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Hu J, Yu Q, Jiang S, Hu X, Li X, Liu Z. Identification and expression analysis of the small auxin-up RNA ( SAUR) gene family in Lycium ruthenicum. PeerJ 2023; 11:e15941. [PMID: 37701838 PMCID: PMC10493089 DOI: 10.7717/peerj.15941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023] Open
Abstract
The plant hormone auxin regulates numerous aspects of plant growth and development, and small auxin-up RNA (SAUR) is the largest family of early auxin response genes in higher plants. SAUR has been implicated in the regulation of multiple biological processes. However, no comprehensive analysis of SAUR genes has been reported in Lycium ruthenicum. L. ruthenicum is a thorny shrub with very pronounced salt and drought tolerance, and studies have shown that stem thorns are related to drought tolerance in L. ruthenicum. In this study, the identification, phylogenetic analysis, and conserved motif prediction of SAUR genes were extensively explored. Furthermore, the tissue expression patterns of selected SAUR genes were assayed with quantitative real-time polymerase chain reaction (RT-qPCR). A total of 33 putative LrSAURs were identified and divided into three clusters in a phylogenetic tree of L. ruthenicum. MEME analysis identified 10 motifs in L. ruthenicum, and the results suggested that motif 1 and motif 3 were widely distributed. Analyzing the transcriptome data of stem thorns at four developmental stages indicated that LrSAURs were differentially expressed in L. ruthenicum, and could be divided into six expression patterns. The RT-qPCR analysis of 21 genes showed that LrSAUR2, LrSAUR8, LrSAUR9, LrSAUR11, LrSAUR12, and LrSAUR19 were mainly expressed in stems and stem thorns, and may be related to stem thorn development.
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Affiliation(s)
- Jing Hu
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Qiushi Yu
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Shengxiu Jiang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Xiaoke Hu
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Xuemin Li
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
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Liu ZM, Faizan M, Chen C, Zheng LH, Yu FY. The Combined Analysis of Transcriptome and Antioxidant Enzymes Revealed the Mechanism of EBL and ZnO NPs Enhancing Styrax tonkinensis Seed Abiotic Stress Resistance. Genes (Basel) 2022; 13:genes13112170. [PMID: 36421844 PMCID: PMC9690584 DOI: 10.3390/genes13112170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
As global climate change worsens, trees will have difficulties adapting to abiotic pressures, particularly in the field, where environmental characteristics are difficult to control. A prospective commercial and ornamental tree species, Styrax tonkinensis, has its seed oil output and quality reduced as a result, which lowers the economic benefits. This necessitates growers to implement efficient strategies to increase the seeds of woody biofuel species' tolerance to abiotic stress. Numerous studies have shown that ZnO nanoparticles (NPs), a new material, and BRs assist plants to increase their resilience to abiotic stress and subsequently adapt to it. However, there have not been many investigations into S. tonkinensis seed resistance. In this study, we examined the changes in antioxidant enzyme activities and transcriptomic results of S. tonkinensis seeds throughout the seed development period to investigate the effects of 24-epibrassinolide (EBL), one of the BRs, and ZnO NPs treatments alone or together on the stress resistance of S. tonkinensis seeds. On 70, 100, and 130 days after flowering (DAF), spraying EBL or ZnO NPs increased the activity of antioxidant enzymes (POD, SOD, and CAT) in S. tonkinensis seeds. Moreover, when the EBL and ZnO NPs were sprayed together, the activities of antioxidant enzymes were the strongest, which suggests that the positive effects of the two can be superimposed. On 70 and 100 DAF, the EBL and ZnO NPs treatments improved seed stress resistance, mostly through complex plant hormone crosstalk signaling, which includes IAA, JA, BR, and ABA signaling. Additionally, ABA played an essential role in hormone crosstalk, while, on 130 DAF, due to the physiological characteristics of seeds themselves in the late stage of maturity, the improvement in seed stress resistance by EBL and ZnO NPs was related to protein synthesis, especially late embryogenesis-abundant protein (LEA), and other nutrient storage in seeds. Spraying EBL and ZnO NPs during the seed growth of S. tonkinensis could significantly increase seed stress resistance. Our findings provide fresh perspectives on how cultural practices can increase abiotic stress tolerance in woody seedlings.
