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Zhao Y, Sun X, Zhou J, Liu L, Huang L, Hu Q. Identification and Functional Exploration of BraGASA Genes Reveal Their Potential Roles in Drought Stress Tolerance and Sexual Reproduction in Brassica rapa L. ssp. pekinensis. Int J Mol Sci 2024; 25:9643. [PMID: 39273590 PMCID: PMC11395553 DOI: 10.3390/ijms25179643] [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: 08/08/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
Gibberellic acid-stimulated Arabidopsis sequences (GASAs) are a subset of the gibberellin (GA)-regulated gene family and play crucial roles in various physiological processes. However, the GASA genes in Brassica rapa have not yet been documented. In this study, we identified and characterized 16 GASA genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Analysis of the conserved motifs revealed significant conservation within the activation segment of BraGASA genes. This gene family contains numerous promoter elements associated with abiotic stress tolerance, including those for abscisic acid (ABA) and methyl jasmonate (MeJA). Expression profiling revealed the presence of these genes in various tissues, including roots, stems, leaves, flowers, siliques, and callus tissues. When plants were exposed to drought stress, the expression of BraGASA3 decreased notably in drought-sensitive genotypes compared to their wild-type counterparts, highlighting the potentially crucial role of BraGASA3 in drought stress. Additionally, BraGASAs exhibited various functions in sexual reproduction dynamics. The findings contribute to the understanding of the function of BraGASAs and provide valuable insights for further exploration of the GASA gene function of the BraGASA gene in Chinese cabbage.
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Affiliation(s)
- Yanting Zhao
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
| | - Xinjie Sun
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (X.S.); (L.H.)
| | - Jingyuan Zhou
- Ziyun & Bifeng Community, Qiushi College, Zhejiang University, Hangzhou 310058, China;
| | - Lixuan Liu
- School of International Studies, Zhejiang University, Hangzhou 310058, China;
| | - Li Huang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (X.S.); (L.H.)
| | - Qizan Hu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
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Gao C, Li Z, Zhang H, Li C, Sun H, Li S, Ma N, Qi X, Cui Y, Yang P, Hu T. Genome-Wide Identification and Characterization of the GASA Gene Family in Medicago truncatula, and Expression Patterns under Abiotic Stress and Hormone Treatments. PLANTS (BASEL, SWITZERLAND) 2024; 13:2364. [PMID: 39273848 PMCID: PMC11396804 DOI: 10.3390/plants13172364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/09/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024]
Abstract
Medicago truncatula is a key model plant for studying legume plants, particularly alfalfa (Medicago sativa), due to its well-defined genetic background. Plant-specific GASA (Gibberellic Acid Stimulated Arabidopsis) genes play various roles in plant growth and development, abiotic stress, and hormone responses. However, limited information is available on GASA research in Medicago. In this study, 26 MtGASAs were identified and analyzed for its structure, evolution, and expressions. Sequence alignments and phylogeny revealed that 26 MtGASAs containing conserved GASA domains were classified into three clades. The chromosomal locations and gene synteny revealed segmental and tandem repetition evolution. Analysis of cis-regulatory elements indicates that family members likely influence various hormone signaling pathways and stress-related mechanisms. Moreover, the RNA-seq and qRT-PCR analyses revealed that 26 MtGASAs were extensively involved in abiotic stresses and hormone responses. Notably, seven MtGASA genes (MtGASA1, 10, 12, 17, 23, 25 and 26) were all dramatically activated by NaCl and Mannitol treatments, and four MtGASAs (MtGASA7, 10, 23 and 24) were significant activated by GA3, PBZ, ABA, and MeJA treatments. Collectively, this study is the first to identify and describe GASA genes in Medicago on a genome-wide scale. The results establish a basis for functional characterization, showing that these proteins are essential in responding to various abiotic stresses and hormonal signals.
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Affiliation(s)
- Cai Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhongxing Li
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hanwen Zhang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chun Li
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiangyu Qi
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yilin Cui
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
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Ben Saad R, Ben Romdhane W, Bouteraa MT, Jemli S, Ben Hsouna A, Hassairi A. Development of a marker-free engineered durum wheat overexpressing Lobularia maritima GASA1 with improved drought tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108775. [PMID: 38810521 DOI: 10.1016/j.plaphy.2024.108775] [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: 03/21/2024] [Revised: 05/09/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024]
Abstract
Due to their fixed lifestyle, plants must adapt to abiotic or biotic stresses by orchestrating various responses, including protective and growth control measures. Growth arrest is provoked upon abiotic stress and can impair plant production. Members of the plant-specific GASA (gibberellic acid-stimulated Arabidopsis) gene family play crucial roles in phytohormone responses, abiotic and biotic stresses, and plant growth. Here, we recognized and examined the LmGASA1 gene from the halophyte plant Lobularia maritima and developed marker-free engineered durum wheat plants overexpressing the gene. The LmGASA1 transcript profile revealed that it's induced by stressful events as well as by phytohormones including GA3, MeJA, and ABA, suggesting that the LmGASA1 gene may contribute to these stress and hormone signal transduction pathways. Transient expression of GFP-LmGASA1 fusion in onion epidermal cells indicated that LmGASA1 is localized to the cell membrane. Further analysis showed that overexpression of LmGASA1 in durum wheat plants enhanced tolerance to drought stress compared with that in non-transgenic (NT) plants, imposing no yield penalty and enabling seed production even following drought stress at the vegetative stage. Altogether, our data indicate that LmGASA1 regulates both the scavenging capacity of the antioxidant enzymatic system and the activation of at least six stress-related genes that function as positive regulators of drought stress tolerance. LmGASA1 appears to be a novel gene useful for further functional analysis and potential engineering for drought stress tolerance in crops.
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Affiliation(s)
- Rania Ben Saad
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P ''1177'', 3018, Sfax -Tunisia
| | - Walid Ben Romdhane
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia.
| | - Mohamed Taieb Bouteraa
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P ''1177'', 3018, Sfax -Tunisia
| | - Sonia Jemli
- Laboratory of Microbial Biotechnology and Enzymes Engineering, Centre of Biotechnology of Sfax, University of Sfax, B.P ''1177'', 3018, Sfax -Tunisia
| | - Anis Ben Hsouna
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P ''1177'', 3018, Sfax -Tunisia; Department of Environmental Sciences and Nutrition, Higher Institute of Applied Sciences and Technology of Mahdia, University of Monastir, Monastir 5000, Tunisia
| | - Afif Hassairi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P ''1177'', 3018, Sfax -Tunisia; Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia
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Pečenková T, Potocký M, Stegmann M. More than meets the eye: knowns and unknowns of the trafficking of small secreted proteins in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3713-3730. [PMID: 38693754 DOI: 10.1093/jxb/erae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/01/2024] [Indexed: 05/03/2024]
Abstract
Small proteins represent a significant portion of the cargo transported through plant secretory pathways, playing crucial roles in developmental processes, fertilization, and responses to environmental stresses. Despite the importance of small secreted proteins, substantial knowledge gaps persist regarding the regulatory mechanisms governing their trafficking along the secretory pathway, and their ultimate localization or destination. To address these gaps, we conducted a comprehensive literature review, focusing particularly on trafficking and localization of Arabidopsis small secreted proteins with potential biochemical and/or signaling roles in the extracellular space, typically those within the size range of 101-200 amino acids. Our investigation reveals that while at least six members of the 21 mentioned families have a confirmed extracellular localization, eight exhibit intracellular localization, including cytoplasmic, nuclear, and chloroplastic locations, despite the presence of N-terminal signal peptides. Further investigation into the trafficking and secretion mechanisms of small protein cargo could not only deepen our understanding of plant cell biology and physiology but also provide a foundation for genetic manipulation strategies leading to more efficient plant cultivation.
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Affiliation(s)
- Tamara Pečenková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Martin Potocký
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Martin Stegmann
- Technical University Munich, School of Life Sciences, Phytopathology, Emil-Ramann-Str. 2, 85354 Freising, Germany
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Guo X, Zhu S, Xue Y, Lin Y, Mao J, Li S, Liang C, Lu X, Tian J. The Stylo Cysteine-Rich Peptide SgSnakin1 Is Involved in Aluminum Tolerance through Enhancing Reactive Oxygen Species Scavenging. Int J Mol Sci 2024; 25:6672. [PMID: 38928379 PMCID: PMC11204226 DOI: 10.3390/ijms25126672] [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: 04/25/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Stylo (Stylosanthes spp.) is an important pasture legume with strong aluminum (Al) resistance. However, the molecular mechanisms underlying its Al tolerance remain fragmentary. Due to the incomplete genome sequence information of stylo, we first conducted full-length transcriptome sequencing for stylo root tips treated with and without Al and identified three Snakin/GASA genes, namely, SgSnakin1, SgSnakin2, and SgSnakin3. Through quantitative RT-PCR, we found that only SgSnakin1 was significantly upregulated by Al treatments in stylo root tips. Histochemical localization assays further verified the Al-enhanced expression of SgSnakin1 in stylo root tips. Subcellular localization in both tobacco and onion epidermis cells showed that SgSnakin1 localized to the cell wall. Overexpression of SgSnakin1 conferred Al tolerance in transgenic Arabidopsis, as reflected by higher relative root growth and cell vitality, as well as lower Al concentration in the roots of transgenic plants. Additionally, overexpression of SgSnakin1 increased the activities of SOD and POD and decreased the levels of O2·- and H2O2 in transgenic Arabidopsis in response to Al stress. These findings indicate that SgSnakin1 may function in Al resistance by enhancing the scavenging of reactive oxygen species through the regulation of antioxidant enzyme activities.
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Affiliation(s)
- Xueqiong Guo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.G.); (Y.L.); (J.M.); (S.L.); (J.T.)
| | - Shengnan Zhu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang 524048, China;
| | - Yingbin Xue
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China;
| | - Yan Lin
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.G.); (Y.L.); (J.M.); (S.L.); (J.T.)
| | - Jingying Mao
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.G.); (Y.L.); (J.M.); (S.L.); (J.T.)
| | - Shuyue Li
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.G.); (Y.L.); (J.M.); (S.L.); (J.T.)
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.G.); (Y.L.); (J.M.); (S.L.); (J.T.)
| | - Xing Lu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.G.); (Y.L.); (J.M.); (S.L.); (J.T.)
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.G.); (Y.L.); (J.M.); (S.L.); (J.T.)
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Li Y, Yuan W, Peng J, Ju J, Ling P, Guo X, Yang J, Ma Q, Lin H, Li J, Wang C, Su J. GhGASA14 regulates the flowering time of upland cotton in response to GA 3. PLANT CELL REPORTS 2024; 43:170. [PMID: 38869848 DOI: 10.1007/s00299-024-03252-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024]
Abstract
KEY MESSAGE The silencing of GhGASA14 and the identification of superior allelic variation in its coding region indicate that GhGASA14 may positively regulate flowering and the response to GA3. Gibberellic acid-stimulated Arabidopsis (GASA), a member of the gibberellin-regulated short amino acid family, has been extensively investigated in several plant species and found to be critical for plant growth and development. However, research on this topic in cotton has been limited. In this study, we identified 38 GhGASAs that were dispersed across 18 chromosomes in upland cotton, and all of these genes had a GASA core domain. Transcriptome expression patterns and qRT-PCR results revealed that GhGASA9 and GhGASA14 exhibited upregulated expression not only in the floral organs but also in the leaves of early-maturing cultivars. The two genes were functionally characterized by virus-induced gene silencing (VIGS), and the budding and flowering times after silencing the target genes were later than those of the control (TRV:00). Compared with that in the water-treated group (MOCK), the flowering period of the different fruiting branches in the GA3-treated group was more concentrated. Interestingly, allelic variation was detected in the coding sequence of GhGASA14 between early-maturing and late-maturing accessions, and the frequency of this favorable allele was greater in high-latitude cotton cultivars than in low-latitude ones. Additionally, a significant linear relationship was observed between the expression level of GhGASA14 and flowering time among the 12 upland cotton accessions. Taken together, these results indicated that GhGASA14 may positively regulate flowering time and respond to GA3. These findings could lead to the use of valuable genetic resources for breeding early-maturing cotton cultivars in the future.
