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Yu L, Xia J, Jiang R, Wang J, Yuan X, Dong X, Chen Z, Zhao Z, Wu B, Zhan L, Zhang R, Tang K, Li J, Xu X. Genome-Wide Identification and Characterization of the CCT Gene Family in Rapeseed ( Brassica napus L.). Int J Mol Sci 2024; 25:5301. [PMID: 38791340 PMCID: PMC11121423 DOI: 10.3390/ijms25105301] [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: 02/29/2024] [Revised: 05/01/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
The CCT gene family is present in plants and is involved in biological processes such as flowering, circadian rhythm regulation, plant growth and development, and stress resistance. We identified 87, 62, 46, and 40 CCTs at the whole-genome level in B. napus, B. rapa, B. oleracea, and A. thaliana, respectively. The CCTs can be classified into five groups based on evolutionary relationships, and each of these groups can be further subdivided into three subfamilies (COL, CMF, and PRR) based on function. Our analysis of chromosome localization, gene structure, collinearity, cis-acting elements, and expression patterns in B. napus revealed that the distribution of the 87 BnaCCTs on the chromosomes of B. napus was uneven. Analysis of gene structure and conserved motifs revealed that, with the exception of a few genes that may have lost structural domains, the majority of genes within the same group exhibited similar structures and conserved domains. The gene collinearity analysis identified 72 orthologous genes, indicating gene duplication and expansion during the evolution of BnaCCTs. Analysis of cis-acting elements identified several elements related to abiotic and biotic stress, plant hormone response, and plant growth and development in the promoter regions of BnaCCTs. Expression pattern and protein interaction network analysis showed that BnaCCTs are differentially expressed in various tissues and under stress conditions. The PRR subfamily genes have the highest number of interacting proteins, indicating their significant role in the growth, development, and response to abiotic stress of B. napus.
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Affiliation(s)
- Liyiqi Yu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Jichun Xia
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Rujiao Jiang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Jiajia Wang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Xiaolong Yuan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Xinchao Dong
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Zhenjie Chen
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Zizheng Zhao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Boen Wu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Lanlan Zhan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Ranfeng Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Kang Tang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xinfu Xu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
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Liu T, Yang Y, Zhu R, Wang Q, Wang Y, Shi M, Kai G. Genome-Wide Identification and Expression Analysis of Sucrose Nonfermenting 1-Related Protein Kinase ( SnRK) Genes in Salvia miltiorrhiza in Response to Hormone. PLANTS (BASEL, SWITZERLAND) 2024; 13:994. [PMID: 38611523 PMCID: PMC11013873 DOI: 10.3390/plants13070994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024]
Abstract
The SnRK gene family is the chief component of plant stress resistance and metabolism through activating the phosphorylation of downstream proteins. S. miltiorrhiza is widely used for the treatment of cardiovascular diseases in Asian countries. However, information about the SnRK gene family of S. miltiorrhiza is not clear. The aim of this study is to comprehensively analyze the SnRK gene family of S. miltiorrhiza and its response to phytohormone. Here, 33 SmSnRK genes were identified and divided into three subfamilies (SmSnRK1, SmSnRK2 and SmSnRK3) according to phylogenetic analysis and domain. SmSnRK genes within same subgroup shared similar protein motif composition and were unevenly distributed on eight chromosomes of S. miltiorrhiza. Cis-acting element analysis showed that the promoter of SmSnRK genes was enriched with ABRE motifs. Expression pattern analysis revealed that SmSnRK genes were preferentially expressed in leaves and roots. Most SmSnRK genes were induced by ABA and MeJA treatment. Correlation analysis showed that SmSnRK3.15 and SmSnRK3.18 might positively regulate tanshinone biosynthesis; SmSnRK3.10 and SmSnRK3.12 might positively regulate salvianolic acid biosynthesis. RNAi-based silencing of SmSnRK2.6 down-regulated the biosynthesis of tanshinones and biosynthetic genes expression. An in vitro phosphorylation assay verified that SmSnRK2.2 interacted with and phosphorylated SmAREB1. These findings will provide a valuable basis for the functional characterization of SmSnRK genes and quality improvement of S. miltiorrhiza.