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Affiliation(s)
- Ze-Mao Liu
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing 210000, China; (Z.-M.L.); (L.-H.Z.)
| | - Mohammad Faizan
- Botany Section, School of Sciences, Maulana Azad National Urdu University, Hyderabad 500032, India;
| | - Chen Chen
- School of Landscape and Horticulture, Yangzhou Polytechnic College, Yangzhou 225009, China;
| | - Li-Hong Zheng
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing 210000, China; (Z.-M.L.); (L.-H.Z.)
| | - Fang-Yuan Yu
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing 210000, China; (Z.-M.L.); (L.-H.Z.)
- Correspondence:
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Lv W, He X, Guo H, Lan H, Jiao Y, Li L, Lian Y, Wang Z, Xin Z, Ren Y, Lin T. Genome-Wide Identification of TaSAUR Gene Family Members in Hexaploid Wheat and Functional Characterization of TaSAUR66-5B in Improving Nitrogen Use Efficiency. Int J Mol Sci 2022; 23:ijms23147574. [PMID: 35886923 PMCID: PMC9319360 DOI: 10.3390/ijms23147574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Excessive input of nitrogen fertilizer not only causes a great waste of resources but brings about a series of ecological and environmental problems. Although Small Auxin Up-regulated RNAs (SAURs) participate in diverse biological processes, the function of SAURs in the nitrogen starvation response has not been well-studied. Here, we identified 308 TaSAURs in wheat and divided them into 10 subfamilies. The promoter regions of most TaSAURs contain hormone responsive elements, and their expression levels change under the treatment of different hormones, such as IAA, MeJA, and ABA. Interestingly, overexpression of one of the TaSAUR family members, a nitrogen starvation responsive gene, TaSAUR66-5B, can promote the growth of Arabidopsis and wheat roots. In addition, overexpression of TaSAUR66-5B in Arabidopsis up-regulates the expression levels of auxin biosynthesis related genes, suggesting that overexpression TaSAUR66-5B may promote root growth by increasing the biosynthesis of auxin. Furthermore, overexpression of TaSAUR66-5B in wheat can increase the biomass and grain yields of transgenic plants, as well as the nitrogen concentration and accumulation of both shoots and grains, especially under low nitrogen conditions. This study provides important genomic information of the TaSAUR gene family and lays a foundation for elucidating the functions of TaSAURs in improving nitrogen utilization efficiency in wheat.
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Affiliation(s)
- Weizeng Lv
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Xue He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Haojuan Guo
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Haibin Lan
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Yanqing Jiao
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Le Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Yanhao Lian
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Zhiqiang Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Zeyu Xin
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Yongzhe Ren
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
- Correspondence: (Y.R.); (T.L.)
| | - Tongbao Lin
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
- Correspondence: (Y.R.); (T.L.)
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Liu Y, Xiao L, Chi J, Li R, Han Y, Cui F, Peng Z, Wan S, Li G. Genome-wide identification and expression of SAUR gene family in peanut (Arachis hypogaea L.) and functional identification of AhSAUR3 in drought tolerance. BMC Plant Biol 2022; 22:178. [PMID: 35387613 PMCID: PMC8988358 DOI: 10.1186/s12870-022-03564-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/25/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Small auxin-upregulated RNAs (SAURs) gene family plays important roles in plant growth, development, and stress responses. However, the function of few SAUR genes is known in the peanut (Arachis hypogaea L.), one of the world's major food legume crops. This study aimed to perform a comprehensive identification of the SAUR gene family from the peanut genome. RESULTS The genome-wide analysis revealed that a total of 162 SAUR genes were identified in the peanut genome. The phylogenetic analysis indicated that the SAUR proteins were classified into eight subfamilies. The SAUR gene family experienced a remarkable expansion after tetraploidization, which contributed to the tandem duplication events first occurring in subgenome A and then segmental duplication events occurring between A and B subgenomes. The expression profiles based on transcriptomic data showed that SAUR genes were dominantly expressed in the leaves, pistils, perianth, and peg tips, and were widely involved in tolerance against abiotic stresses. A total of 18 AhSAUR genes selected from different subfamilies randomly presented 4 major expression patterns according to their expression characteristics in response to indole-3-acetic acid. The members from the same subfamily showed a similar expression pattern. Furthermore, the functional analysis revealed that AhSAUR3 played a negative role in response to drought tolerance. CONCLUSIONS This study provided insights into the evolution and function of the SAUR gene family and may serve as a resource for further functional research on AhSAUR genes.