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Affiliation(s)
- Ying Li
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wenmin Yuan
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jialuo Peng
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jisheng Ju
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Pingjie Ling
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xuefeng Guo
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Junning Yang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Qi Ma
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Hai Lin
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Jilian Li
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Caixiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Junji Su
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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Kumar A, Mushtaq M, Kumar P, Sharma DP, Gahlaut V. Insights into flowering mechanisms in apple (Malus × domestica Borkh.) amidst climate change: An exploration of genetic and epigenetic factors. Biochim Biophys Acta Gen Subj 2024; 1868:130593. [PMID: 38408683 DOI: 10.1016/j.bbagen.2024.130593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/05/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
Apple (Malus × domestica Borkh.) holds a prominent position among global temperate fruit crops, with flowering playing a crucial role in both production and breeding. This review delves into the intricate mechanisms governing apple flowering amidst the backdrop of climate change, acknowledging the profound influence of external and internal factors on biennial bearing, flower bud quality, and ultimately, fruit quality. Notably, the challenge faced in major apple production regions is not an inadequacy of flowers but an excess, leading to compromised fruit quality necessitating thinning practices. Climate change exacerbates these challenges, rendering apple trees more susceptible to crop failure due to unusual weather events, such as reduced winter snowfall, early spring cold weather, and hailstorms during flowering and fruit setting. Altered climatic conditions, exemplified by increased spring warming coupled with sub-freezing temperatures, negatively impact developing flower buds and decrease overall crop production. Furthermore, changing winter conditions affect chilling accumulation, disrupting flower development and synchronicity. Although the physiological perception of apple flowering has been reviewed in the past, the genetic, epigenetic, and multi-omics regulatory mechanisms governing floral induction and flowering are still rarely discussed in the case of apple flowering. This article comprehensively reviews the latest literature encompassing all aspects of apple flowering, aiming to broaden our understanding and address flowering challenges while also laying a solid foundation for future research in developing cultivars that are ideally adapted to climate change.
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Affiliation(s)
- Anshul Kumar
- MS Swaminathan School of Agriculture, Shoolini University, Bhajol, Solan, Himachal Pradesh 173229, India
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University, Bhajol, Solan, Himachal Pradesh 173229, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. YS Parmar University of Horticulture and Forestry Nauni Solan, Himachal Pradesh 173230, India.
| | - Dharam Paul Sharma
- Department of Fruit Science, Dr. YS Parmar University of Horticulture and Forestry Nauni Solan, Himachal Pradesh 173230, India
| | - Vijay Gahlaut
- University Centre for Research & Development, Chandigarh University, Punjab 140413, India.
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Nahirñak V, Almasia NI, Lia VV, Hopp HE, Vazquez Rovere C. Unveiling the defensive role of Snakin-3, a member of the subfamily III of Snakin/GASA peptides in potatoes. PLANT CELL REPORTS 2024; 43:47. [PMID: 38302779 DOI: 10.1007/s00299-023-03108-4] [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: 09/01/2023] [Accepted: 11/05/2023] [Indexed: 02/03/2024]
Abstract
KEY MESSAGE The first in-depth characterization of a subfamily III Snakin/GASA member was performed providing experimental evidence on promoter activity and subcellular localization and unveiling a role of potato Snakin-3 in defense Snakin/GASA proteins share 12 cysteines in conserved positions in the C-terminal region. Most of them were involved in different aspects of plant growth and development, while a small number of these peptides were reported to have antimicrobial activity or participate in abiotic stress tolerance. In potato, 18 Snakin/GASA genes were identified and classified into three groups based on phylogenetic analysis. Snakin-1 and Snakin-2 are members of subfamilies I and II, respectively, and were reported to be implicated not only in defense against pathogens but also in plant development. In this work, we present the first in-depth characterization of Snakin-3, a member of the subfamily III within the Snakin/GASA gene family of potato. Transient co-expression of Snakin-3 fused to the green fluorescent protein and organelle markers revealed that it is located in the endoplasmic reticulum. Furthermore, expression analyses via pSnakin-3::GUS transgenic plants showed GUS staining mainly in roots and vascular tissues of the stem. Moreover, GUS expression levels were increased after inoculation with Pseudomonas syringae pv. tabaci or Pectobacterium carotovorum subsp. carotovorum and also after auxin treatment mainly in roots and stems. To gain further insights into the function of Snakin-3 in planta, potato overexpressing lines were challenged against P. carotovorum subsp. carotovorum showing enhanced tolerance to this bacterial pathogen. In sum, here we report the first functional characterization of a Snakin/GASA gene from subfamily III in Solanaceae. Our findings provide experimental evidence on promoter activity and subcellular localization and reveal a role of potato Snakin-3 in plant defense.
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Affiliation(s)
- Vanesa Nahirñak
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina
| | - Natalia Inés Almasia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina
| | - Verónica Viviana Lia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Horacio Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cecilia Vazquez Rovere
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina.
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Syed Nabi RB, Lee MH, Cho KS, Tayade R, Kim S, Kim JI, Kim MY, Lee E, Lee J, Kim SW, Oh E. Genome-Wide Identification and Comprehensive Analysis of the GASA Gene Family in Peanuts ( Arachis hypogaea L.) under Abiotic Stress. Int J Mol Sci 2023; 24:17117. [PMID: 38069439 PMCID: PMC10707693 DOI: 10.3390/ijms242317117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/08/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Peanut (Arachis hypogaea L.) is a globally cultivated crop of significant economic and nutritional importance. The role of gibberellic-acid-stimulated Arabidopsis (GASA) family genes is well established in plant growth, development, and biotic and abiotic stress responses. However, there is a gap in understanding the function of GASA proteins in cultivated peanuts, particularly in response to abiotic stresses such as drought and salinity. Thus, we conducted comprehensive in silico analyses to identify and verify the existence of 40 GASA genes (termed AhGASA) in cultivated peanuts. Subsequently, we conducted biological experiments and performed expression analyses of selected AhGASA genes to elucidate their potential regulatory roles in response to drought and salinity. Phylogenetic analysis revealed that AhGASA genes could be categorized into four distinct subfamilies. Under normal growth conditions, selected AhGASA genes exhibited varying expressions in young peanut seedling leaves, stems, and roots tissues. Notably, our findings indicate that certain AhGASA genes were downregulated under drought stress but upregulated under salt stress. These results suggest that specific AhGASA genes are involved in the regulation of salt or drought stress. Further functional characterization of the upregulated genes under both drought and salt stress will be essential to confirm their regulatory roles in this context. Overall, our findings provide compelling evidence of the involvement of AhGASA genes in the mechanisms of stress tolerance in cultivated peanuts. This study enhances our understanding of the functions of AhGASA genes in response to abiotic stress and lays the groundwork for future investigations into the molecular characterization of AhGASA genes.
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Affiliation(s)
- Rizwana Begum Syed Nabi
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
| | - Myoung Hee Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
| | - Kwang-Soo Cho
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
| | - Rupesh Tayade
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Sungup Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
| | - Jung-In Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
| | - Min-Young Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
| | - Eunsoo Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
| | - Jungeun Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
| | - Sang-Woo Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
| | - Eunyoung Oh
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Republic of Korea; (R.B.S.N.); (J.-I.K.)
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10
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Yang M, Liu C, Zhang W, Wu J, Zhong Z, Yi W, Liu H, Leng Y, Sun W, Luan A, He Y. Genome-Wide Identification and Characterization of Gibberellic Acid-Stimulated Arabidopsis Gene Family in Pineapple ( Ananas comosus). Int J Mol Sci 2023; 24:17063. [PMID: 38069384 PMCID: PMC10706908 DOI: 10.3390/ijms242317063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays a crucial role in growth, development, and stress response, and it is specific to plants. This gene family has been extensively studied in various plant species, and its functional role in pineapple has yet to be characterized. In this study, 15 AcGASA genes were identified in pineapple through a genome-wide scan and categorized into three major branches based on a phylogenetic tree. All AcGASA proteins share a common structural domain with 12 cysteine residues, but they exhibit slight variations in their physicochemical properties and motif composition. Predictions regarding subcellular localization suggest that AcGASA proteins are present in the cell membrane, Golgi apparatus, nucleus, and cell wall. An analysis of gene synteny indicated that both tandem and segmental repeats have a significant impact on the expansion of the AcGASA gene family. Our findings demonstrate the differing regulatory effects of these hormones (GA, NAA, IAA, MeJA, and ABA) on the AcGASA genes. We analyzed the expression profiles of GASA genes in different pineapple tissue parts, and the results indicated that AcGASA genes exhibit diverse expression patterns during the development of different plant tissues, particularly in the regulation of floral organ development. This study provides a comprehensive understanding of GASA family genes in pineapple. It serves as a valuable reference for future studies on the functional characterization of GASA genes in other perennial herbaceous plants.
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Affiliation(s)
- Mingzhe Yang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.Y.); (C.L.); (W.Z.); (J.W.); (Z.Z.); (W.Y.); (H.L.); (Y.L.)
| | - Chaoyang Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.Y.); (C.L.); (W.Z.); (J.W.); (Z.Z.); (W.Y.); (H.L.); (Y.L.)
| | - Wei Zhang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.Y.); (C.L.); (W.Z.); (J.W.); (Z.Z.); (W.Y.); (H.L.); (Y.L.)
| | - Jing Wu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.Y.); (C.L.); (W.Z.); (J.W.); (Z.Z.); (W.Y.); (H.L.); (Y.L.)
| | - Ziqin Zhong
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.Y.); (C.L.); (W.Z.); (J.W.); (Z.Z.); (W.Y.); (H.L.); (Y.L.)
| | - Wen Yi
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.Y.); (C.L.); (W.Z.); (J.W.); (Z.Z.); (W.Y.); (H.L.); (Y.L.)
| | - Hui Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.Y.); (C.L.); (W.Z.); (J.W.); (Z.Z.); (W.Y.); (H.L.); (Y.L.)
| | - Yan Leng
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.Y.); (C.L.); (W.Z.); (J.W.); (Z.Z.); (W.Y.); (H.L.); (Y.L.)
| | - Weisheng Sun
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China;
| | - Aiping Luan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yehua He
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.Y.); (C.L.); (W.Z.); (J.W.); (Z.Z.); (W.Y.); (H.L.); (Y.L.)
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11
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Wang Y, Guo X, Xu Y, Sun R, Cai X, Zhou Z, Qin T, Tao Y, Li B, Hou Y, Wang Q, Liu F. Genome-wide association study for boll weight in Gossypium hirsutum races. Funct Integr Genomics 2023; 23:331. [PMID: 37940771 DOI: 10.1007/s10142-023-01261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
High yield has always been an essential target in almost all of the cotton breeding programs. Boll weight (BW) is a key component of cotton yield. Numerous linkage mapping and genome-wide association studies (GWAS) have been performed to understand the genetic mechanism of BW, but information on the markers/genes controlling BW remains limited. In this study, we conducted a GWAS for BW using 51,268 high-quality single-nucleotide polymorphisms (SNPs) and 189 Gossypium hirsutum accessions across five different environments. A total of 55 SNPs significantly associated with BW were detected, of which 29 and 26 were distributed in the A and D subgenomes, respectively. Five SNPs were simultaneously detected in two environments. For TM5655, TM8662, TM36371, and TM50258, the BW grouped by alleles of each SNP was significantly different. The ± 550 kb regions around these four key SNPs contained 262 genes. Of them, Gh_A02G1473, Gh_A10G1765, and Gh_A02G1442 were expressed highly at 0 to 1 days post-anthesis (dpa), - 3 to 0 dpa, and - 3 to 0 dpa in ovule of TM-1, respectively. They were presumed as the candidate genes for fiber cell differentiation, initiation, or elongation based on gene annotation of their homologs. Overall, these results supplemented valuable information for dissecting the genetic architecture of BW and might help to improve cotton yield through molecular marker-assisted selection breeding and molecular design breeding.
