscience, Wageningen University and Research, Wageningen, Netherlands
| | - Julie Ferreira de Carvalho
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Kitty Vijverberg
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
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13
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Gao H, Suo X, Zhao L, Ma X, Cheng R, Wang G, Zhang H. Molecular evolution, diversification, and expression assessment of MADS gene family in Setaria italica, Setaria viridis, and Panicum virgatum. PLANT CELL REPORTS 2023; 42:1003-1024. [PMID: 37012438 DOI: 10.1007/s00299-023-03009-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE This paper sheds light on the evolution and expression patterns of MADS genes in Setaria and Panicum virgatum. SiMADS51 and SiMADS64 maybe involved in the ABA-dependent pathway of drought response. The MADS gene family is a key regulatory factor family that controls growth, reproduction, and response to abiotic stress in plants. However, the molecular evolution of this family is rarely reported. Here, a total of 265 MADS genes were identified in Setaria italica (foxtail millet), Setaria viridis (green millet), and Panicum virgatum (switchgrass) and analyzed by bioinformatics, including physicochemical characteristics, subcellular localization, chromosomal position and duplicate, motif distribution, genetic structure, genetic evolvement, and expression patterns. Phylogenetic analysis was used to categorize these genes into M and MIKC types. The distribution of motifs and gene structure were similar for the corresponding types. According to a collinearity study, the MADS genes have been mostly conserved during evolution. The principal cause of their expansion is segmental duplication. However, the MADS gene family tends to shrink in foxtail millet, green millet, and switchgrass. The MADS genes were subjected to purifying selection, but several positive selection sites were also identified in three species. And most of the promoters of MADS genes contain cis-elements related to stress and hormonal response. RNA-seq and quantitative Real-time PCR (qRT-PCR) analysis also were examined. SiMADS genes expression levels are considerably changed in reaction to various treatments, following qRT-PCR analysis. This sheds fresh light on the evolution and expansion of the MADS family in foxtail millet, green millet, and switchgrass, and lays the foundation for further research on their functions.
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Affiliation(s)
- Hui Gao
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xiaoman Suo
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ling Zhao
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xinlei Ma
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Genping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Haoshan Zhang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
- Chinese Academy of Agricultural Sciences Institute of Crop Sciences, Beijing, 100081, China.
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14
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Li M, Li M, Wang L, Li M, Wei J. Apiaceae Medicinal Plants in China: A Review of Traditional Uses, Phytochemistry, Bolting and Flowering (BF), and BF Control Methods. Molecules 2023; 28:4384. [PMID: 37298861 PMCID: PMC10254214 DOI: 10.3390/molecules28114384] [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: 04/30/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Apiaceae plants have been widely used in traditional Chinese medicine (TCM) for the removing dampness, relieving superficies, and dispelling cold, etc. In order to exploit potential applications as well as improve the yield and quality of Apiaceae medicinal plants (AMPs), the traditional use, modern pharmacological use, phytochemistry, effect of bolting and flowering (BF), and approaches for controlling BF were summarized. Currently, about 228 AMPs have been recorded as TCMs, with 6 medicinal parts, 79 traditional uses, 62 modern pharmacological uses, and 5 main kinds of metabolites. Three different degrees (i.e., significantly affected, affected to some extent, and not significantly affected) could be classed based on the yield and quality. Although the BF of some plants (e.g., Angelica sinensis) could be effectively controlled by standard cultivation techniques, the mechanism of BF has not yet been systemically revealed. This review will provide useful references for the reasonable exploration and high-quality production of AMPs.
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Affiliation(s)
- Meiling Li
- State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (M.L.); (M.L.)
| | - Min Li
- State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (M.L.); (M.L.)
| | - Li Wang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen 518120, China;
| | - Mengfei Li
- State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (M.L.); (M.L.)
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
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15
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Jiu S, Chen B, Dong X, Lv Z, Wang Y, Yin C, Xu Y, Zhang S, Zhu J, Wang J, Liu X, Sun W, Yang G, Li M, Li S, Zhang Z, Liu R, Wang L, Manzoor MA, José QG, Wang S, Lei Y, Yang L, Dirlewanger E, Dong Y, Zhang C. Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L. HORTICULTURE RESEARCH 2023; 10:uhad062. [PMID: 37220556 PMCID: PMC10200261 DOI: 10.1093/hr/uhad062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/02/2023] [Indexed: 05/25/2023]
Abstract
Prunus pusilliflora is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled P. pusilliflora genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we de novo assembled a chromosome-scale P. pusilliflora genome using Oxford Nanopore, Illumina, and chromosome conformation capture sequencing. The assembled genome size was 309.62 Mb, with 76 scaffolds anchored to eight pseudochromosomes. We predicted 33 035 protein-coding genes, functionally annotated 98.27% of them, and identified repetitive sequences covering 49.08% of the genome. We found that P. pusilliflora is closely related to Prunus serrulata and Prunus yedoensis, having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that P. pusilliflora has 643 expanded and 1128 contracted gene families. Furthermore, we found that P. pusilliflora is more resistant to Colletotrichum viniferum, Phytophthora capsici, and Pseudomonas syringae pv. tomato (Pst) DC3000 infections than cultivated Prunus avium. P. pusilliflora also has considerably more nucleotide-binding site-type resistance gene analogs than P. avium, which explains its stronger disease resistance. The cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in P. pusilliflora. Furthermore, 81 MADS-box genes were identified in P. pusilliflora, accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality P. pusilliflora genome will be valuable for further research on cherries and molecular breeding.