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Affiliation(s)
- Tingyao Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yinkai Yang
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Ruiyan Zhu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Qichao Wang
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yao Wang
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Min Shi
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Guoyin Kai
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Zheng H, Xie Y, Mu C, Cheng W, Bai Y, Gao J. Deciphering the regulatory role of PheSnRK genes in Moso bamboo: insights into hormonal, energy, and stress responses. BMC Genomics 2024; 25:252. [PMID: 38448813 PMCID: PMC10916206 DOI: 10.1186/s12864-024-10176-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
The SnRK (sucrose non-fermentation-related protein kinase) plays an important role in regulating various signals in plants. However, as an important bamboo shoot and wood species, the response mechanism of PheSnRK in Phyllostachys edulis to hormones, low energy and stress remains unclear. In this paper, we focused on the structure, expression, and response of SnRK to hormones and sugars. In this study, we identified 75 PheSnRK genes from the Moso bamboo genome, which can be divided into three groups according to the evolutionary relationship. Cis-element analysis has shown that the PheSnRK gene can respond to various hormones, light, and stress. The PheSnRK2.9 proteins were localized in the nucleus and cytoplasm. Transgenic experiments showed that overexpression of PheSnRK2.9 inhibited root development, the plants were salt-tolerant and exhibited slowed starch consumption in Arabidopsis in the dark. The results of yeast one-hybrid and dual luciferase assay showed that PheIAAs and PheNACs can regulate PheSnRK2.9 gene expression by binding to the promoter of PheSnRK2.9. This study provided a comprehensive understanding of PheSnRK genes of Moso bamboo, which provides valuable information for further research on energy regulation mechanism and stress response during the growth and development of Moso bamboo.
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Affiliation(s)
- Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
- College of Life Science, Leshan Normal University, Leshan, China
| | - Yali Xie
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China.
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Zhang JF, Chu HH, Liao D, Ma GJ, Tong YK, Liu YY, Li J, Ren F. Comprehensive Evolution and Expression anaLysis of PHOSPHATE 1 Gene Family in Allotetraploid Brassica napus and Its Diploid Ancestors. Biochem Genet 2023; 61:2330-2347. [PMID: 37036640 DOI: 10.1007/s10528-023-10375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
The members of PHOSPHATE 1 (PHO1) family play important roles in plant phosphate (Pi) transport and adaptation to Pi deficiency. The functions of PHO1 family proteins have been reported in several plant species, with the exception of Brassica species. Here, we identified 23, 23, and 44 putative PHO1 family genes in Brassica rapa, Brassica oleracea, and Brassica napus by whole genome analysis, respectively. The phylogenetic analysis divided PHO1 family proteins into eight groups, which represented the orthologous relationships among PHO1 members. The gene structure and the conserved motif analysis indicated that the most PHO1 family genes had similar gene structures and the PHO1 proteins shared mutual conserved motifs. The chromosome distribution analysis showed that the majority of BnPHO1 family genes distributed analogously at chromosomes with BrPHO1 and BoPHO1 family genes. The data showed that PHO1 family genes were highly conserved during evolution from diploid to tetraploid. Furthermore, the expression analysis showed that PHO1 family genes had different expression patterns in plant tissues, suggesting the diversity of gene functions in Brassica species. Meanwhile, the expression analysis also revealed that some PHO1 family genes were significantly responsive to Pi deficiency, suggesting that PHO1 family genes play critical roles in Pi uptake and homeostasis under low Pi stress. Altogether, the characteristics of PHO1 family genes provide a reliable groundwork for further dissecting their functions in Brassica species.