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Affiliation(s)
- Yuanyuan Wang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xinlei Guo
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Runrun Sun
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory / National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Tengfei Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ye Tao
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Baihui Li
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qinglian Wang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Hainan Yazhou Bay Seed Laboratory / National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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12
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Sun B, Zhao X, Gao J, Li J, Xin Y, Zhao Y, Liu Z, Feng H, Tan C. Genome-wide identification and expression analysis of the GASA gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Genomics 2023; 24:668. [PMID: 37932701 PMCID: PMC10629197 DOI: 10.1186/s12864-023-09773-9] [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: 03/27/2023] [Accepted: 10/29/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The Gibberellic Acid-Stimulated Arabidopsis (GASA) gene family is widely involved in the regulation of plant growth, development, and stress response. However, information on the GASA gene family has not been reported in Chinese cabbage (Brassica rapa L. ssp. pekinensis). RESULTS Here, we conducted genome-wide identification and analysis of the GASA genes in Chinese cabbage. In total, 15 GASA genes were identified in the Chinese cabbage genome, and the physicochemical property, subcellular location, and tertiary structure of the corresponding GASA proteins were elucidated. Phylogenetic analysis, conserved motif, and gene structure showed that the GASA proteins were divided into three well-conserved subfamilies. Synteny analysis proposed that the expansion of the GASA genes was influenced mainly by whole-genome duplication (WGD) and transposed duplication (TRD) and that duplication gene pairs were under negative selection. Cis-acting elements of the GASA promoters were involved in plant development, hormonal and stress responses. Expression profile analysis showed that the GASA genes were widely expressed in different tissues of Chinese cabbage, but their expression patterns appeared to diverse. The qRT-PCR analysis of nine GASA genes confirmed that they responded to salt stress, heat stress, and hormonal triggers. CONCLUSIONS Overall, this study provides a theoretical basis for further exploring the important role of the GASA gene family in the functional genome of Chinese cabbage.
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Affiliation(s)
- Bingxin Sun
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Xianlei Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Jiahui Gao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Jie Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yue Xin
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yonghui Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Chong Tan
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
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13
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Iqbal A, Khan RS. Snakins: antimicrobial potential and prospects of genetic engineering for enhanced disease resistance in plants. Mol Biol Rep 2023; 50:8683-8690. [PMID: 37578577 DOI: 10.1007/s11033-023-08734-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
Snakins of the Snakin/Gibberellic Acid Stimulated in Arabidopsis (GASA) family are short sequenced peptides consisting of three different regions: a C-terminal GASA domain, an N-terminal signal sequence and a variable region. The GASA domain is comprised of 12 conserved cysteine residues responsible for the structural stability of the peptide. Snakins are playing a variety of roles in response to various biotic stresses such as bacterial, fungal, and nematodes infections and abiotic stress like water scarcity, saline condition, and reactive oxygen species. These properties make snakins very effective biotechnological tools for possible therapeutic and agricultural applications. This review was attempted to highlight and summarize the antifungal and antibacterial potential of snakins, also emphasizing their sequence characteristics, distributions, expression patterns and biological activities. In addition, further details of transgene expression in various plant species for enhanced fungal and bacterial resistance is also discussed, with special emphasis on their potential applications in crop protection and combating plant pathogens.
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Affiliation(s)
- Aneela Iqbal
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Raham Sher Khan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan.
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14
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Lei S, Zhao L, Chen Y, Xu G. Identification and promoter analysis of a GA-stimulated transcript 1 gene from Jatropha curcas. PLANT CELL REPORTS 2023:10.1007/s00299-023-03034-5. [PMID: 37355482 DOI: 10.1007/s00299-023-03034-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/12/2023] [Indexed: 06/26/2023]
Abstract
KEY MESSAGE Overexpression of JcGAST1 promotes plant growth but inhibits pistil development. The pyrimidine box and CGTCA motif of the JcGAST1 promoter were responsible for the GA and MeJA responses. Members of the gibberellic acid-stimulated Arabidopsis (GASA) gene family play roles in plant growth and development, particularly in flower induction and seed development. However, there is still relatively limited knowledge of GASA genes in Jatropha curcas. Herein, we identified a GASA family gene from Jatropha curcas, namely, JcGAST1, which encodes a protein containing a conserved GASA domain. Sequence alignment showed that the JcGAST1 protein shares 76% sequence identity and 80% sequence similarity with SlGAST1. JcGAST1 had higher expression and protein levels in the female flowers than in the male flowers. Overexpression of JcGAST1 in tobacco promotes plant growth but inhibits pistil development. JcGAST1 expression was upregulated by GA and downregulated by MeJA. Promoter analysis indicated that the pyrimidine box and CGTCA motif were the GA- and MeJA-responsive elements of the JcGAST1 promoter. Using a Y1H screen, six transcription factors were found to interact with the pyrimidine box, and three transcription factors were found to interact with the CGTCA motif. Overall, the results of this study improve our understanding of the JcGAST1 gene and provide useful information for further studies.
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Affiliation(s)
- Shikang Lei
- School of Traditional Chinese Medicine Resource/ Key Laboratory of State Administration of Traditional Chinese Medicine for Production & Development of Cantonese Medicinal Materials, Guangdong Pharmaceutical University, Guangzhou, 510006, China
- Key Laboratory of Biology and Genetic Breeding, Guangzhou Academy of Agricultural Sciences, Guangzhou, 510000, China
| | | | - Yuqian Chen
- Institute for Forest Resources and Environment of Guizhou/College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Gang Xu
- School of Traditional Chinese Medicine Resource/ Key Laboratory of State Administration of Traditional Chinese Medicine for Production & Development of Cantonese Medicinal Materials, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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15
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Serajazari M, Torkamaneh D, Gordon E, Lee E, Booker H, Pauls KP, Navabi A. Identification of fusarium head blight resistance markers in a genome-wide association study of CIMMYT spring synthetic hexaploid derived wheat lines. BMC PLANT BIOLOGY 2023; 23:290. [PMID: 37259061 DOI: 10.1186/s12870-023-04306-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Fusarium head blight (FHB), caused by Fusarium graminearum, is one of the most destructive wheat diseases worldwide. FHB infection can dramatically reduce grain yield and quality due to mycotoxins contamination. Wheat resistance to FHB is quantitatively inherited and many low-effect quantitative trait loci (QTL) have been mapped in the wheat genome. Synthetic hexaploid wheat (SHW) represents a novel source of FHB resistance derived from Aegilops tauschii and Triticum turgidum that can be transferred into common wheat (T. aestivum). In this study, a panel of 194 spring Synthetic Hexaploid Derived Wheat (SHDW) lines from the International Maize and Wheat Improvement Center (CIMMYT) was evaluated for FHB response under field conditions over three years (2017-2019). A significant phenotypic variation was found for disease incidence, severity, index, number of Fusarium Damaged Kernels (FDKs), and deoxynivalenol (DON) content. Further, 11 accessions displayed < 10 ppm DON in 2017 and 2019. Genotyping of the SHDW panel using a 90 K Single Nucleotide Polymorphism (SNP) chip array revealed 31 K polymorphic SNPs with a minor allele frequency (MAF) > 5%, which were used for a Genome-Wide Association Study (GWAS) of FHB resistance. A total of 52 significant marker-trait associations for FHB resistance were identified. These included 5 for DON content, 13 for the percentage of FDKs, 11 for the FHB index, 3 for disease incidence, and 20 for disease severity. A survey of genes associated with the markers identified 395 candidate genes that may be involved in FHB resistance. Collectively, our results strongly support the view that utilization of synthetic hexaploid wheat in wheat breeding would enhance diversity and introduce new sources of resistance against FHB into the common wheat gene pool. Further, validated SNP markers associated with FHB resistance may facilitate the screening of wheat populations for FHB resistance.
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Affiliation(s)
- Mitra Serajazari
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, Québec, G1V 0A6, Canada
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec City, Québec, G1V 0A6, Canada
| | - Emily Gordon
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Elizabeth Lee
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Helen Booker
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Karl Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
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16
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Bouteraa MT, Ben Romdhane W, Baazaoui N, Alfaifi MY, Chouaibi Y, Ben Akacha B, Ben Hsouna A, Kačániová M, Ćavar Zeljković S, Garzoli S, Ben Saad R. GASA Proteins: Review of Their Functions in Plant Environmental Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2023; 12:2045. [PMID: 37653962 PMCID: PMC10223810 DOI: 10.3390/plants12102045] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 09/02/2023]
Abstract
Gibberellic acid-stimulated Arabidopsis (GASA) gene family is a class of functional cysteine-rich proteins characterized by an N-terminal signal peptide and a C-terminal-conserved GASA domain with 12 invariant cysteine (Cys) residues. GASA proteins are widely distributed among plant species, and the majority of them are involved in the signal transmission of plant hormones, the regulation of plant development and growth, and the responses to different environmental constraints. To date, their action mechanisms are not completely elucidated. This review reports an overview of the diversity, structure, and subcellular localization of GASA proteins, their involvement in hormone crosstalk and redox regulation during development, and plant responses to abiotic and biotic stresses. Knowledge of this complex regulation can be a contribution to promoting multiple abiotic stress tolerance with potential agricultural applications through the engineering of genes encoding GASA proteins and the production of transgenic plants.
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Affiliation(s)
- Mohamed Taieb Bouteraa
- Biotechnology and Plant Improvement Laboratory, Center of Biotechnology of Sfax, B.P “1177”, Sfax 3018, Tunisia
- Faculty of Sciences of Bizerte UR13ES47, University of Carthage, BP W, Bizerte 7021, Tunisia
| | - Walid Ben Romdhane
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Narjes Baazaoui
- Biology Department, College of Sciences and Arts Muhayil Assir, King Khalid University, Abha 61421, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha 9004, Saudi Arabia
| | - Yosra Chouaibi
- Biotechnology and Plant Improvement Laboratory, Center of Biotechnology of Sfax, B.P “1177”, Sfax 3018, Tunisia
| | - Bouthaina Ben Akacha
- Biotechnology and Plant Improvement Laboratory, Center of Biotechnology of Sfax, B.P “1177”, Sfax 3018, Tunisia
| | - Anis Ben Hsouna
- Biotechnology and Plant Improvement Laboratory, Center of Biotechnology of Sfax, B.P “1177”, Sfax 3018, Tunisia
- Department of Environmental Sciences and Nutrition, Higher Institute of Applied Sciences and Technology of Mahdia, University of Monastir, Mahdia 5100, Tunisia
| | - Miroslava Kačániová
- Institute of Horticulture, Faculty of Horticulture, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia
- Department of Bioenergy, Food Technology and Microbiology, Institute of Food Technology and Nutrition, University of Rzeszow, 4 Zelwerowicza St, 35601 Rzeszow, Poland
| | - Sanja Ćavar Zeljković
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 29, 77900 Olomouc, Czech Republic
- Czech Advanced Technology and Research Institute, Palacky University, Šlechtitelů 27, 77900 Olomouc, Czech Republic
| | - Stefania Garzoli
- Department of Chemistry and Technologies of Drug, Sapienza University, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Rania Ben Saad
- Biotechnology and Plant Improvement Laboratory, Center of Biotechnology of Sfax, B.P “1177”, Sfax 3018, Tunisia
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17
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Panji A, Ismaili A, Sohrabi SM. Genome-wide identification and expression profiling of snakin/GASA genes under drought stress in barley ( Hordeum vulgare L.). 3 Biotech 2023; 13:126. [PMID: 37064004 PMCID: PMC10090255 DOI: 10.1007/s13205-023-03545-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/28/2023] [Indexed: 04/18/2023] Open
Abstract
Gibberellic Acid-Stimulated Arabidopsis (GASA) proteins are present in various plants and have a role in plant growth, stress responses, and hormone crosstalk. GASA coding sequences in barley were discovered in this study. We then investigated gene and protein structure, physicochemical characteristics, evolutionary and phylogenetic relationships, promoter region, post-translational modification, and in silico gene expression. Finally, real-time quantitative PCR (RT-qPCR) was used to examine the expression of GASA genes in root and shoot tissues under drought stress. We found 11 GASA genes spread across six of seven chromosomes in the barley genome. A conserved GASA domain and 12-cysteine residues at the C-terminus were included in the proteins. All GASA genes contained secretory signal peptides. The GASA genes in Hordeum vulgare (HvGASA) have been classified into three subfamilies based on evolutionary analysis. According to synteny analyses, segmental duplications are significant in forming the GASA gene family. According to the cis-elements analyses, GASA genes may be induced by a variety of phytohormones and stresses. Tissue-specific expression analysis indicated that GASA genes had varied expression patterns in different tissues. Contrary to common perception, the expression study of GASA genes under biotic and abiotic stresses revealed that GASA genes are more induced by abiotic stresses than biotic stresses. The qPCR confirmed the response of GASA genes to abiotic stresses and showed different expression patterns of these genes under drought stress. Overall, these results can improve our knowledge about the function of GASA genes and provide data for future researches. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03545-8.