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Affiliation(s)
| | | | - Xiao Dong
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Zhengxin Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yuxuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Chunjin Yin
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Sen Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Jijun Zhu
- Shanghai Botanical Garden, Shanghai, 200231, P. R. China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Wanxia Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Guoqian Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Meng Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu Province, 200037, P. R. China
| | - Shufeng Li
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Zhuo Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ruie Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Quero-García José
- INRAe, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d'Ornon, France
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yahui Lei
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Ling Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
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16
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Cheng S, Jia M, Su L, Liu X, Chu Q, He Z, Zhou X, Lu W, Jiang C. Genome-Wide Identification of the MADS-Box Gene Family during Male and Female Flower Development in Chayote (Sechium edule). Int J Mol Sci 2023; 24:ijms24076114. [PMID: 37047083 PMCID: PMC10094161 DOI: 10.3390/ijms24076114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/25/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
The MADS-box gene plays an important role in plant growth and development. As an important vegetable of Cucurbitaceae, chayote has great edible and medicinal value. So far, there is little molecular research on chayote, and there are no reports on the MADS-box transcription factor of chayote. In this study, the MADS-box gene family of chayote was analyzed for the first time, and a total of 70 MADS-box genes were identified, including 14 type I and 56 type II MICK MADS genes. They were randomly distributed on 13 chromosomes except for chromosome 11. The light response element, hormone response element and abiotic stress response element were found in the promoter region of 70 MADS genes, indicating that the MADS gene can regulate the growth and development of chayote, resist abiotic stress, and participate in hormone response; GO and KEGG enrichment analysis also found that SeMADS genes were mainly enriched in biological regulation and signal regulation, which further proved the important role of MADS-box gene in plant growth and development. The results of collinearity showed that segmental duplication was the main driving force of MADS gene expansion in chayote. RNA-seq showed that the expression levels of SeMADS06, SeMADS13, SeMADS26, SeMADS28, SeMADS36 and SeMADS37 gradually increased with the growth of chayote, indicating that these genes may be related to the development of root tubers of 'Tuershao'. The gene expression patterns showed that 12 SeMADS genes were specifically expressed in the male flower in 'Tuershao' and chayote. In addition, SeMADS03 and SeMADS52 may be involved in regulating the maturation of male flowers of 'Tuershao' and chayote. SeMADS21 may be the crucial gene in the development stage of the female flower of 'Tuershao'. This study laid a theoretical foundation for the further study of the function of the MADS gene in chayote in the future.
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Affiliation(s)
- Shaobo Cheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingyue Jia
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Lihong Su
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuanxuan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianwen Chu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongqun He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoting Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengyao Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
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17
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Cheng Z, Song W, Zhang X. Genic male and female sterility in vegetable crops. HORTICULTURE RESEARCH 2022; 10:uhac232. [PMID: 36643746 PMCID: PMC9832880 DOI: 10.1093/hr/uhac232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Vegetable crops are greatly appreciated for their beneficial nutritional and health components. Hybrid seeds are widely used in vegetable crops for advantages such as high yield and improved resistance, which require the participation of male (stamen) and female (pistil) reproductive organs. Male- or female-sterile plants are commonly used for production of hybrid seeds or seedless fruits in vegetables. In this review we will focus on the types of genic male sterility and factors affecting female fertility, summarize typical gene function and research progress related to reproductive organ identity and sporophyte and gametophyte development in vegetable crops [mainly tomato (Solanum lycopersicum) and cucumber (Cucumis sativus)], and discuss the research trends and application perspectives of the sterile trait in vegetable breeding and hybrid production, in order to provide a reference for fertility-related germplasm innovation.
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Affiliation(s)
- Zhihua Cheng
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiyuan Song
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaolan Zhang
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
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18
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Genome-Wide Identification, Evolution, and Expression Characterization of the Pepper (Capsicum spp.) MADS-box Gene Family. Genes (Basel) 2022; 13:genes13112047. [PMID: 36360285 PMCID: PMC9690561 DOI: 10.3390/genes13112047] [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: 10/13/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
MADS domain transcription factors play roles throughout the whole lifecycle of plants from seeding to flowering and fruit-bearing. However, systematic research into MADS-box genes of the economically important vegetable crop pepper (Capsicum spp.) is still lacking. We identified 174, 207, and 72 MADS-box genes from the genomes of C. annuum, C. baccatum, and C. chinense, respectively. These 453 MADS-box genes were divided into type I (Mα, Mβ, Mγ) and type II (MIKC* and MIKCC) based on their phylogenetic relationships. Collinearity analysis identified 144 paralogous genes and 195 orthologous genes in the three Capsicum species, and 70, 114, and 10 MADS-box genes specific to C. annuum, C. baccatum, and C. chinense, respectively. Comparative genomic analysis highlighted functional differentiation among homologous MADS-box genes during pepper evolution. Tissue expression analysis revealed three main expression patterns: highly expressed in roots, stems, leaves, and flowers (CaMADS93/CbMADS35/CcMADS58); only expressed in roots; and specifically expressed in flowers (CaMADS26/CbMADS31/CcMADS11). Protein interaction network analysis showed that type II CaMADS mainly interacted with proteins related to flowering pathway and flower organ development. This study provides the basis for an in-depth study of the evolutionary features and biological functions of pepper MADS-box genes.