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Affiliation(s)
- Yiyang Liu
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 Shandong Province China
| | - Lina Xiao
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 Shandong Province China
| | - Jingxian Chi
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 Shandong Province China
- Key Lab of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, 250014 Shandong Province China
| | - Rongchong Li
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 Shandong Province China
| | - Yan Han
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 Shandong Province China
| | - Feng Cui
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 Shandong Province China
| | - Zhenying Peng
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 Shandong Province China
| | - Shubo Wan
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 Shandong Province China
| | - Guowei Li
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 Shandong Province China
- Key Lab of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, 250014 Shandong Province China
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Iqbal MA, Miyamoto K, Yumoto E, Parveen S, Mutanda I, Inafuku M, Oku H. Plant hormone profile and control over isoprene biosynthesis in a tropical tree Ficus septica. Plant Biol (Stuttg) 2022; 24:492-501. [PMID: 35050526 DOI: 10.1111/plb.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Plant hormone signalling and the circadian clock have been implicated in the transcriptional control of isoprene biosynthesis. To gain more insight into the hormonal control of isoprene biosynthesis, the present study measured plant hormone concentrations in jasmonic acid (JA)-treated leaves of our previous model study, examined their relationship with gene expression of isoprene synthase (IspS) and hormone signalling transcription factors. Of the plant hormones, IAA and JA-Ile and their related transcription factors (MYC2 and SAUR21) were significantly correlated with IspS gene expression. Concentrations of cytokinins, isopentenyladenine (iP), trans-zeatin riboside (tZR) and cis-zeatin riboside (cZR), were similarly significantly correlated with IspS expression. However, there was no significant correlation between their related transcription factor (ARR-B) and IspS expression. The circadian clock-related gene PRR7, but not the transcription factor LHY, was highly correlated with IspS expression. These results suggest that the hormonal balance between JA-Ile and IAA plays a central role in transcriptional regulation of IspS through the transcription factors MYC2 and SAUR21, the early auxin responsive genes. The putative cis-acting elements for SAUR on the IspS promoter (TGTCNN and CATATG), in addition to the G-box for MYC2, support the above proposal. These results provide insightful information on the core components of plant hormone-related regulation of IspS under coordination with the circadian clock genes.