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Affiliation(s)
- Anahita Panji
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Seyyed Mohsen Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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18
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Lee SH, Yoon JS, Jung WJ, Kim DY, Seo YW. Genome-wide identification and characterization of the lettuce GASA family in response to abiotic stresses. BMC PLANT BIOLOGY 2023; 23:106. [PMID: 36814195 PMCID: PMC9945619 DOI: 10.1186/s12870-023-04101-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Lettuce is one of the most extensively farmed vegetables in the world, and it prefers cool growing conditions. High temperatures promote premature bolt formation, reducing quality and yield. The gibberellic acid-stimulated Arabidopsis (GASA) family genes play critical roles in plant growth, development, and stress responses. However, the biological functions of GASA proteins in lettuce have yet to be thoroughly investigated. RESULTS Using genome-wide analysis, 20 GASAs were identified in lettuce including, three groups of LsGASA proteins based on the phylogenetic analysis. Except for one, all GASA proteins included a conserved GASA domain with 12 cysteine residues. Cis-element analysis showed that LsGASAs were closely associated with light, phytohormones, and stress resistance. Five segmental and three tandem duplication events were observed in the LsGASA family based on duplication analysis. GASA synteny analysis among lettuce, Arabidopsis, tobacco, and rice revealed that LsGASA5 is highly collinear with all species. Six of the 20 LsGASA showed increased expression patterns at specific time points in the shoot apical meristem when subjected to heat stress. According to gene expression analysis, the majority of GASA were highly expressed in flowers compared to other organs, and six GASA exhibited highly increased expression levels in response to NaCl, abscisic acid, and gibberellin treatment. Furthermore, LsGASA proteins are predominantly found in the plasma membrane and/or the cytosol. CONCLUSIONS This study provides a comprehensive characterization of LsGASA genes for their diversity and biological functions. Moreover, our results will be useful for further studies on the function of lettuce GASA in abiotic stress- and heat-induced bolting signaling.
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Affiliation(s)
- Sun Ho Lee
- Department of Plant Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jin Seok Yoon
- Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, Republic of Korea
| | - Woo Joo Jung
- Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea
| | - Dae Yeon Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, South Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
- Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, Republic of Korea.
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19
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Li X, Zhang MS, Zhao LQ, Ling-Hu QQ, Xu G. The study on interacting factors and functions of GASA6 in Jatropha curcas L. BMC PLANT BIOLOGY 2023; 23:99. [PMID: 36800929 PMCID: PMC9938578 DOI: 10.1186/s12870-023-04067-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The gibberellic acid-stimulated Arabidopsis (GASA) gene encodes a class of cysteine-rich functional proteins and is ubiquitous in plants. Most GASA proteins are influence the signal transmission of plant hormones and regulate plant growth and development, however, their function in Jatropha curcas is still unknown. RESULTS In this study, we cloned JcGASA6, a member of the GASA family, from J. curcas. The JcGASA6 protein has a GASA-conserved domain and is located in the tonoplast. The three-dimensional structure of the JcGASA6 protein is highly consistent with the antibacterial protein Snakin-1. Additionally, the results of the yeast one-hybrid (Y1H) assay showed that JcGASA6 was activated by JcERF1, JcPYL9, and JcFLX. The results of the Y2H assay showed that both JcCNR8 and JcSIZ1 could interact with JcGASA6 in the nucleus. The expression of JcGASA6 increased continuously during male flower development, and the overexpression of JcGASA6 was associated with filament elongation of the stamens in tobacco. CONCLUSION JcGASA6, a member of the GASA family in J. curcas, play an important role in growth regulation and floral development (especially in male flower). It is also involved in the signal transduction of hormones, such as ABA, ET, GA, BR, and SA. Also, JcGASA6 is a potential antimicrobial protein determined by its three-dimensional structure.
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Affiliation(s)
- Xue Li
- School of Chinese Ethnic Medicine, Guizhou Minzu University, Guiyang, 550025, Guizhou, China
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China
- School of Life Sciences/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Ming-Sheng Zhang
- School of Life Sciences/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | | | - Qian-Qian Ling-Hu
- School of Life Sciences/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Gang Xu
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China.
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20
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Bouteraa MT, Ben Romdhane W, Ben Hsouna A, Amor F, Ebel C, Ben Saad R. Genome-wide characterization and expression profiling of GASA gene family in Triticum turgidum ssp. durum (desf.) husn. (Durum wheat) unveils its involvement in environmental stress responses. PHYTOCHEMISTRY 2023; 206:113544. [PMID: 36464102 DOI: 10.1016/j.phytochem.2022.113544] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 11/27/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Family members within the plant-specific gibberellic acid-stimulated Arabidopsis (GASA) gene serve a crucial role in plant growth and development, particularly in flower induction and seed development. Through a genome-wide analysis of Triticum turgidum ssp. Durum (durum wheat), we identified 19 GASA genes, designated as TdGASA1‒19. Moreover, the chromosomal locations, exon-intron distribution and the physiochemical properties of these genes were determined and the subcellular localization of their encoded proteins was estimated. Analyses of their domain structure, motif arrangements, and phylogeny revealed four distinct groups that share a conserved GASA domain. Additionally, a real-time q-PCR analysis revealed differential expression patterns of TdGASA genes in various tissues (including leaves, roots, stems, and seeds) and in response to salinity, osmotic stress, and treatment with exogenous phytohormones (abscisic and gibberellic acid), implying that these genes may play a role in the growth, development, and stress responses of Triticum turgidum. Heterologous expression of TdGASA1, TdGASA4, TdGASA14, and TdGASA19 in Saccharomyces cerevisiae improved its tolerance to salt, osmotic, oxidative, and heat stresses, which suggests the involvement of these genes in abiotic stress tolerance mechanisms. The present study is the first to identify and analyze the expression profile of T. turgidum GASA genes, therefore offering novel insights for their further functional characterization, which may serve as a novel resource for molecular breeding of durum wheat.
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Affiliation(s)
- Mohamed Taieb Bouteraa
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018, Sfax, Tunisia; University of Carthage, Faculty of Sciences of Bizerte UR13ES47, BP W, 7021 Jarzouna, Bizerte, Tunisia
| | - Walid Ben Romdhane
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia
| | - Anis Ben Hsouna
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018, Sfax, Tunisia; Department of Environmental Sciences and Nutrition, Higher Institute of Applied Sciences and Technology of Mahdia, University of Monastir, 5100, Mahdia, Tunisia
| | - Fatma Amor
- Plant Physiology and Functional Genomics Unit; Institute of Biotechnology, University of Sfax, BP B1175, 3038, Sfax, Tunisia
| | - Chantal Ebel
- Plant Physiology and Functional Genomics Unit; Institute of Biotechnology, University of Sfax, BP B1175, 3038, Sfax, Tunisia
| | - Rania Ben Saad
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018, Sfax, Tunisia.
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21
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Wu T, Liu K, Chen M, Jiang B, Gong Q, Zhong Y. Transcriptome and metabolome analyses of Shatian pomelo ( Citrus grandis var. Shatinyu Hort) leaves provide insights into the overexpression of the gibberellin-induced gene CcGASA4. FRONTIERS IN PLANT SCIENCE 2022; 13:1022961. [PMID: 36407630 PMCID: PMC9671072 DOI: 10.3389/fpls.2022.1022961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
The gibberellic acid (GA)-stimulated Arabidopsis (GASA) gene family is highly specific to plants and plays crucial roles in plant growth and development. CcGASA4 is a member of the GASA gene family in citrus plants; however, the current understanding of its function in citrus is limited. We used CcGASA4-overexpression transgenic citrus (OEGA) and control (CON) plants to study the role of CcGASA4 in Shatian pomelo. The RNA sequencing (RNA-seq) analysis showed that 3,522 genes, including 1,578 upregulated and 1,944 downregulated genes, were significantly differentially expressed in the CON versus OEGA groups. The Gene Ontology enrichment analysis showed that 178 of the differentially-expressed genes (DEGs) were associated with flowers. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were enriched in 134 pathways, including "plant-pathogen interaction", "MAPK signaling pathway-plant", "phenylpropane biosynthesis", "plant hormone signal transduction", "phenylalanine, tyrosine and tryptophan biosynthesis", and "flavonoid and flavonol biosynthesis". The most significantly-enriched pathway was "plant-pathogen interaction", in which 203 DEGs were enriched (126 DEGs were upregulated and 78 were downregulated). The metabolome analysis showed that 644 metabolites were detected in the OEGA and CON samples, including 294 differentially-accumulated metabolites (DAMs; 83 upregulated versus 211 downregulated in OEGA compared to CON). The metabolic pathway analysis showed that these DAMs were mainly involved in the metabolic pathways of secondary metabolites, such as phenylpropanoids, phenylalanine, flavone, and flavonol biosynthesis. Thirteen flavonoids and isoflavones were identified as DAMs in OEGA and CON. We also discovered 25 OEGA-specific accumulated metabolites and found 10 that were associated with disease resistance. CcGASA4 may therefore play a functional role in activating the expression of MAPK signaling transduction pathway and disease resistance genes, inhibiting the expression of auxin- and ethylene-related genes, and activating or inhibiting the expression of brassinosteroid biosynthesis- and abscisic acid-related genes. CcGASA4 may also play a role in regulating the composition and abundance of flavonoids, isoflavones, amino acids, purines, and phenolic compounds. This study provides new insights into the molecular mechanisms of action of CcGASA4 in citrus plants.
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Affiliation(s)
- Tianli Wu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Min Chen
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Bo Jiang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qijing Gong
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Yun Zhong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangzhou, China
- Key Laboratory of Tropical and Subtropical of Fruit Tree Research, Science and Technology Department of Guangdong Province, Guangzhou, China
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22
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Zhang M, Wang Z, Jian S. Genome-Wide Identification and Functional Analysis of the GASA Gene Family Responding to Multiple Stressors in Canavalia rosea. Genes (Basel) 2022; 13:1988. [PMID: 36360226 PMCID: PMC9690345 DOI: 10.3390/genes13111988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 08/15/2023] Open
Abstract
In plants, the Gibberellic Acid-Stimulated Arabidopsis (GASA) gene family is unique and responds to ubiquitous stress and hormones, playing important regulatory roles in the growth and development of plants, as well as in the resistance mechanisms to biotic and abiotic stress. In this study, a total of 23 CrGASAs were characterized in C. rosea using a genome-wide approach, and their phylogenetic relationships, gene structures, conserved motifs, chromosomal locations, gene duplications, and promoter regions were systematically analyzed. Expression profile analysis derived from transcriptome data showed that CrGASAs are expressed at higher levels in the flowers or fruit than in the leaves, vines, and roots. The expression of CrGASAs also showed habitat- and environmental-stress-regulated patterns in C. rosea analyzed by transcriptome and quantitative reverse transcription PCR (qRT-PCR). The heterologous induced expression of some CrGASAs in yeast enhanced the tolerance to H2O2, and some CrGASAs showed elevated heat tolerance and heavy metal (HM) Cd/Cu tolerance. These findings will provide an important foundation to elucidate the biological functions of CrGASA genes, especially their role in the ecological adaptation of specific plant species to tropical islands and reefs in C. rosea.