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Hu M, Qi Z, Ren Z, Tong J, Wang B, Wu Z, Hao J, Liu N. Genome-Wide Analysis of Auxin Response Factors in Lettuce ( Lactuca sativa L.) Reveals the Positive Roles of LsARF8a in Thermally Induced Bolting. Int J Mol Sci 2022; 23:13509. [PMID: 36362292 PMCID: PMC9653848 DOI: 10.3390/ijms232113509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Warm temperatures induce plant bolting accompanied by flower initiation, where endogenous auxin is dynamically associated with accelerated growth. Auxin signaling is primarily regulated by a family of plant-specific transcription factors, AUXIN RESPONSE FACTORS (ARFs), which either activate or repress the expression of downstream genes in response to developmental and environmental cues. However, the relationship between ARFs and bolting has not been completely understood in lettuce yet. Here, we identified 24 LsARFs (Lactuca sativa ARFs) in the lettuce genome. The phylogenetic tree indicated that LsARFs could be classified into three clusters, which was well supported by the analysis of exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis revealed that more than half of the LsARFs were ubiquitously expressed in all tissues examined, whereas a small number of LsARFs responded to UV or cadmium stresses. qRT-PCR analysis indicated that the expression of most LsARFs could be activated by more than one phytohormone, underling their key roles as integrative hubs of different phytohormone signaling pathways. Importantly, the majority of LsARFs displayed altered expression profiles under warm temperatures, implying that their functions were tightly associated with thermally accelerated bolting in lettuce. Importantly, we demonstrated that silencing of LsARF8a, expression of which was significantly increased by elevated temperatures, resulted in delayed bolting under warm temperatures, suggesting that LsARF8a might conduce to the thermally induced bolting. Together, our results provide molecular insights into the LsARF gene family in lettuce, which will facilitate the genetic improvement of the lettuce in an era of global warming.
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Affiliation(s)
- Manman Hu
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhengyang Qi
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zheng Ren
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Jing Tong
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Baoju Wang
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhanhui Wu
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jinghong Hao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Ning Liu
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Li Y, Zhu J, Feng Y, Li Z, Ren Z, Liu N, Liu C, Hao J, Han Y. LsARF3 mediates thermally induced bolting through promoting the expression of LsCO in lettuce ( Lactuca sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:958833. [PMID: 36160965 PMCID: PMC9498183 DOI: 10.3389/fpls.2022.958833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/09/2022] [Indexed: 06/16/2023]
Abstract
Lettuce (Lactuca sativa L.) is a leafy vegetable whose edible organs usually are leaf or stems, and thus high-temperature induced bolting followed by flower initiation is an undesirable trait in lettuce production. However, the molecular mechanism that controls lettuce bolting and flowering upon thermal treatments is largely unknown. Here, we identified a Lettuce auxin response factor 3 (LsARF3), the expression of which was enhanced by heat and auxin treatments. Interestingly, LsARF3 is preferentially expressed in stem apex, suggesting it might be associated with lettuce bolting. Transgenic lettuce overexpressing LsARF3 displayed early bolting and flowering, whereas knockout of LsARF3 dramatically delayed bolting and flowering in lettuce under normal or high temperature conditions. Furthermore, Exogenous application of IAA failed to rescue the late-bolting and -flowering phenotype of lsarf3 mutants. Several floral integrator genes including LsCO, LsFT, and LsLFY were co-expressed with LsARF3 in the overexpression and knockout lettuce plants. Yeast one-hybrid (Y1H) experiments suggested that LsARF3 could physically interact with the LsCO promoter, which was further confirmed by a dual luciferase assay in tobacco leaves. The results indicated that LsARF3 might directly modulate the expression of LsCO in lettuce. Therefore, these results demonstrate that LsARF3 could promote lettuce bolting in response to the high temperature by directly or indirectly activating the expression of floral genes such as LsCO, which provides new insights into lettuce bolting in the context of ARFs signaling and heat response.
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Affiliation(s)
- Yunfeng Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jiaqi Zhu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yixuan Feng
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Zhenfeng Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Zheng Ren
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Ning Liu
- National Engineering Research Center for Vegetables, Institute of Vegetable Science, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chaojie Liu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jinghong Hao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yingyan Han
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
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21
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Bull T, Michelmore R. Molecular Determinants of in vitro Plant Regeneration: Prospects for Enhanced Manipulation of Lettuce ( Lactuca sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:888425. [PMID: 35615120 PMCID: PMC9125155 DOI: 10.3389/fpls.2022.888425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 05/12/2023]
Abstract
In vitro plant regeneration involves dedifferentiation and molecular reprogramming of cells in order to regenerate whole organs. Plant regeneration can occur via two pathways, de novo organogenesis and somatic embryogenesis. Both pathways involve intricate molecular mechanisms and crosstalk between auxin and cytokinin signaling. Molecular determinants of both pathways have been studied in detail in model species, but little is known about the molecular mechanisms controlling de novo shoot organogenesis in lettuce. This review provides a synopsis of our current knowledge on molecular determinants of de novo organogenesis and somatic embryogenesis with an emphasis on the former as well as provides insights into applying this information for enhanced in vitro regeneration in non-model species such as lettuce (Lactuca sativa L.).
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Affiliation(s)
- Tawni Bull
- The Genome Center, University of California, Davis, Davis, CA, United States
- Graduate Group in Horticulture and Agronomy, University of California, Davis, Davis, CA, United States
| | - Richard Michelmore
- The Genome Center, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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22
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Xue Y, Ma L, Wang H, Hao P, Cheng S, Su Z, Li L, Yu S, Wei H. The MADS transcription factor GhFYF is involved in abiotic stress responses in upland cotton (Gossypium hirsutum L.). Gene 2022; 815:146138. [PMID: 34979233 DOI: 10.1016/j.gene.2021.146138] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Cotton is an important textile industry raw material crops, which plays a critical role in the development of society. MADS transcription factors (TFs) play a key role about the flowering time, flower development, and abiotic stress responses in plants, but little is known about their functions on abiotic stress in cotton. In this study, a MIKCC subfamily gene from cotton, GhFYF (FOREVER YOUNG FLOWER), was isolated and characterized. Our data showed that GhFYF localized to the nucleus. A β-glucuronidase (GUS) activity assay revealed that the promoter of GhFYF was mainly expressed in the flower and seed of ProGhFYF::GUS transgenic A. thaliana plants. The GUS staining of flowers and seeds was deepened after drought, salt treatment, and the expression level of the GUS gene and corresponding stress genes AtERD10, AtAnnexin1 are up-regulated in the inflorescence. Overexpression GhFYF in A. thaliana could promote the seed germination and growth under different salt concentrations, and determin the proline content. Yeast two-hybrid (Y2H) assays showed that GhFYF interacted with the HAD-like protein GhGPP2, which has responds to abiotic stress. Our findings indicate that GhFYF is involved in abiotic stress responses, especially for salt stress. This work establishes a solid foundation for further functional analysis of the GhFYF gene in cotton.