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Affiliation(s)
- Md A Iqbal
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - K Miyamoto
- Department of Biosciences, Teikyo University, Utsunomiya, Tochigi, Japan
| | - E Yumoto
- Advanced Instrumental Analysis Center, Teikyo University, Tochigi, Japan
| | - S Parveen
- Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - I Mutanda
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, Jiangsu, China
| | - M Inafuku
- Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan
| | - H Oku
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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Li G, Wang Q, Lu L, Wang S, Chen X, Khan MHU, Zhang Y, Yang S. Identification of the soybean small auxin upregulated RNA (SAUR) gene family and specific haplotype for drought tolerance. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01010-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhang H, Yu Z, Yao X, Chen J, Chen X, Zhou H, Lou Y, Ming F, Jin Y. Genome-wide identification and characterization of small auxin-up RNA (SAUR) gene family in plants: evolution and expression profiles during normal growth and stress response. BMC Plant Biol 2021; 21:4. [PMID: 33407147 PMCID: PMC7789510 DOI: 10.1186/s12870-020-02781-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/02/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Auxin is critical to plant growth and development, as well as stress responses. Small auxin-up RNA (SAUR) is the largest family of early auxin responsive genes in higher plants. However, the function of few SAUR genes is known owing to functional redundancy among the many family members. RESULTS In this study, we conducted a phylogenetic analysis using protein sequences of 795 SAURs from Anthoceros angustus, Marchantia polymorpha, Physcomitrella patens, Selaginella moellendorffii, Ginkgo biloba, Gnetum montanum, Amborella trichopoda, Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Medicago truncatula and Setaria italica. The phylogenetic trees showed that the SAUR proteins could be divided into 10 clades and three subfamilies, and that SAUR proteins of three bryophyte species were only located in subfamily III, which suggested that they may be ancestral. From bryophyta to anthophyta, SAUR family have appeared very large expansion. The number of SAUR gene in Fabaceae species was considerably higher than that in other plants, which may be associated with independent whole genome duplication event in the Fabaceae lineages. The phylogenetic trees also showed that SAUR genes had expanded independently monocotyledons and dicotyledons in angiosperms. Conserved motif and protein structure prediction revealed that SAUR proteins were highly conserved among higher plants, and two leucine residues in motif I were observed in almost all SAUR proteins, which suggests the residues plays a critical role in the stability and function of SAUR proteins. Expression analysis of SAUR genes using publicly available RNA-seq data from rice and soybean indicated functional similarity of members in the same clade, which was also further confirmed by qRT-PCR. Summarization of SAUR functions also showed that SAUR functions were usually consistent within a subclade. CONCLUSIONS This study provides insights into the evolution and function of the SAUR gene family from bryophyta to anthophyta, particularly in Fabaceae plants. Future investigation to understand the functions of SAUR family members should employ a clade as the study unit.
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Affiliation(s)
- Hao Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Zhenjia Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Xiaodie Yao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Jingli Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Xing Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Huiwen Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Yuxia Lou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Feng Ming
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China.
| | - Yue Jin
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China.
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Wang P, Lu S, Xie M, Wu M, Ding S, Khaliq A, Ma Z, Mao J, Chen B. Identification and expression analysis of the small auxin-up RNA (SAUR) gene family in apple by inducing of auxin. Gene 2020; 750:144725. [PMID: 32360839 DOI: 10.1016/j.gene.2020.144725] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 12/14/2022]
Abstract
The small auxin-up RNA (SAUR) family plays a vital role in the regulation of plant growth and development. We identified 80 MdSAUR genes in this study. Phylogenetic analysis indicated that the SAUR proteins from Arabidopsis, rice, and apple were divided into six groups. Of the 80 MdSAURs, 71 were randomly distributed along the 17 chromosomes, while the remaining genes were located along unassigned scafoolds. Among them, a comprehensive overview of SAUR gene family is presented, including gene structures, chromosome locations, duplication and selection pressure analyses, synteny and promoter analyses, and protein interaction. The expression profiles based on microarray data found that 80 genes showed increased expression levels in at least one tissue including seed, seedling, root, stem, leaf, flower, fruit 100daa, and harvested fruit. MdSAUR7 possibly regulate the development of flower organs, and MdSAUR15, MdSAUR24, and MdSAUR80 promote the growth of fruits by regulating cell division. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated the expression levels of 79 MdSAUR genes in leaves under exogenous IAA treatment. MdSAUR4, MdSAUR22, MdSAUR37, MdSAUR38, MdSAUR49, and MdSAUR54 were up-regulated after IAA treatment compared with the control, indicating that they may play specific roles in the IAA signaling transduction pathway. This work provided a foundation for further investigations for the functional analyses of SAURs in apple.
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Affiliation(s)
- Ping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Min Xie
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Maodong Wu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Sunlei Ding
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Abdul Khaliq
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China.