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Affiliation(s)
- Mei Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhengfeng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shuguang Jian
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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23
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Su D, Liu K, Yu Z, Li Y, Zhang Y, Zhu Y, Wu Y, He H, Zeng X, Chen H, Grierson D, Deng H, Liu M. Genome-wide characterization of the tomato GASA family identifies SlGASA1 as a repressor of fruit ripening. HORTICULTURE RESEARCH 2022; 10:uhac222. [PMID: 36643743 PMCID: PMC9832878 DOI: 10.1093/hr/uhac222] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
Gibberellins (GAs) play crucial roles in a wide range of developmental processes and stress responses in plants. However, the roles of GA-responsive genes in tomato (Solanum lycopersicum) fruit development remain largely unknown. Here, we identify 17 GASA (Gibberellic Acid-Stimulated Arabidopsis) family genes in tomato. These genes encode proteins with a cleavable signal peptide at their N terminus and a conserved GASA domain at their C terminus. The expression levels of all tomato GASA family genes were responsive to exogenous GA treatment, but adding ethylene eliminated this effect. Comprehensive expression profiling of SlGASA family genes showed that SlGASA1 follows a ripening-associated expression pattern, with low expression levels during fruit ripening, suggesting it plays a negative role in regulating ripening. Overexpressing SlGASA1 using a ripening-specific promoter delayed the onset of fruit ripening, whereas SlGASA1-knockdown fruits displayed accelerated ripening. Consistent with their delayed ripening, SlGASA1-overexpressing fruits showed significantly reduced ethylene production and carotenoid contents compared to the wild type. Moreover, ripening-related genes were downregulated in SlGASA1-overexpressing fruits but upregulated in SlGASA1-knockdown fruits compared to the wild type. Yeast two-hybrid, co-immunoprecipitation, transactivation, and DNA pull-down assays indicated that SlGASA1 interacts with the key ripening regulator FRUITFULL1 and represses its activation of the ethylene biosynthesis genes ACS2 and ACO1. Our findings shed new light on the role and mode of action of a GA-responsive gene in tomato fruit ripening.
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Affiliation(s)
| | | | - Zhuoshu Yu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Ying Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yaoxin Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yunqi Zhu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yi Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Hongyu He
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Xiaodan Zeng
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Honglin Chen
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Don Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Heng Deng
- Correspondence author: Mingchun Liu Tel: 02885400432, Fax: 02885400432 Heng Deng Tel: 02885400432, Fax: 02885400432
| | - Mingchun Liu
- Correspondence author: Mingchun Liu Tel: 02885400432, Fax: 02885400432 Heng Deng Tel: 02885400432, Fax: 02885400432
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24
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Genome-Wide Identification, Evolution, and Expression Analysis of GASA Gene Family in Prunus mume. Int J Mol Sci 2022; 23:ijms231810923. [PMID: 36142832 PMCID: PMC9506367 DOI: 10.3390/ijms231810923] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
The Gibberellic Acid Stimulated Arabidopsis/Gibberellin Stimulated Transcript (GASA/GAST) gene family is a group of plant-specific genes encoding cysteine-rich peptides essential to plant growth, development, and stress responses. Although GASA family genes have been identified in various plant species, their functional roles in Prunus mume are still unknown. In this study, a total of 16 PmGASA genes were identified via a genome-wide scan in Prunus mume and were grouped into three major gene clades based on the phylogenetic tree. All PmGASA proteins possessed the conserved GASA domain, consisting of 12-cysteine residues, but varied slightly in protein physiochemical properties and motif composition. With evolutionary analysis, we observed that duplications and purifying selection are major forces driving PmGASA family gene evolution. By analyzing PmGASA promoters, we detected a number of hormonal-response related cis-elements and constructed a putative transcriptional regulatory network for PmGASAs. To further understand the functional role of PmGASA genes, we analyzed the expression patterns of PmGASAs across different organs and during various biological processes. The expression analysis revealed the functional implication of PmGASA gene members in gibberellic acid-, abscisic acid-, and auxin-signaling, and during the progression of floral bud break in P. mume. To summarize, these findings provide a comprehensive understanding of GASA family genes in P. mume and offer a theoretical basis for future research on the functional characterization of GASA genes in other woody perennials.
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25
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Jiang R, Yuan W, Yao W, Jin X, Wang X, Wang Y. A regulatory GhBPE-GhPRGL module maintains ray petal length in Gerbera hybrida. MOLECULAR HORTICULTURE 2022; 2:9. [PMID: 37789358 PMCID: PMC10515009 DOI: 10.1186/s43897-022-00030-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/08/2022] [Indexed: 10/05/2023]
Abstract
The molecular mechanism regulating petal length in flowers is not well understood. Here we used transient transformation assays to confirm that GhPRGL (proline-rich and GASA-like)-a GASA (gibberellic acid [GA] stimulated in Arabidopsis) family gene-promotes the elongation of ray petals in gerbera (Gerbera hybrida). Yeast one-hybrid screening assay identified a bHLH transcription factor of the jasmonic acid (JA) signaling pathway, here named GhBPE (BIGPETAL), which binds to the GhPRGL promoter and represses its expression, resulting in a phenotype of shortened ray petal length when GhBPE is overexpressed. Further, the joint response to JA and GA of GhBPE and GhPRGL, together with their complementary expression profiles in the early stage of petal growth, suggests a novel GhBPE-GhPRGL module that controls the size of ray petals. GhPRGL promotes ray petal elongation in its early stage especially, while GhBPE inhibits ray petal elongation particularly in the late stage by inhibiting the expression of GhPRGL. JA and GA operate in concert to regulate the expression of GhBPE and GhPRGL genes, providing a regulatory mechanism by which ray petals could grow to a fixed length in gerbera species.
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Affiliation(s)
- Rui Jiang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Weichao Yuan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Wei Yao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xuefeng Jin
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xiaojing Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yaqin Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangdong Laboratory for Lingnan Modern Agricultural, Guangzhou, 510642, China.
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26
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Li Z, Gao J, Wang G, Wang S, Chen K, Pu W, Wang Y, Xia Q, Fan X. Genome-Wide Identification and Characterization of GASA Gene Family in Nicotiana tabacum. Front Genet 2022; 12:768942. [PMID: 35178069 PMCID: PMC8844377 DOI: 10.3389/fgene.2021.768942] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
The gibberellic acid stimulated Arabidopsis (GASA) gene family is critical for plant growth, development, and stress response. GASA gene family has been studied in various plant species, however, the GASA gene family in tobacco (Nicotiana tabacum) have not been characterized in detail. In this study, we identified 18 GASA genes in the tobacco genome, which were distributed to 13 chromosomes. All the proteins contained a conserved GASA domain and highly specific 12-cysteine residues at the C-terminus. Phylogenetic analysis divided the NtGASA genes into three well-conserved subfamilies. Synteny analysis suggested that tandem and segmental duplications played an important role in the expansion of the NtGASA gene family. Cis-elements analysis showed that NtGASA genes might influence different phytohormone and stress responses. Tissue expression analysis revealed that NtGASA genes displayed unique or distinct expression patterns in different tissues, suggesting their potential roles in plant growth and development. We also found that the expression of NtGASA genes were mostly regulated by abscisic and gibberellic acid, signifying their roles in the two phytohormone signaling pathways. Overall, these findings improve our understanding of NtGASA genes and provided useful information for further studies on their molecular functions.
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Affiliation(s)
- Zhaowu Li
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Junping Gao
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Genhong Wang
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Shuaibin Wang
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Kai Chen
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Wenxuan Pu
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Yaofu Wang
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
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27
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Wu K, Qu Y, Rong H, Han X, Tian Y, Xu L. Identification and Expression Analysis of the Populus trichocarpa GASA-Gene Family. Int J Mol Sci 2022; 23:ijms23031507. [PMID: 35163431 PMCID: PMC8835824 DOI: 10.3390/ijms23031507] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/22/2022] [Accepted: 01/22/2022] [Indexed: 02/04/2023] Open
Abstract
The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays an important regulatory role in the growth and development of plants. In this study, we identified 19 GASA genes using bioinformatics-based methods in Populus trichocarpa, and these PtGASA genes could be divided into three categories based on their phylogenetic relationships. Based on an analysis of the structure and motifs of these genes, it was concluded that PtGASA class II members are more conserved than class I and class III members are, and the results of collinearity analysis showed that members of class II are collinearly related in poplar. Expression analysis of Populus trichocarpa roots, stems, and leaves showed that most of the PtGASA genes are expressed at higher levels in the stems or roots than in the leaves; a similar expression pattern was found in Vitis vinifera, indicating that the GASA-family members mainly play a role in the morphogenesis of poplar. Considering the phenomenon of gene amplification, we found that the higher the similarity of homologous genes was, the more similar the expression patterns. This study represents the first whole-genome identification and expression-profile analysis of the GASA-gene family in poplar, a model species, laying a foundation for functional studies of poplar GASA genes and serving as a reference for related research on other woody plant species.
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Affiliation(s)
| | | | | | | | | | - Li’an Xu
- Correspondence: ; Tel.: +86-25-8542-7882
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Wu T, Zhong Y, Chen M, Wu B, Wang T, Jiang B, Zhong G. Analysis of CcGASA family members in Citrus clementina (Hort. ex Tan.) by a genome-wide approach. BMC PLANT BIOLOGY 2021; 21:565. [PMID: 34852791 PMCID: PMC8638133 DOI: 10.1186/s12870-021-03326-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
The Gibberellic Acid Stimulated Arabidopsis (GASA) proteins were investigated in the study to help understand their possible roles in fruit trees, particularly in Citrus. A total of 18 CcGASA proteins were identified and characterized in Citrus clementina via a genome-wide approach. It was shown that the CcGASA proteins structurally shared a conserved GASA domain but varied considerably in primary sequences and motif compositions. Thus, they could be classified into three major phylogenetic groups, G1~G3, and two groups, G1 and G3 could be further classified into subgroups. The cis- elements on all CcGASA promoters were identified and categorized, and the associated transcription factors were predicted. In addition, the possible interactions between the CcGASA proteins and other proteins were predicted. All the clues suggested that these genes should be involved in defense against biotic and abiotic stresses and in growth and development. The notion was further supported by gene expression analysis that showed these genes were more or less responsive to the treatments of plant hormones (GA3, SA, ABA and IAA), and infections of citrus canker pathogen Xanthomonas citri. It was noted that both the segmental and the tandem duplications had played a role in the expansion of the CcGASA gene family in Citrus. Our results showed that the members of the CcGASA gene family should have structurally and functionally diverged to different degrees, and hence, the representative group members should be individually investigated to dissect their specific roles.
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Affiliation(s)
- Tianli Wu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yun Zhong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, China
| | - Min Chen
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bo Wu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ting Wang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bo Jiang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Guangyan Zhong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
- Key Laboratory of Tropical and Subtropical of Fruit Tree Research, Science and Technology Department of Guangdong Province, Guangzhou, 510640, China.
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Structural and functional analysis of CCT family genes in pigeonpea. Mol Biol Rep 2021; 49:217-226. [PMID: 34800230 DOI: 10.1007/s11033-021-06860-6] [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: 07/16/2021] [Accepted: 10/12/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Pigeonpea (Cajanus cajan L.) is a photoperiod-sensitive short-day plant. Understanding the flowering-related genes is critical to developing photoperiod insensitive cultivars. METHODS The CCT family genes were identified using 'CCT DOMAIN PROTEIN' as a keyword and localized on the chromosomes using the BLAST search option available at the LIS database. The centromeric positions were identified through BLAST search using the centromeric repeat sequence of C. cajan as a query against the chromosome-wise FASTA files downloaded from the NCBI database. The CCT family genes were classified based on additional domains and/or CCT domains. The orthologous and phylogenetic relationships were inferred using the OrthoFinder and MEGA 10.1 software, respectively. The CCT family genes' expression level in photoperiod-sensitive and insensitive genotypes was compared using RNA-seq data and qRT-PCR analysis. RESULTS We identified 33 CCT family genes in C. cajan distributed on ten chromosomes and nine genomic scaffolds. They were classified into CMF-type, COL-type, PRR-type, and GTCC- type. The CCT family genes of legumes exhibited an extensive orthologous relationship. Glycine max showed the maximum similarity of CCT family genes with C. cajan. The expression analysis of CCT family genes using photoperiod insensitive (ICP20338) and photoperiod sensitive (MAL3) genotypes of C. cajan demonstrated that CcCCT4 and CcCCT23 are the active CONSTANS in ICP20338. In contrast, only CcCCT23 is active in MAL3. CONCLUSION The CCT family genes in C. cajan vary considerably in structure and domain types. They are maximally similar to soybean's CCT family genes. The differential photoperiod response of pigeonpea genotypes, ICP20338 and MAL3, is possibly due to the difference in the number and types of active CONSTANS in them.