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Affiliation(s)
- Yujun Xue
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Zhengzheng Su
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Lin Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
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23
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Fu J, Huang S, Qian J, Qing H, Wan Z, Cheng H, Zhang C. Genome-Wide Identification of Petunia HSF Genes and Potential Function of PhHSF19 in Benzenoid/Phenylpropanoid Biosynthesis. Int J Mol Sci 2022; 23:ijms23062974. [PMID: 35328393 PMCID: PMC8951162 DOI: 10.3390/ijms23062974] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
Volatile benzenoids/phenylpropanoids are the main flower scent compounds in petunia (Petunia hybrida). Heat shock factors (HSFs), well known as the main regulator of heat stress response, have been found to be involved in the biosynthesis of benzenoid/phenylpropanoid and other secondary metabolites. In order to figure out the potential function of HSFs in the regulation of floral scent in petunia, we systematically identified the genome-wide petunia HSF genes and analyzed their expression and then the interaction between the key petunia HSF gene with target gene involved in benzenoid/phenylpropanoid biosynthesis. The results revealed that 34 HSF gene family members were obtained in petunia, and most petunia HSFs contained one intron. The phylogenetic analysis showed that 23 petunia HSFs were grouped into the largest subfamily HSFA, while only two petunia HSFs were in HSFC subfamily. The DBD domain and NLS motif were well conserved in most petunia HSFs. Most petunia HSF genes’ promoters contained STRE motifs, the highest number of cis-acting element. PhHSF19 is highly expressed in petal tubes, followed by peduncles and petal limbs. During flower development, the expression level of PhHSF19 was dramatically higher at earlier flower opening stages than that at the bud stage, suggesting that PhHSF19 may have potential roles in regulating benzenoid/phenylpropanoid biosynthesis. The expression pattern of PhHSF19 is positively related with PhPAL2, which catalyzes the first committed step in the phenylpropanoid pathway. In addition, there are three STRE elements in the promoter of PhPAL2. PhHSF19 was proven to positively regulate the expression of PhPAL2 according to the yeast one hybrid and dual luciferase assays. These results lay a theoretical foundation for further studies of the regulation of HSFs on plant flower scent biosynthesis.
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24
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Wang S, Luo C, Sun L, Ning K, Chen Z, Yang J, Wang Y, Wang Q. LsRGL1 controls the bolting and flowering times of lettuce by modulating the gibberellin pathway. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111175. [PMID: 35151458 DOI: 10.1016/j.plantsci.2021.111175] [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: 09/04/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Bolting, which is a serious problem during lettuce (Lactuca sativa L.) production, is responsible for substantial annual yield and quality losses. Gibberellin plays a critical role in the regulation of lettuce bolting. Additionally, DELLA proteins negatively regulate the gibberellin signaling pathway. However, it is unclear if DELLA proteins are involved in the regulation of lettuce bolting. Therefore, in this study, we identified four DELLA-encoding genes in lettuce, including LsRGL1, which was highly expressed in the stem and negatively correlated with bolting. Knocking down this gene in lettuce promoted bolting, whereas its overexpression inhibited bolting and the biosynthesis of gibberellin and auxin. A transcriptome analysis revealed that genes involved in gibberellin and auxin biosynthesis and flowering were affected in the LsRGL1-overexpressing lines. The yeast two-hybrid and yeast one-hybrid assay results indicated that LsRGL1 can interact with LsGA3ox and the LsYUC4 promoter region. Considered together, the results of this study suggest LsRGL1 negatively regulates lettuce bolting. Furthermore, its function may depend on modifications to gibberellin and auxin levels mediated at the transcript and protein levels.
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Affiliation(s)
- Shenglin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Chen Luo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Kang Ning
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zijing Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jingjing Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yixin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Qian Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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Zhang Q, Hou S, Sun Z, Chen J, Meng J, Liang D, Wu R, Guo Y. Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao. Genes (Basel) 2021; 12:genes12111799. [PMID: 34828404 PMCID: PMC8622960 DOI: 10.3390/genes12111799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023] Open
Abstract
The MADS-box family gene is a class of transcription factors that have been extensively studied and involved in several plant growth and development processes, especially in floral organ specificity, flowering time and initiation and fruit development. In this study, we identified 69 candidate MADS-box genes and clustered these genes into five subgroups (Mα: 11; Mβ: 2; Mγ: 14; Mδ: 9; MIKC: 32) based on their phylogenetical relationships with Arabidopsis. Most TcMADS genes within the same subgroup showed a similar gene structure and highly conserved motifs. Chromosomal distribution analysis revealed that all the TcMADS genes were evenly distributed in 10 chromosomes. Additionally, the cis-acting elements of promoter, physicochemical properties and subcellular localization were also analyzed. This study provides a comprehensive analysis of MADS-box genes in Theobroma cacao and lays the foundation for further functional research.