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Deng G, Huang X, Xie L, Tan S, Gbokie T Jr, Bao Y, Xie Z, Yi K. Identification and Expression of SAUR Genes in the CAM Plant Agave. Genes (Basel) 2019; 10:E555. [PMID: 31340544 DOI: 10.3390/genes10070555] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 01/04/2023] Open
Abstract
Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for fiber production in Brazil, China, and African countries. Small Auxin Up-regulated RNA (SAUR) genes have broad effect on auxin signaling-regulated plant growth and development, while only few SAUR genes have been reported in Agave species. In this study, we identified 43, 60, 24, and 21 SAUR genes with full-length coding regions in A. deserti, A. tequilana, A. H11648, and A. americana, respectively. Although phylogenetic analysis revealed that rice contained a species-specific expansion pattern of SAUR gene, no similar phenomena were observed in Agave species. The in silico expression indicated that SAUR genes had a distinct expression pattern in A. H11648 compared with other Agave species; and four SAUR genes were differentially expressed during CAM diel cycle in A. americana. Additionally, an expression analysis was conducted to estimate SAUR gene expression during different leaf developmental stages, abiotic and biotic stresses in A. H11648. Together, we first characterized the SAUR genes of Agave based on previously published transcriptome datasets and emphasized the potential functions of SAUR genes in Agave's leaf development and stress responses. The identification of which further expands our understanding on auxin signaling-regulated plant growth and development in Agave species.
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Guo P, Zheng Y, Peng D, Liu L, Dai L, Chen C, Wang B. Identification and expression characterization of the Phloem Protein 2 (PP2) genes in ramie (Boehmeria nivea L. Gaudich). Sci Rep 2018; 8:10734. [PMID: 30013165 PMCID: PMC6048116 DOI: 10.1038/s41598-018-28953-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 06/28/2018] [Indexed: 11/20/2022] Open
Abstract
Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in sieve elements and companion cells, which play important roles in the maintenance of morphology, photoassimilate transportation and wound protection in higher plants, but to date, no PP2 (BnPP2) genes had been identified in ramie. Here, a total of 15 full-length BnPP2 genes were identified. These BnPP2 genes exhibited different responses to abiotic stresses. Interestingly, the BnPP2 genes are more sensitive to insect pests than to other stresses. A study of the BnPP2-15 promoter revealed that pBnPP2-15 could drive specific GUS expression in the petiole, root and stamen and could also be induced by mechanical wounding and aphid infection in transgenic Arabidopsis lines. The subcellular localization of six BnPP2 proteins showed that GFP-BnPP2-1, GFP-BnPP2-6, GFP-BnPP2-7, GFP-BnPP2-9, GFP-BnPP2-11 and GFP-BnPP2-12 were predominantly located in the cytoplasm. These results provide useful information elucidating the functions of BnPP2 genes in ramie.
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Affiliation(s)
- Pingan Guo
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Yancheng Zheng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Lijun Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Lunjin Dai
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Cong Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Bo Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China.
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11
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Hu W, Yan H, Luo S, Pan F, Wang Y, Xiang Y. Genome-wide analysis of poplar SAUR gene family and expression profiles under cold, polyethylene glycol and indole-3-acetic acid treatments. Plant Physiol Biochem 2018; 128:50-65. [PMID: 29758473 DOI: 10.1016/j.plaphy.2018.04.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Small auxin-up RNA (SAUR) proteins play an important role in the regulation of plant growth and development. Here, we identified 105 SAUR genes and comprehensively analyzed them in Populus trichocarpa. Based on the phylogenetic relationships, the PtSAURs were classified into ten subfamilies. Of the 105 PtSAURs, 100 were randomly distributed along the nineteen chromosomes, while the remaining genes were located along unassigned scafoolds. These genes mainly evolved through segmental duplications. In total, 94 PtSAURs contained no introns, and each group had a similar conserved motif structure. A promoter analysis revealed various cis-elements related to growth, development and stress responses, and a synteny analysis established orthologous relationships among SAURs in Arabidopsis, rice, grape and poplar. The qRT-PCR and tissue expression analyses indicated that PtSAURs show different expression levels in various tissues in response to different treatments. PtSAUR53 was located on the nuclear and plasma membrane by conducting subcellular localization analysis. This study provides a comprehensive overview of poplar SAUR proteins and a foundation for further investigations for functional analysis of SAURs in poplar growth and development. At the same time, it will be valuable to further study the poplar SAUR genes to reveal their biological effects.