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Han S, Jiao Z, Niu MX, Yu X, Huang M, Liu C, Wang HL, Zhou Y, Mao W, Wang X, Yin W, Xia X. Genome-Wide Comprehensive Analysis of the GASA Gene Family in Populus. Int J Mol Sci 2021; 22:ijms222212336. [PMID: 34830215 PMCID: PMC8624709 DOI: 10.3390/ijms222212336] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/20/2022] Open
Abstract
Gibberellic acid-stimulated Arabidopsis (GASA) proteins, as cysteine-rich peptides (CRPs), play roles in development and reproduction and biotic and abiotic stresses. Although the GASA gene family has been identified in plants, the knowledge about GASAs in Populus euphratica, the woody model plant for studying abiotic stress, remains limited. Here, we referenced the well-sequenced Populus trichocarpa genome, and identified the GASAs in the whole genome of P. euphratica and P. trichocarpa. 21 candidate genes in P. trichocarpa and 19 candidate genes in P. euphratica were identified and categorized into three subfamilies by phylogenetic analysis. Most GASAs with signal peptides were located extracellularly. The GASA genes in Populus have experienced multiple gene duplication events, especially in the subfamily A. The evolution of the subfamily A, with the largest number of members, can be attributed to whole-genome duplication (WGD) and tandem duplication (TD). Collinearity analysis showed that WGD genes played a leading role in the evolution of GASA genes subfamily B. The expression patterns of P. trichocarpa and P. euphratica were investigated using the PlantGenIE database and the real-time quantitative PCR (qRT-PCR), respectively. GASA genes in P. trichocarpa and P. euphratica were mainly expressed in young tissues and organs, and almost rarely expressed in mature leaves. GASA genes in P. euphratica leaves were also widely involved in hormone responses and drought stress responses. GUS activity assay showed that PeuGASA15 was widely present in various organs of the plant, especially in vascular bundles, and was induced by auxin and inhibited by mannitol dramatically. In summary, this present study provides a theoretical foundation for further research on the function of GASA genes in P. euphratica.
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Affiliation(s)
- Shuo Han
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (S.H.); (Z.J.); (M.-X.N.); (X.Y.); (M.H.); (C.L.); (H.-L.W.)
| | - Zhiyin Jiao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (S.H.); (Z.J.); (M.-X.N.); (X.Y.); (M.H.); (C.L.); (H.-L.W.)
| | - Meng-Xue Niu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (S.H.); (Z.J.); (M.-X.N.); (X.Y.); (M.H.); (C.L.); (H.-L.W.)
| | - Xiao Yu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (S.H.); (Z.J.); (M.-X.N.); (X.Y.); (M.H.); (C.L.); (H.-L.W.)
| | - Mengbo Huang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (S.H.); (Z.J.); (M.-X.N.); (X.Y.); (M.H.); (C.L.); (H.-L.W.)
| | - Chao Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (S.H.); (Z.J.); (M.-X.N.); (X.Y.); (M.H.); (C.L.); (H.-L.W.)
| | - Hou-Ling Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (S.H.); (Z.J.); (M.-X.N.); (X.Y.); (M.H.); (C.L.); (H.-L.W.)
| | - Yangyan Zhou
- Salver Academy of Botany, Rizhao 276800, China; (Y.Z.); (W.M.); (X.W.)
| | - Wei Mao
- Salver Academy of Botany, Rizhao 276800, China; (Y.Z.); (W.M.); (X.W.)
| | - Xiaofei Wang
- Salver Academy of Botany, Rizhao 276800, China; (Y.Z.); (W.M.); (X.W.)
| | - Weilun Yin
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (S.H.); (Z.J.); (M.-X.N.); (X.Y.); (M.H.); (C.L.); (H.-L.W.)
- Correspondence: (W.Y.); (X.X.); Tel.: +86-10-62336400 (X.X.)
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (S.H.); (Z.J.); (M.-X.N.); (X.Y.); (M.H.); (C.L.); (H.-L.W.)
- Correspondence: (W.Y.); (X.X.); Tel.: +86-10-62336400 (X.X.)
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Chen B, Sun Y, Tian Z, Fu G, Pei X, Pan Z, Nazir MF, Song S, Li H, Wang X, Qin N, Shang J, Miao Y, He S, Du X. GhGASA10-1 promotes the cell elongation in fiber development through the phytohormones IAA-induced. BMC PLANT BIOLOGY 2021; 21:448. [PMID: 34615467 PMCID: PMC8493757 DOI: 10.1186/s12870-021-03230-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/23/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cotton is an important cash crop. The fiber length has always been a hot spot, but multi-factor control of fiber quality makes it complex to understand its genetic basis. Previous reports suggested that OsGASR9 promotes germination, width, and thickness by GAs in rice, while the overexpression of AtGASA10 leads to reduced silique length, which is likely to reduce cell wall expansion. Therefore, this study aimed to explore the function of GhGASA10 in cotton fibers development. RESULTS To explore the molecular mechanisms underlying fiber elongation regulation concerning GhGASA10-1, we revealed an evolutionary basis, gene structure, and expression. Our results emphasized the conservative nature of GASA family with its origin in lower fern plants S. moellendorffii. GhGASA10-1 was localized in the cell membrane, which may synthesize and transport secreted proteins to the cell wall. Besides, GhGASA10-1 promoted seedling germination and root extension in transgenic Arabidopsis, indicating that GhGASA10-1 promotes cell elongation. Interestingly, GhGASA10-1 was upregulated by IAA at fiber elongation stages. CONCLUSION We propose that GhGASA10-1 may promote fiber elongation by regulating the synthesis of cellulose induced by IAA, to lay the foundation for future research on the regulation networks of GASA10-1 in cotton fiber development.
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Affiliation(s)
- Baojun Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
| | - Yaru Sun
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Zailong Tian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Guoyong Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
| | - Xinxin Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
| | - Mian Faisal Nazir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
| | - Song Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
| | - Hongge Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
| | - Xiaoyang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
| | - Ning Qin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China
| | - Jiandong Shang
- National Supercomputing Center in Zhengzhou, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China.
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China.
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Ghorbani F, Abolghasemi R, Haghighi M, Etemadi N, Wang S, Karimi M, Soorni A. Global identification of long non-coding RNAs involved in the induction of spinach flowering. BMC Genomics 2021; 22:704. [PMID: 34587906 PMCID: PMC8482690 DOI: 10.1186/s12864-021-07989-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait. Results In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. Conclusions This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07989-1.
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Affiliation(s)
- Fatemeh Ghorbani
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - 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
| | - Marzieh Karimi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.,Department of Plant Breeding and Biotechnology, College of Agriculture, University of Shahrekord, Shahrekord, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
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Abdullah, Faraji S, Mehmood F, Malik HMT, Ahmed I, Heidari P, Poczai P. The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis. AGRONOMY 2021; 11:1425. [DOI: 10.3390/agronomy11071425] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants and involved in various physiological and biological processes. These genes also provide resistance to abiotic and biotic stresses, including antimicrobial, antiviral, and antifungal. We are interested in characterizing the GASA gene family and determining its role in various physiological and biological process in Theobroma cacao. Here, we report 17 tcGASA genes distributed on six chromosomes in T. cacao. The gene structure, promoter region, protein structure and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. Among 17 tcGASA genes, nine segmentally duplicating genes were identified which formed four pairs and cluster together in phylogenetic tree. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The differential expression of tcGASAs was recorded between the tolerant and susceptible cultivars of cacao, which indicating their possible role as fungal resistant. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T.cacao and may suggest new target genes for development of fungi-resistant cacao varieties in breeding programs.
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Hetherington FM, Kakkar M, Topping JF, Lindsey K. Gibberellin signaling mediates lateral root inhibition in response to K+-deprivation. PLANT PHYSIOLOGY 2021; 185:1198-1215. [PMID: 33793923 PMCID: PMC8133588 DOI: 10.1093/plphys/kiaa093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/10/2020] [Indexed: 05/16/2023]
Abstract
The potassium ion (K+) is vital for plant growth and development, and K+-deprivation leads to reduced crop yields. Here we describe phenotypic, transcriptomic, and mutant analyses to investigate the signaling mechanisms mediating root architectural changes in Arabidopsis (Arabidopsis thaliana) Columbia. We showed effects on root architecture are mediated through a reduction in cell division in the lateral root (LR) meristems, the rate of LR initiation is reduced but LR density is unaffected, and primary root growth is reduced only slightly. This was primarily regulated through gibberellic acid (GA) signaling, which leads to the accumulation of growth-inhibitory DELLA proteins. The short LR phenotype was rescued by exogenous application of GA but not of auxin or by the inhibition of ethylene signaling. RNA-seq analysis showed upregulation by K+-deprivation of the transcription factors JUNGBRUNNEN1 (JUB1) and the C-repeat-binding factor (CBF)/dehydration-responsive element-binding factor 1 regulon, which are known to regulate GA signaling and levels that regulate DELLAs. Transgenic overexpression of JUB1 and CBF1 enhanced responses to K+ stress. Attenuation of the reduced LR growth response occurred in mutants of the CBF1 target gene SFR6, implicating a role for JUB1, CBF1, and SFR6 in the regulation of LR growth in response to K+-deprivation via DELLAs. We propose this represents a mechanism to limit horizontal root growth in conditions where K+ is available deeper in the soil.
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Affiliation(s)
| | - Medhavi Kakkar
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | | | - Keith Lindsey
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
- Author for communication:
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The Cysteine-Rich Peptide Snakin-2 Negatively Regulates Tubers Sprouting through Modulating Lignin Biosynthesis and H 2O 2 Accumulation in Potato. Int J Mol Sci 2021; 22:ijms22052287. [PMID: 33669030 PMCID: PMC7956376 DOI: 10.3390/ijms22052287] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/10/2023] Open
Abstract
Potato tuber dormancy is critical for the post-harvest quality. Snakin/Gibberellic Acid Stimulated in Arabidopsis (GASA) family genes are involved in the plants’ defense against pathogens and in growth and development, but the effect of Snakin-2 (SN2) on tuber dormancy and sprouting is largely unknown. In this study, a transgenic approach was applied to manipulate the expression level of SN2 in tubers, and it demonstrated that StSN2 significantly controlled tuber sprouting, and silencing StSN2 resulted in a release of dormancy and overexpressing tubers showed a longer dormant period than that of the control. Further analyses revealed that the decrease expression level accelerated skin cracking and water loss. Metabolite analyses revealed that StSN2 significantly down-regulated the accumulation of lignin precursors in the periderm, and the change of lignin content was documented, a finding which was consistent with the precursors’ level. Subsequently, proteomics found that cinnamyl alcohol dehydrogenase (CAD), caffeic acid O-methyltransferase (COMT) and peroxidase (Prx), the key proteins for lignin synthesis, were significantly up-regulated in silencing lines, and gene expression and enzyme activity analyses also supported this effect. Interestingly, we found that StSN2 physically interacts with three peroxidases catalyzing the oxidation and polymerization of lignin. In addition, SN2 altered the hydrogen peroxide (H2O2) content and the activities of superoxide dismutase (SOD) and catalase (CAT). These results suggest that StSN2 negatively regulates lignin biosynthesis and H2O2 accumulation, and ultimately inhibits the sprouting of potato tubers.