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Affiliation(s)
- Qianqian Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Sijia Hou
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Zhenmei Sun
- Institute of Marine Materials Science and Engineering, College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China;
| | - Jing Chen
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Jianqiao Meng
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Dan Liang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Yunqian Guo
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
- Correspondence:
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26
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Rosental L, Still DW, You Y, Hayes RJ, Simko I. Mapping and identification of genetic loci affecting earliness of bolting and flowering in lettuce. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3319-3337. [PMID: 34196730 DOI: 10.1007/s00122-021-03898-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Photoperiod and temperature conditions elicit different genetic regulation over lettuce bolting and flowering. This study identifies environment-specific QTLs and putative genes and provides information for genetic marker assay. Bolting, defined as stem elongation, marks the plant life cycle transition from vegetative to reproductive stage. Lettuce is grown for its leaf rosettes, and premature bolting may reduce crop quality resulting in economic losses. The transition to reproductive stage is a complex process that involves many genetic and environmental factors. In this study, the effects of photoperiod and ambient temperature on bolting and flowering regulation were studied by utilizing a lettuce mapping population to identify quantitative trait loci (QTL) and by gene expression analyses of genotypes with contrasting phenotypes. A recombinant inbred line (RIL) population, derived from a cross between PI 251246 (early bolting) and cv. Salinas (late bolting), was grown in four combinations of short (8 h) and long (16 h) days and low (20 °C) and high (35 °C) temperature. QTL models revealed both genetic (G) and environmental (E) effects, and GxE interactions. A major QTL for bolting and flowering time was found on chromosome 7 (qFLT7.2), and two candidate genes were identified by fine mapping, homology, and gene expression studies. In short days and high temperature conditions, qFLT7.2 had no effect on plant development, while several small-effect loci on chromosomes 2, 3, 6, 8, and 9 were associated with bolting and flowering. Of these, the QTL on chromosome 2, qBFr2.1, co-located with the Flowering Locus T (LsFT) gene. Polymorphisms between parent genotypes in the promotor region may explain identified gene expression differences and were used to design a genetic marker which may be used to identify the late bolting trait.
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Affiliation(s)
- Leah Rosental
- Agricultural Research Service, Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Salinas, CA, USA
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - David W Still
- Agriculture Research Institute, California State University, Cal Poly Pomona, Pomona, CA, USA
- Department of Plant Sciences, Cal Poly Pomona, Pomona, CA, USA
| | - Youngsook You
- Department of Plant Sciences, Cal Poly Pomona, Pomona, CA, USA
| | - Ryan J Hayes
- Agricultural Research Service, Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Salinas, CA, USA
- Agricultural Research Service, Forage Seed and Cereal Research Unit, U.S. Department of Agriculture, Corvallis, OR, USA
| | - Ivan Simko
- Agricultural Research Service, Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Salinas, CA, USA.
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27
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Genome-Wide Identification MIKC-Type MADS-Box Gene Family and Their Roles during Development of Floral Buds in Wheel Wingnut ( Cyclocarya paliurus). Int J Mol Sci 2021; 22:ijms221810128. [PMID: 34576289 PMCID: PMC8471257 DOI: 10.3390/ijms221810128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
MADS-box transcription factors (TFs) have fundamental roles in regulating floral organ formation and flowering time in flowering plants. In order to understand the function of MIKC-type MADS-box family genes in Cyclocarya paliurus (Batal.) Iljinskaja, we first implemented a genome-wide analysis of MIKC-type MADS-box genes in C. paliurus. Here, the phylogenetic relationships, chromosome location, conserved motif, gene structure, promoter region, and gene expression profile were analyzed. The results showed that 45 MIKC-type MADS-box were divided into 14 subfamilies: BS (3), AGL12 (1), AP3-PI (3), MIKC* (3), AGL15 (3), SVP (5), AGL17 (2), AG (3), TM8 (1), AGL6 (2), SEP (5), AP1-FUL (6), SOC1 (7), and FLC (1). The 43 MIKC-type MADS-box genes were distributed unevenly in 14 chromosomes, but two members were mapped on unanchored scaffolds. Gene structures were varied in the same gene family or subfamily, but conserved motifs shared similar distributions and sequences. The element analysis in promoters’ regions revealed that MIKC-type MADS-box family genes were associated with light, phytohormone, and temperature responsiveness, which may play important roles in floral development and differentiation. The expression profile showed that most MIKC-type MADS-box genes were differentially expressed in six tissues (specifically expressed in floral buds), and the expression patterns were also visibly varied in the same subfamily. CpaF1st24796 and CpaF1st23405, belonging to AP3-PI and SEP subfamilies, exhibited the high expression levels in PA-M and PG-F, respectively, indicating their functions in presenting heterodichogamy. We further verified the MIKC-type MADS-box gene expression levels on the basis of transcriptome and qRT-PCR analysis. This study would provide a theoretical basis for classification, cloning, and regulation of flowering mechanism of MIKC-type MADS-box genes in C. paliurus.
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28
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Vijverberg K, Welten M, Kraaij M, van Heuven BJ, Smets E, Gravendeel B. Sepal Identity of the Pappus and Floral Organ Development in the Common Dandelion ( Taraxacum officinale; Asteraceae). PLANTS 2021; 10:plants10081682. [PMID: 34451727 PMCID: PMC8398263 DOI: 10.3390/plants10081682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022]
Abstract
The dry one-seeded fruits (cypselae) of the Asteraceae are often crowned with a pappus, an appendage of hairs or scales that assists in dispersal. It is generally assumed, but little investigated, that the pappus represents the outer floral whorl where the sepals are usually located. We analysed pappus–sepal homology in dandelions using micromorphological and floral gene expression analyses. We show that the pappus initiates from a ring primordium at the base of the corolla, heterochronic to the petals. Pappus parts form from this ring, with those in the alternipetalaous position usually being ahead in growth, referring to sepal identity. Tof-APETALLA1 expression increased during floret development and was highest in mature pappus. Tof-PISTILLATA expression was high and confined to the floral tissues containing the petals and stamens, consistent with expectations for sepals. Apart from the pappus, the dispersal structure of dandelion consists of the upper part of the fruit, the beak, which originates from the inner floral whorl. Thus, our results support the homology of the pappus with the sepals, but show that it is highly derived. Together with our floral stage definitions and verified qPCR reference genes, they provide a basis for evolution and development studies in dandelions and possibly other Asteraceae.