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Affiliation(s)
- Wenfang Hu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture University, Hefei, 230036, China.
| | - Shuangshuang Luo
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Feng Pan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yue Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture University, Hefei, 230036, China.
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12
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Li X, Liu G, Geng Y, Wu M, Pei W, Zhai H, Zang X, Li X, Zhang J, Yu S, Yu J. A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton. BMC Genomics 2017; 18:815. [PMID: 29061116 PMCID: PMC5654091 DOI: 10.1186/s12864-017-4224-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 10/17/2017] [Indexed: 11/10/2022] Open
Abstract
Background Small auxin-up RNA (SAUR) gene family is the largest family of early auxin response genes in higher plants, which have been implicated in the regulation of multiple biological processes. However, no comprehensive analysis of SAUR genes has been reported in cotton (Gossypium spp.). Results In the study, we identified 145, 97, 214, and 176 SAUR homologous genes in the sequenced genomes of G. raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. A phylogenetic analysis revealed that the SAUR genes can be classified into 10 groups. A further analysis of chromosomal locations and gene duplications showed that tandem duplication and segmental duplication events contributed to the expansion of the SAUR gene family in cotton. An exon-intron organization and motif analysis revealed the conservation of SAUR-specific domains, and the auxin responsive elements existed in most of the upstream sequences. The expression levels of 16 GhSAUR genes in response to an exogenous application of IAA were determined by a quantitative RT-PCR analysis. The genome-wide RNA-seq data and qRT-PCR analysis of selected SAUR genes in developing fibers revealed their differential expressions. The physical mapping showed that 20 SAUR genes were co-localized with fiber length quantitative trait locus (QTL) hotspots. Single nucleotide polymorphisms (SNPs) were detected for 12 of these 20 genes between G. hirsutum and G. barbadense, but no SNPs were identified between two backcross inbred lines with differing fiber lengths derived from a cross between the two cultivated tetraploids. Conclusions This study provides an important piece of genomic information for the SAUR genes in cotton and lays a solid foundation for elucidating the functions of SAUR genes in auxin signaling pathways to regulate cotton growth. Electronic supplementary material The online version of this article (10.1186/s12864-017-4224-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xihua Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China.,College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Guoyuan Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Yanhui Geng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Honghong Zhai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Xinshan Zang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Xingli Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 88003, USA.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China. .,College of Agronomy, Northwest A&F University, Yangling, 712100, China.
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China.
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Zhang N, Huang X, Bao Y, Wang B, Zeng H, Cheng W, Tang M, Li Y, Ren J, Sun Y. Genome-wide identification of SAUR genes in watermelon ( Citrullus lanatus). Physiol Mol Biol Plants 2017; 23:619-628. [PMID: 28878500 PMCID: PMC5567703 DOI: 10.1007/s12298-017-0442-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 05/22/2023]
Abstract
The early auxin responsive SAUR family is an important gene family in auxin signal transduction. We here present the first report of a genome-wide identification of SAUR genes in watermelon genome. We successfully identified 65 ClaSAURs and provide a genomic framework for future study on these genes. Phylogenetic result revealed a Cucurbitaceae-specific SAUR subfamily and contribute to understanding of the evolutionary pattern of SAUR genes in plants. Quantitative RT-PCR analysis demonstrates the existed expression of 11 randomly selected SAUR genes in watermelon tissues. ClaSAUR36 was highly expressed in fruit, for which further study might bring a new prospective for watermelon fruit development. Moreover, correlation analysis revealed the similar expression profiles of SAUR genes between watermelon and Arabidopsis during shoot organogenesis. This work gives us a new support for the conserved auxin machinery in plants.
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Affiliation(s)
- Na Zhang
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, #4 Xueyuan Road, Longhua District, Haikou, 571101 China
| | - Yaning Bao
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province China
| | - Bo Wang
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province China
| | - Hongxia Zeng
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Weishun Cheng
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Mi Tang
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Yuhua Li
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Jian Ren
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Yuhong Sun
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
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