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Abdullah, Faraji S, Mehmood F, Malik HMT, Ahmed I, Heidari P, Poczai P. The GASA Gene Family in Theobroma cacao: Genome wide Identification and Expression Analysis.. [DOI: 10.1101/2021.01.27.425041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractThe gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20–25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.
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Liu H, Luo C, Chen D, Wang Y, Guo S, Chen X, Bai J, Li M, Huang X, Cheng X, Huang C. Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium. BMC Genom Data 2021; 22:2. [PMID: 33568073 PMCID: PMC7853313 DOI: 10.1186/s12863-021-00959-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes remains an enigma. We analyzed a cut-flower chrysanthemum variety that produces normal capitula composed of ray florets with normally developed pistils and purple corollas and mutant capitula comprising ray florets with green corollas and vegetative buds instead of pistils. RESULTS We conducted a whole-transcriptome analysis of the differentially expressed genes (DEGs) in the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified the DEGs between the mutant and normal capitula to reveal important regulators underlying the differential development. Many transcription factors and genes related to the photoperiod and GA pathways, floral organ identity, and the anthocyanin biosynthesis pathway were differentially expressed between the normal and mutant capitula. A qualitative analysis of the pigments in the florets of normal and mutant capitula indicated anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. These results provide clues regarding the molecular basis of the replacement of Chrysanthemum morifolium ray florets with normally developed pistils and purple corollas with mutant ray florets with green corollas and vegetative buds. Additionally, the study findings will help to elucidate the molecular mechanisms underlying floral organ development and contribute to the development of techniques for studying the regulation of flower shape and color, which may enhance chrysanthemum breeding. CONCLUSIONS The whole-transcriptome analysis of DEGs in mutant and normal C. morifolium capitula described herein indicates the anthocyanin deficiency of the mutant capitula may be related to the mutation that replaces ray floret pistils with vegetative buds. Moreover, pistils may be required for the anthocyanin biosynthesis in the corollas of chrysanthemum ray florets.
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Affiliation(s)
- Hua Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Chang Luo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Dongliang Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Yaqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shuang Guo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xiaoxi Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Jingyi Bai
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Mingyuan Li
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xinlei Huang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xi Cheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Conglin Huang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China.
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Liu H, Luo C, Chen D, Wang Y, Guo S, Chen X, Bai J, Li M, Huang X, Cheng X, Huang C. Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium. BMC Genom Data 2021; 22:2. [PMID: 33568073 DOI: 10.21203/rs.3.rs-27505/v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/05/2021] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes remains an enigma. We analyzed a cut-flower chrysanthemum variety that produces normal capitula composed of ray florets with normally developed pistils and purple corollas and mutant capitula comprising ray florets with green corollas and vegetative buds instead of pistils. RESULTS We conducted a whole-transcriptome analysis of the differentially expressed genes (DEGs) in the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified the DEGs between the mutant and normal capitula to reveal important regulators underlying the differential development. Many transcription factors and genes related to the photoperiod and GA pathways, floral organ identity, and the anthocyanin biosynthesis pathway were differentially expressed between the normal and mutant capitula. A qualitative analysis of the pigments in the florets of normal and mutant capitula indicated anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. These results provide clues regarding the molecular basis of the replacement of Chrysanthemum morifolium ray florets with normally developed pistils and purple corollas with mutant ray florets with green corollas and vegetative buds. Additionally, the study findings will help to elucidate the molecular mechanisms underlying floral organ development and contribute to the development of techniques for studying the regulation of flower shape and color, which may enhance chrysanthemum breeding. CONCLUSIONS The whole-transcriptome analysis of DEGs in mutant and normal C. morifolium capitula described herein indicates the anthocyanin deficiency of the mutant capitula may be related to the mutation that replaces ray floret pistils with vegetative buds. Moreover, pistils may be required for the anthocyanin biosynthesis in the corollas of chrysanthemum ray florets.
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Affiliation(s)
- Hua Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Chang Luo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Dongliang Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Yaqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shuang Guo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xiaoxi Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Jingyi Bai
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Mingyuan Li
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xinlei Huang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xi Cheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Conglin Huang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China.
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Su T, Han M, Cao D, Xu M. Molecular and Biological Properties of Snakins: The Foremost Cysteine-Rich Plant Host Defense Peptides. J Fungi (Basel) 2020; 6:jof6040220. [PMID: 33053707 PMCID: PMC7711543 DOI: 10.3390/jof6040220] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/01/2020] [Accepted: 10/10/2020] [Indexed: 12/21/2022] Open
Abstract
Plant host defense peptides (HDPs), also known as antimicrobial peptides (AMPs), are regarded as one of the most prevalent barriers elaborated by plants to combat various infective agents. Among the multiple classes of HDPs, the Snakin class attracts special concern, as they carry 12 cysteine residues, being the foremost cysteine-rich peptides of the plant HDPs. Also, their cysteines are present at very highly conserved positions and arranged in an extremely similar way among different members. Like other plant HDPs, Snakins have been shown to exhibit strong antifungal and antibacterial activity against a wide range of plant pathogens. Moreover, they display diversified biological activities in many aspects of plant growth and the development process. This review is devoted to present the general characters of the Snakin class of plant HDPs, as well as the individual features of different Snakin family members. Specifically, the sequence properties, spatial structures, distributions, expression patterns and biological activities of Snakins are described. In addition, further detailed classification of the Snakin family members, along with their possible mode of action and potential applications in the field of agronomy and pathology are discussed.
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Affiliation(s)
- Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (D.C.); (M.X.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
| | - Mei Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (D.C.); (M.X.)
- Correspondence: ; Tel.:+86-1589-598-9551
| | - Dan Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (D.C.); (M.X.)
| | - Mingyue Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (D.C.); (M.X.)
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Identification of nitric oxide (NO)-responsive genes under hypoxia in tomato (Solanum lycopersicum L.) root. Sci Rep 2020; 10:16509. [PMID: 33020554 PMCID: PMC7536229 DOI: 10.1038/s41598-020-73613-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/14/2020] [Indexed: 12/04/2022] Open
Abstract
Flooding periods, as one probable consequence of climate change, will lead more frequently to plant hypoxic stress. Hypoxia sensing and signaling in the root, as the first organ encountering low oxygen, is therefore crucial for plant survival under flooding. Nitric oxide has been shown to be one of the main players involved in hypoxia signaling through the regulation of ERFVII transcription factors stability. Using SNP as NO donor, we investigated the NO-responsive genes, which showed a significant response to hypoxia. We identified 395 genes being differentially regulated under both hypoxia and SNP-treatment. Among them, 251 genes showed up- or down-regulation under both conditions which were used for further biological analysis. Functional classification of these genes showed that they belong to different biological categories such as primary carbon and nitrogen metabolism (e.g. glycolysis, fermentation, protein and amino acid metabolism), nutrient and metabolites transport, redox homeostasis, hormone metabolism, regulation of transcription as well as response to biotic and abiotic stresses. Our data shed light on the NO-mediated gene expression modulation under hypoxia and provides potential targets playing a role in hypoxia tolerance. These genes are interesting candidates for further investigating their role in hypoxia signaling and survival.
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Dos Santos-Silva CA, Zupin L, Oliveira-Lima M, Vilela LMB, Bezerra-Neto JP, Ferreira-Neto JR, Ferreira JDC, de Oliveira-Silva RL, Pires CDJ, Aburjaile FF, de Oliveira MF, Kido EA, Crovella S, Benko-Iseppon AM. Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era. Bioinform Biol Insights 2020; 14:1177932220952739. [PMID: 32952397 PMCID: PMC7476358 DOI: 10.1177/1177932220952739] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.
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Affiliation(s)
| | - Luisa Zupin
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy
| | - Marx Oliveira-Lima
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | - José Diogo Cavalcanti Ferreira
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil.,Departamento de Genética, Instituto Federal de Pernambuco, Pesqueira, Brazil
| | | | | | | | | | - Ederson Akio Kido
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | - Sergio Crovella
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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Rezaee S, Ahmadizadeh M, Heidari P. Genome-wide characterization, expression profiling, and post-transcriptional study of GASA gene family. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Shi CL, Dong NQ, Guo T, Ye WW, Shan JX, Lin HX. A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1174-1188. [PMID: 32365409 DOI: 10.1111/tpj.14793] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 05/18/2023]
Abstract
Grain size is one of the essential components determining rice yield and is a target for both domestication and artificial breeding. Gibberellins (GAs) are diterpenoid phytohormones that influence diverse aspects of plant growth and development. Several quantitative trait loci (QTLs) have been identified that control grain size through phytohormone regulation. However, little is known about the role of GAs in the control of grain size. Here we report the cloning and characterization of a QTL, GW6 (GRAIN WIDTH 6), which encodes a GA-regulated GAST family protein and positively regulates grain width and weight. GW6 is highly expressed in the young panicle and increases grain width by promoting cell expansion in the spikelet hull. Knockout of GW6 exhibits reduced grain size and weight, whereas overexpression of GW6 results in increased grain size and weight. GW6 is induced by GA and its knockout downregulates the expression of GA biosynthesis genes and decreases GA content in the young panicle. We found that a natural variation in the cis element CAAT-box in the promoter of GW6 is associated with its expression level and grain width and weight. Furthermore, introduction of GW6 to Oryza indica variety HJX74 can lead to a 10.44% increase in rice grain yield, indicating that GW6 has great potential to improve grain yield in rice.
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Affiliation(s)
- Chuan-Lin Shi
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
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Wang Z, Ma W, Zhu T, Lu N, Ouyang F, Wang N, Yang G, Kong L, Qu G, Zhang S, Wang J. Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey. BMC Genomics 2020; 21:508. [PMID: 32698759 PMCID: PMC7376858 DOI: 10.1186/s12864-020-06918-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Floral transition plays an important role in development, and proper time is necessary to improve the value of valuable ornamental trees. The molecular mechanisms of floral transition remain unknown in perennial woody plants. "Bairihua" is a type of C. bungei that can undergo floral transition in the first planting year. RESULTS Here, we combined short-read next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing to provide a more complete view of transcriptome regulation during floral transition in C. bungei. The circadian rhythm-plant pathway may be the critical pathway during floral transition in early flowering (EF) C. bungei, according to horizontal and vertical analysis in EF and normal flowering (NF) C. bungei. SBP and MIKC-MADS-box were seemingly involved in EF during floral transition. A total of 61 hub genes were associated with floral transition in the MEturquoise model with Weighted Gene Co-expression Network Analysis (WGCNA). The results reveal that ten hub genes had a close connection with the GASA homologue gene (Cbu.gene.18280), and the ten co-expressed genes belong to five flowering-related pathways. Furthermore, our study provides new insights into the complexity and regulation of alternative splicing (AS). The ratio or number of isoforms of some floral transition-related genes is different in different periods or in different sub-genomes. CONCLUSIONS Our results will be a useful reference for the study of floral transition in other perennial woody plants. Further molecular investigations are needed to verify our sequencing data.
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Affiliation(s)
- Zhi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Fangqun Ouyang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Nan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Guijuan Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Lisheng Kong
- Department of Biology Centre for Forest Biology, University of Victoria, Victoria, BC 11 Canada
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 PR China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
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Genome-Wide Characterization and Expression Profiling of GASA Genes during Different Stages of Seed Development in Grapevine ( Vitis vinifera L.) Predict Their Involvement in Seed Development. Int J Mol Sci 2020; 21:ijms21031088. [PMID: 32041336 PMCID: PMC7036793 DOI: 10.3390/ijms21031088] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 01/19/2023] Open
Abstract
Members of the plant-specific GASA (gibberellic acid-stimulated Arabidopsis) gene family have multiple potential roles in plant growth and development, particularly in flower induction and seed development. However, limited information is available about the functions of these genes in fruit plants, particularly in grapes. We identified 14 GASA genes in grapevine (Vitis vinifera L.) and performed comprehensive bioinformatics and expression analyses. In the bioinformatics analysis, the locations of genes on chromosomes, physiochemical properties of proteins, protein structure, and subcellular positions were described. We evaluated GASA proteins in terms of domain structure, exon-intron distribution, motif arrangements, promoter analysis, phylogenetic, and evolutionary history. According to the results, the GASA domain is conserved in all proteins and the proteins are divided into three well-conserved subgroups. Synteny analysis proposed that segmental and tandem duplication have played a role in the expansion of the GASA gene family in grapes, and duplicated gene pairs have negative selection pressure. Most of the proteins were predicted to be in the extracellular region, chloroplasts, and the vacuole. In silico promoter analysis suggested that the GASA genes may influence different hormone signaling pathways and stress-related mechanisms. Additionally, we performed a comparison of the expression between seedless (Thompson seedless) and seeded (Red globe) cultivars in different plant parts, including the ovule during different stages of development. Furthermore, some genes were differentially expressed in different tissues, signifying their role in grapevine growth and development. Several genes (VvGASA2 and 7) showed different expression levels in later phases of seed development in Red globe and Thompson seedless, suggesting their involvement in seed development. Our study presents the first genome-wide identification and expression profiling of grapevine GASA genes and provides the basis for functional characterization of GASA genes in grapes. We surmise that this information may provide new potential resources for the molecular breeding of grapes.