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Affiliation(s)
- Kitty Vijverberg
- Evolutionary Ecology, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; (M.W.); (B.J.v.H.); (E.S.); (B.G.)
- Experimental Plant Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6500 GL Nijmegen, The Netherlands
- Correspondence: ; Tel.: +31-(0)715271910
| | - Monique Welten
- Evolutionary Ecology, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; (M.W.); (B.J.v.H.); (E.S.); (B.G.)
| | - Marjan Kraaij
- Evolutionary Genetics, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands;
| | - Bertie Joan van Heuven
- Evolutionary Ecology, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; (M.W.); (B.J.v.H.); (E.S.); (B.G.)
| | - Erik Smets
- Evolutionary Ecology, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; (M.W.); (B.J.v.H.); (E.S.); (B.G.)
| | - Barbara Gravendeel
- Evolutionary Ecology, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; (M.W.); (B.J.v.H.); (E.S.); (B.G.)
- Experimental Plant Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6500 GL Nijmegen, The Netherlands
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Dong X, Deng H, Ma W, Zhou Q, Liu Z. Genome-wide identification of the MADS-box transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under abiotic stress. BMC Genomics 2021; 22:603. [PMID: 34362293 PMCID: PMC8348820 DOI: 10.1186/s12864-021-07911-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Background Alfalfa, the “queen of forage”, is the most extensively cultivated forage legume in the world. The development and yield of alfalfa are seriously limited by abiotic stress. MADS-box transcription factors are one of the largest gene families and play a pivotal role in plant development and abiotic stress. However, little is known regarding the MADS-box transcription factors in autotetraploid cultivated alfalfa. Results In the present study, we identified 120 MsMADS-box genes in the alfalfa genome. Phylogenetic analysis indicated that 75 type-I MsMADS-box genes were classified into the Mα, Mβ, and Mγ subgroups, and 45 type-II MsMADS-box genes were classified into 11 subgroups. The promoter region of MsMADS-box genes containing several hormone and stress related elements. Chromosomal location analysis revealed that 117 MsMADS-box genes were unevenly distributed on 32 chromosomes, and the remaining three genes were located on unmapped scaffolds. A total of nine pairs of segmental duplications and four groups of tandem duplications were found. Expression analysis showed that MsMADS-box genes were differentially expressed in various tissues and under abiotic stresses. qRT-PCR analysis revealed that the expression profiles of eight selected MsMADS-box genes were distinct under various stresses. Conclusions In this study, MsMADS-box genes were identified in the cultivated alfalfa genome based on autotetraploid level, and further confirmed by Gene Ontology (GO) analysis, phylogenetic analysis, sequence features and expression analysis. Taken together, these findings will provide clues for further study of MsMADS-box functions and alfalfa molecular breeding. Our study is the first to systematically identify and characterize the MADS-box transcription factors in autotetraploid cultivated alfalfa (Medicago sativa L.), and eight MsMADS-box genes were significantly involved in response to various stresses. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07911-9.
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Affiliation(s)
- Xueming Dong
- 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, 730000, Lanzhou, People's Republic of China
| | - Hao Deng
- 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, 730000, Lanzhou, People's Republic of China
| | - Wenxue Ma
- 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, 730000, Lanzhou, People's Republic of China
| | - Qiang Zhou
- 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, 730000, Lanzhou, People's Republic of China
| | - Zhipeng Liu
- 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, 730000, Lanzhou, People's Republic of China.
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Abolghasemi R, Haghighi M, Etemadi N, Wang S, Soorni A. Transcriptome architecture reveals genetic networks of bolting regulation in spinach. BMC PLANT BIOLOGY 2021; 21:179. [PMID: 33853527 PMCID: PMC8045288 DOI: 10.1186/s12870-021-02956-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/31/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Bolting refers to the early flowering stem production on agricultural and horticultural crops before harvesting. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components, which cause a large reduction in the quality and productivity of vegetable crops like spinach. However, little is known about the signaling pathways and molecular functions involved in bolting mechanisms in spinach. The genetic information regarding the transition from vegetative growth to the reproductive stage in spinach would represent an advantage to regulate bolting time and improvement of resistant cultivars to minimize performance loss. RESULTS To investigate the key genes and their genetic networks controlling spinach bolting, we performed RNA-seq analysis on early bolting accession Kashan and late-bolting accession Viroflay at both vegetative and reproductive stages and found a significant number of differentially expressed genes (DEGs) ranging from 195 to 1230 in different comparisons. These genes were mainly associated with the signaling pathways of vernalization, photoperiod/circadian clock, gibberellin, autonomous, and aging pathways. Gene ontology analysis uncovered terms associated with carbohydrate metabolism, and detailed analysis of expression patterns for genes of Fructose-1, 6-bisphosphate aldolase, TREHALOSE-6-PHOSPHATE SYNTHASE 1, FLOWERING PROMOTING FACTOR 1, EARLY FLOWERING, GIGANTEA, and MADS-box proteins revealed their potential roles in the initiating or delaying of bolting. CONCLUSION This study is the first report on identifying bolting and flowering-related genes based on transcriptome sequencing in spinach, which provides insight into bolting control and can be useful for molecular breeding programs and further study in the regulation of the genetic mechanisms related to bolting in other vegetable crops.
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Affiliation(s)
- Reza Abolghasemi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Maryam Haghighi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Shui Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
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Luo C, Wang S, Ning K, Chen Z, Wang Y, Yang J, Qi M, Wang Q. The APETALA2 transcription factor LsAP2 regulates seed shape in lettuce. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2463-2476. [PMID: 33340036 DOI: 10.1093/jxb/eraa592] [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: 10/20/2020] [Accepted: 12/15/2020] [Indexed: 05/28/2023]
Abstract
Seeds are major vehicles of propagation and dispersal in plants. A number of transcription factors, including APETALA2 (AP2), play crucial roles during the seed development process in various plant species. However, genes essential for seed development and the regulatory networks that operate during seed development remain unclear in lettuce. Here, we identified a lettuce AP2 (LsAP2) gene that was highly expressed during the early stages of seed development. LsAP2 knockout plants obtained by the CRISPR/Cas9 system were used to explore the biological function of LsAP2. Compared with the wild type, the seeds of Lsap2 mutant plants were longer and narrower, and developed an extended tip at the seed top. After further investigating the structural characteristics of the seeds of Lsap2 mutant plants, we proposed a new function of LsAP2 in seed dispersal. Moreover, we identified several interactors of LsAP2. Our results showed that LsAP2 directly interacted with the lettuce homolog of BREVIPEDICELLUS (LsBP) and promoted the expression of LsBP. Transcriptome analysis revealed that LsAP2 might also be involved in brassinosteroid biosynthesis and signaling pathways. Taken together, our data indicate that LsAP2 has a significant function in regulating seed shape in lettuce.
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Affiliation(s)
- Chen Luo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Shenglin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Kang Ning
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Zijing Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Yixin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Jingjing Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Meixia Qi
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Qian Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
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Han R, Truco MJ, Lavelle DO, Michelmore RW. A Composite Analysis of Flowering Time Regulation in Lettuce. FRONTIERS IN PLANT SCIENCE 2021; 12:632708. [PMID: 33763095 PMCID: PMC7982828 DOI: 10.3389/fpls.2021.632708] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/16/2021] [Indexed: 05/08/2023]
Abstract
Plants undergo profound physiological changes when transitioning from vegetative to reproductive growth. These changes affect crop production, as in the case of leafy vegetables. Lettuce is one of the most valuable leafy vegetable crops in the world. Past genetic studies have identified multiple quantitative trait loci (QTLs) that affect the timing of the floral transition in lettuce. Extensive functional molecular studies in the model organism Arabidopsis provide the opportunity to transfer knowledge to lettuce to explore the mechanisms through which genetic variations translate into changes in flowering time. In this review, we integrated results from past genetic and molecular studies for flowering time in lettuce with orthology and functional inference from Arabidopsis. This summarizes the basis for all known genetic variation underlying the phenotypic diversity of flowering time in lettuce and how the genetics of flowering time in lettuce projects onto the established pathways controlling flowering time in plants. This comprehensive overview reveals patterns across experiments as well as areas in need of further study. Our review also represents a resource for developing cultivars with delayed flowering time.
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Affiliation(s)
- Rongkui Han
- The Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, United States
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, United States
| | - Maria José Truco
- The Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, United States
| | - Dean O. Lavelle
- The Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, United States
| | - Richard W. Michelmore
- The Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- *Correspondence: Richard W. Michelmore,
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Won SY, Jung JA, Kim JS. Genome-wide analysis of the MADS-Box gene family in Chrysanthemum. Comput Biol Chem 2020; 90:107424. [PMID: 33340990 DOI: 10.1016/j.compbiolchem.2020.107424] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/19/2020] [Accepted: 11/28/2020] [Indexed: 10/22/2022]
Abstract
MADS-box family transcription factors play key roles in various developmental processes in plants. Here, we identified 108 MADS-box genes in the genome of chrysanthemum (Chrysanthemum nankingense). We classified these genes based on their phylogenetic relationships with MADS-box genes in Arabidopsis thaliana and lettuce (Lactuca sativa). Type I genes were subdivided into classes Mα (19 genes), Mβ (12 genes), and Mγ (10 genes), and type II genes were subdivided into classes MIKCC (64 genes) and MIKC* (3 genes). The MIKCC class genes were further divided into 16 subclasses that included genes described in the ABCDE flower development model. Each group of MADS-box genes showed a specific pattern of conserved protein motifs and exon-intron structure. We analyzed the expression levels of each MADS-box gene in root, stem, leaf, flower bud, disc floret, and ray floret tissues. Subfamilies AGL18, FLC, and SVP contained more members in chrysanthemum. The asterid-specific TM8 subfamily and eleven Asteraceae Specific-MADS CnMADS genes were present in chrysanthemum. Chrysanthemum is the lacking members of the AGL15 subfamily. Among the genes responsible for the ABCDE model, B-class genes were expanded in chrysanthemum with three AP3 and four PI genes. One AP3 homolog functions in marginal ray floret development, whereas the two other AP3 homologs function in the development of the central disc floret. Two of the four PI genes are expressed in chrysanthemum, specifically in both types of florets. The results of this study lay the foundation for further studies of the roles of MADS-box genes in flower development in chrysanthemum and of the evolution of MADS-box genes in plants.