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Huang L, Feng G, Yan H, Zhang Z, Bushman BS, Wang J, Bombarely A, Li M, Yang Z, Nie G, Xie W, Xu L, Chen P, Zhao X, Jiang W, Zhang X. Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:373-388. [PMID: 31276273 PMCID: PMC6953241 DOI: 10.1111/pbi.13205] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/27/2019] [Accepted: 06/29/2019] [Indexed: 05/18/2023]
Abstract
Orchardgrass (Dactylis glomerata L.) is an important forage grass for cultivating livestock worldwide. Here, we report an ~1.84-Gb chromosome-scale diploid genome assembly of orchardgrass, with a contig N50 of 0.93 Mb, a scaffold N50 of 6.08 Mb and a super-scaffold N50 of 252.52 Mb, which is the first chromosome-scale assembled genome of a cool-season forage grass. The genome includes 40 088 protein-coding genes, and 69% of the assembled sequences are transposable elements, with long terminal repeats (LTRs) being the most abundant. The LTRretrotransposons may have been activated and expanded in the grass genome in response to environmental changes during the Pleistocene between 0 and 1 million years ago. Phylogenetic analysis reveals that orchardgrass diverged after rice but before three Triticeae species, and evolutionarily conserved chromosomes were detected by analysing ancient chromosome rearrangements in these grass species. We also resequenced the whole genome of 76 orchardgrass accessions and found that germplasm from Northern Europe and East Asia clustered together, likely due to the exchange of plants along the 'Silk Road' or other ancient trade routes connecting the East and West. Last, a combined transcriptome, quantitative genetic and bulk segregant analysis provided insights into the genetic network regulating flowering time in orchardgrass and revealed four main candidate genes controlling this trait. This chromosome-scale genome and the online database of orchardgrass developed here will facilitate the discovery of genes controlling agronomically important traits, stimulate genetic improvement of and functional genetic research on orchardgrass and provide comparative genetic resources for other forage grasses.
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Affiliation(s)
- Linkai Huang
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Guangyan Feng
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Haidong Yan
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
- School of Plant and Environmental SciencesVirginia TechBlacksburgVAUSA
| | | | | | - Jianping Wang
- Agronomy DepartmentUniversity of FloridaGainesvilleFLUSA
| | | | - Mingzhou Li
- Animal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Zhongfu Yang
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Gang Nie
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Wengang Xie
- State Key Laboratory of Grassland Agro‐EcosystemsCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Lei Xu
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Peilin Chen
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Xinxin Zhao
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | | | - Xinquan Zhang
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
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Cheng X, Wang S, Xu D, Liu X, Li X, Xiao W, Cao J, Jiang H, Min X, Wang J, Zhang H, Chang C, Lu J, Ma C. Identification and Analysis of the GASR Gene Family in Common Wheat ( Triticum aestivum L.) and Characterization of TaGASR34, a Gene Associated With Seed Dormancy and Germination. Front Genet 2019; 10:980. [PMID: 31681420 PMCID: PMC6813915 DOI: 10.3389/fgene.2019.00980] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/13/2019] [Indexed: 11/13/2022] Open
Abstract
Seed dormancy and germination are important agronomic traits in wheat (Triticum aestivum L.) because they determine pre-harvest sprouting (PHS) resistance and thus affect grain production. These processes are regulated by Gibberellic Acid-Stimulated Regulator (GASR) genes. In this study, we identified 37 GASR genes in common wheat, which were designated TaGASR1-37. Moreover, we identified 40 pairs of paralogous genes, of which only one had a Ka/Ks value greater than 1, indicating that most TaGASR genes have undergone negative selection. Chromosomal location and duplication analysis revealed 25 pairs of segmentally duplicated genes and seven pairs of tandemly duplicated genes, suggesting that large-scale duplication events may have contributed to the expansion of TaGASR gene family. Microarray analysis of the expression of 18 TaGASR genes indicated that these genes play diverse roles in different biological processes. Using wheat varieties with contrasting seed dormancy phenotypes, we investigated the expression patterns of TaGASR genes and the corresponding seed germination index phenotypes in response to water imbibition, exogenous ABA and GA treatment, and low- and high-temperature treatment. Based on these data, we identified the TaGASR34 gene as potentially associated with seed dormancy and germination. Further, we used a SNP mutation of the TaGASR34 promoter (-16) to develop the CAPS marker GS34-7B, which was then used to validate the association of TaGASR34 with seed dormancy and germination by evaluating two natural populations across environments. Notably, the frequency of the high-dormancy GS34-7Bb allele was significantly lower than that of the low-dormancy GS34-7Ba allele, implying that the favorable GS34-7Bb allele has not previously been used in wheat breeding. These results provide valuable information for further functional analysis of TaGASR genes and present a useful gene and marker combination for future improvement of PHS resistance in wheat.
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Affiliation(s)
- Xinran Cheng
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Shengxing Wang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Dongmei Xu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Xue Liu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Xinyu Li
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Weiwei Xiao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jiajia Cao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Hao Jiang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Xiaoyu Min
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jianfeng Wang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Haiping Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
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48
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Huang F, Yuan W, Tian S, Zheng Q, He Y. SIN3 LIKE genes mediate long-day induction of flowering but inhibit the floral transition in short days through histone deacetylation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:101-113. [PMID: 31168864 DOI: 10.1111/tpj.14430] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/27/2023]
Abstract
Day length or photoperiod changes are crucial for plants to align the timing of the floral transition with seasonal changes. Through the photoperiod pathway, day length changes induce the expression of the florigenic FLOWERING LOCUS T (FT) to promote flowering. In the facultative long days (LDs) plant Arabidopsis thaliana, LD signals induce flowering, whereas short days (SDs) inhibit flowering. Here, we show that in Arabidopsis SIN3 LIKE (SNL) family genes, encoding a scaffold protein for assembly of histone deacetylase complexes, directly repress the expression of an FT activator and three FT repressors to regulate the transition to flowering in SDs and LDs, respectively. Under inductive LDs, SNLs including SIN3 LIKE 1 (SNL1) to SNL5, function in partial redundancy to repress the expression of three AP2 family transcription factors that repress FT expression, and therefore mediate LD induction of FT expression and promote the transition to flowering. In contrast, under non-inductive SDs SNLs act to inhibit the floral transition, partly through direct repression of a MADS box transcriptional factor that promotes FT expression. Therefore, our results reveal that SNLs, through histone deacetylation, play a dual role for the control of flowering in the LD plant Arabidopsis: inhibiting flowering when the day length is shorter and promoting the floral transition when days become longer than a threshold length.
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Affiliation(s)
- Fei Huang
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenya Yuan
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
| | - Shu Tian
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qijie Zheng
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuehui He
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
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49
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Li X, Shi S, Tao Q, Tao Y, Miao J, Peng X, Li C, Yang Z, Zhou Y, Liang G. OsGASR9 positively regulates grain size and yield in rice (Oryza sativa). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 286:17-27. [PMID: 31300138 DOI: 10.1016/j.plantsci.2019.03.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/04/2019] [Accepted: 03/13/2019] [Indexed: 05/22/2023]
Abstract
The plant-specific gibberellic acid (GA)-stimulated transcript gene family is critical for plant growth and development. There are 10 family members in rice (Oryza sativa), known as OsGASRs. However, few have been functionally characterized. Here, we investigated the function of OsGASR9 in rice. OsGASR9 transcripts were detected in various tissues, with the lowest and highest levels in leaves and panicles, respectively. Greater mRNA levels accumulated in young, compared with in old, panicles and spikelets. OsGASR9 localized to the plasma membrane, cytoplasm and nucleus. Transgenic RNA interference-derived lines in the Zhonghua 11 background exhibited reduced plant height, grain size and yield compared with the wild-type. The two osgasr9 mutants in the Nipponbare background showed similar phenotypes. Conversely, the overexpression of OsGASR9 in the two backgrounds increased plant height and grain size. A significantly increased grain yield per plant was also observed in the overexpression lines having a Nipponbare background. Furthermore, by measuring the GA-induced lengths of the second leaf sheaths and α-amylase activity levels of seeds, we concluded that OsGASR9 is a positive regulator of responses to GA in rice. Thus, OsGASR9 may regulate plant height, grain size and yield through the GA pathway and could have an application value in breeding.
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Affiliation(s)
- Xiangbo Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Shuangyue Shi
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Quandan Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Yajun Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Jun Miao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Xiuron Peng
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Chang Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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50
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Ahmad MZ, Sana A, Jamil A, Nasir JA, Ahmed S, Hameed MU, Abdullah. A genome-wide approach to the comprehensive analysis of GASA gene family in Glycine max. PLANT MOLECULAR BIOLOGY 2019; 100:607-620. [PMID: 31123969 DOI: 10.1007/s11103-019-00883-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/16/2019] [Indexed: 05/24/2023]
Abstract
A vital role of short amino acid gene family, gibberellic acid stimulated arabidopsis (GASA), has been reported in plant growth and development. Although, little information is available about these cysteine rich short proteins in different plant species and this is the first comprehensive approach to exploit available genomic data and to analyze the GASA family in G. max. The phylogenetic and sequence composition analysis distributed the 37 identified GmGASA genes into three groups. Further investigation of the tissue expression pattern, phylogenetic analysis, motif, gene structure, chromosome distributions, duplication patterns, positive-selection pressure and cis-element analysis of 37 GmGASA genes. A conserved GASA domain was found in all identified GmGASA genes and exhibited similar characteristics. The online gene expression profile based analysis of GmGASA genes reveled that these genes were highly expressed in almost all soybean parts and some have high expression in flower which indicates that GmGASA genes displayed special or distinct expression pattern among different tissues. The segmental duplication was found in five pairs from 37 GmGASA genes and was distributed on 15 different chromosomes. The Ka/Ks ratio of 5 pairs of segmentally duplicated gene indicated that after the occurrence of duplication events, the duplicated gene pairs were purified and selected after restrictive functional differentiation. This investigated study of GmGASA gene will useful to support the statement about GASA genes role during flower induction in flowering plants.
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Affiliation(s)
- Muhammad Zulfiqar Ahmad
- Department of Plant Breeding and Genetics, Faculty of Agriculture, Gomal University, Dera Ismail Khan, KP, Pakistan.
| | - Aiman Sana
- Department of Plant Breeding and Genetics, Faculty of Agriculture, Gomal University, Dera Ismail Khan, KP, Pakistan
| | - Arshad Jamil
- Department of Plant Breeding and Genetics, Faculty of Agriculture, Gomal University, Dera Ismail Khan, KP, Pakistan
| | - Jamal Abdul Nasir
- Department of Plant Breeding and Genetics, Faculty of Agriculture, Gomal University, Dera Ismail Khan, KP, Pakistan
| | - Shakeel Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Muhammad Uzair Hameed
- Department of Horticulture, Faculty of Agriculture, Gomal University, Dera Ismail Khan, KP, Pakistan
| | - Abdullah
- Department of Plant Breeding and Genetics, Faculty of Agriculture, Gomal University, Dera Ismail Khan, KP, Pakistan
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