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Affiliation(s)
- So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea.
| | - Jae-A Jung
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
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Hui WK, Liu MQ, Wu GJ, Wang JY, Zhong Y, Li HY, Tang HL, Zeng W, Ma LX, Zhang Y, Xiang L, Chen XY, Gong W. Ectopic expression of an AGAMOUS homologue gene in Jatropha curcas causes early flowering and heterostylous phenotypes. Gene 2020; 766:145141. [PMID: 32911031 DOI: 10.1016/j.gene.2020.145141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 01/06/2023]
Abstract
Jatropha curcasseeds are abundant in biodiesel, and low seed yields are linked to poor quality female flowers, which creates a bottleneck for Jatropha seed utilization. Therefore, identifying the genes associated with flowering is crucial for the genetic enrichment of seed yields. Here, we identified an AGAMOUS homologue gene (JcAG) from J. curcas. We found that reproductive organs had higher JcAG expression than vegetative organs, particularly the carpel. Rosette leaves were small and misshapen in 35S:JcAG transgenic lines in comparison with those in wild-type plants. JcAG overexpression caused an extremely early flowering, delayed perianth and stamen filament development, small flowers, and significantly shorter Arabidopsis plants with little fruit. In the JcAG-overexpressing line, the homeotic transformation of sepals into pistillate organs was observed, and floral meristem and organ identity genes were regulated. This study provides insights into the JcAG's function and benefits to our knowledge of the underlying the genetic mechanisms related to floral sex differentiation in Jatropha.
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Affiliation(s)
- Wen-Kai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Ming-Qian Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, Preparation Office of South China Agricultural Museum, South China Agricultural University, Guangzhou 510642, China
| | - Guo-Jiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jing-Yan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - He-Yue Li
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Hai-Long Tang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Zeng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Le-Xun Ma
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Xiang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiao-Yang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, Preparation Office of South China Agricultural Museum, South China Agricultural University, Guangzhou 510642, China.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China.
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Su MH, Azwar E, Yang Y, Sonne C, Yek PNY, Liew RK, Cheng CK, Show PL, Lam SS. Simultaneous removal of toxic ammonia and lettuce cultivation in aquaponic system using microwave pyrolysis biochar. JOURNAL OF HAZARDOUS MATERIALS 2020; 396:122610. [PMID: 32298865 DOI: 10.1016/j.jhazmat.2020.122610] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/24/2020] [Accepted: 03/27/2020] [Indexed: 05/22/2023]
Abstract
This study examined an aquaponic approach of circulating water containing ammonia excretions from African catfish grown in an aquaculture tank for bacterial conversion into nitrates, which then acted as a nutrient substance to cultivate lettuce in hydroponic tank. We found that microwave pyrolysis biochar (450 g) having microporous (1.803 nm) and high BET surface area (419 m2/g) was suitable for use as biological carrier to grow nitrifying bacteria (63 g of biofilm mass) that treated the water quality through removing the ammonia (67%) and total suspended solids (68%), resulting in low concentration of remaining ammonia (0.42 mg/L) and total suspended solid (59.40 mg/L). It also increased the pH (6.8), converted the ammonia into nitrate (29.7 mg/L), and increased the nitrogen uptake by the lettuce (110 mg of nitrogen per plant), resulting in higher growth in lettuce (0.0562 %/day) while maintaining BOD5 level (3.94 mg/L) at acceptable level and 100% of catfish survival rate. Our results demonstrated that microwave pyrolysis biochar can be a promising solution for growing nitrifying bacteria in aquaponic system for simultaneous toxic ammonia remediation and generation of nitrate for growing vegetable in aquaculture industry.
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Affiliation(s)
- Man Huan Su
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; Pyrolysis Technology Research Group, Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Elfina Azwar
- Pyrolysis Technology Research Group, Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - YaFeng Yang
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Christian Sonne
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000, Roskilde, Denmark
| | - Peter Nai Yuh Yek
- Pyrolysis Technology Research Group, Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; School of Engineering and Technology, University College of Technology Sarawak, Lot 88, Persiaran Brooke, 96000 Sibu, Sarawak, Malaysia
| | - Rock Keey Liew
- NV WESTERN PLT, No. 208B, Jalan Macalister, Georgetown, Pulau Pinang 10400, Malaysia
| | - Chin Kui Cheng
- Faculty of Chemical & Natural Resources Engineering, Lebuhraya Tun Razak, Universiti Malaysia Pahang, Gambang Kuantan, Pahang 26300, Malaysia
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Su Shiung Lam
- Pyrolysis Technology Research Group, Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.
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Bai G, Yang DH, Cao P, Yao H, Zhang Y, Chen X, Xiao B, Li F, Wang ZY, Yang J, Xie H. Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco ( Nicotiana tabacum L.). Int J Mol Sci 2019; 20:E5043. [PMID: 31614589 PMCID: PMC6829366 DOI: 10.3390/ijms20205043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/06/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
MADS-box genes play a pivotal role in various processes, including floral and seed development, controlling flowering time, regulation of fruits ripening, and respond to abiotic and biotic stressors in planta. Tobacco (Nicotiana tabacum) has been widely used as a model plant for analyzing the gene function, however, there has been less information on the regulation of flowering, and the associated genes. In the present study, a total of 168 NtMADS-box genes were identified from tobacco, and their phylogenetic relationship, chromosome locations, and gene structures were further analyzed. NtMADS-box genes can be clustered into four sub-families of Mα, Mγ, MIKC*, and MIKCC. A total of 111 NtMADS-box genes were distributed on 20 chromosomes, and 57 NtMADS-box genes were located on the unanchored scaffolds due to the complex and incomplete assembly of the tobacco genome. Expression profiles of NtMADS-box genes by microarray from 23 different tissues indicated that members in different NtMADS-box gene subfamilies might play specific roles in the growth and flower development, and the transcript levels of 24 NtMADS-box genes were confirmed by quantitative real-time PCR. Importantly, overexpressed NtSOC1/NtMADS133 could promote early flowering and dwarfism in transgenic tobacco plants. Therefore, our findings provide insights on the characterization of NtMADS-box genes to further study their functions in plant development.
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Affiliation(s)
- Ge Bai
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Da-Hai Yang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Peijian Cao
- China Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - Heng Yao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Yihan Zhang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Xuejun Chen
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Bingguang Xiao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Feng Li
- China Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - Zhen-Yu Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China.
| | - Jun Yang
- China Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - He Xie
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
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