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Affiliation(s)
- Jian-Feng Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Hui-Hui Chu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Dan Liao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Guang-Jing Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yi-Kai Tong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ying-Ying Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
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Feng X, Meng Q, Zeng J, Yu Q, Xu D, Dai X, Ge L, Ma W, Liu W. Genome-wide identification of sucrose non-fermenting-1-related protein kinase genes in maize and their responses to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1087839. [PMID: 36618673 PMCID: PMC9815513 DOI: 10.3389/fpls.2022.1087839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Protein kinases play an important role in plants in response to environmental changes through signal transduction. As a large family of protein kinases, sucrose non-fermenting-1 (SNF1)-related kinases (SnRKs) were found and functionally verified in many plants. Nevertheless, little is known about the SnRK family of Zea mays. METHODS Evolutionary relationships, chromosome locations, gene structures, conserved motifs, and cis-elements in promoter regions were systematically analyzed. Besides, tissue-specific and stress-induced expression patterns of ZmSnRKs were determined. Finally, functional regulatory networks between ZmSnRKs and other proteins or miRNAs were constructed. RESULTS AND DISCUSSION In total, 60 SnRK genes located on 10 chromosomes were discovered in maize. ZmSnRKs were classified into three subfamilies (ZmSnRK1, ZmSnRK2, and ZmSnRK3), consisting of 4, 14, and 42 genes, respectively. Gene structure analysis showed that 33 of the 42 ZmSnRK3 genes contained only one exon. Most ZmSnRK genes contained at least one ABRE, MBS, and LTR cis-element and a few ZmSnRK genes had AuxRR-core, P-box, MBSI, and SARE ciselements in their promoter regions. The Ka:Ks ratio of 22 paralogous ZmSnRK gene pairs revealed that the ZmSnRK gene family had experienced a purifying selection. Meanwhile, we analyzed the expression profiles of ZmSnRKs, and they exhibited significant differences in various tissues and abiotic stresses. In addition, A total of eight ZmPP2Cs, which can interact with ZmSnRK proteins, and 46 miRNAs, which can target 24 ZmSnRKs, were identified. Generally, these results provide valuable information for further function verification of ZmSnRKs, and improve our understanding of the role of ZmSnRKs in the climate resilience of maize.
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Affiliation(s)
- Xue Feng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Quan Meng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Qian Yu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Xuehuan Dai
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Lei Ge
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Wenxing Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
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Li R, Radani Y, Ahmad B, Movahedi A, Yang L. Identification and characteristics of SnRK genes and cold stress-induced expression profiles in Liriodendron chinense. BMC Genomics 2022; 23:708. [PMID: 36253733 PMCID: PMC9578244 DOI: 10.1186/s12864-022-08902-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/09/2022] [Indexed: 12/23/2022] Open
Abstract
Background The sucrose non-fermenting 1 (SNF1)-related protein kinases (SnRKs) play a vivid role in regulating plant metabolism and stress response, providing a pathway for regulation between metabolism and stress signals. Conducting identification and stress response studies on SnRKs in plants contributes to the development of strategies for tree species that are more tolerant to stress conditions. Results In the present study, a total of 30 LcSnRKs were identified in Liriodendron chinense (L. chinense) genome, which was distributed across 15 chromosomes and 4 scaffolds. It could be divided into three subfamilies: SnRK1, SnRK2, and SnRK3 based on phylogenetic analysis and domain types. The LcSnRK of the three subfamilies shared the same Ser/Thr kinase structure in gene structure and motif composition, while the functional domains, except for the kinase domain, showed significant differences. A total of 13 collinear gene pairs were detected in L. chinense and Arabidopsis thaliana (A. thaliana), and 18 pairs were detected in L. chinense and rice, suggesting that the LcSnRK family genes may be evolutionarily more closely related to rice. Cis-regulation element analysis showed that LcSnRKs were LTR and TC-rich, which could respond to different environmental stresses. Furthermore, the expression patterns of LcSnRKs are different at different times under low-temperature stress. LcSnRK1s expression tended to be down-regulated under low-temperature stress. The expression of LcSnRK2s tended to be up-regulated under low-temperature stress. The expression trend of LcSnRK3s under low-temperature stress was mainly up-or down-regulated. Conclusion The results of this study will provide valuable information for the functional identification of the LcSnRK gene in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08902-0.
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Affiliation(s)
- Rongxue Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Yasmina Radani
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Baseer Ahmad
- Muhammad Nawaz Sharif University of Agriculture, Multan, Punjab, 25000, Pakistan
| | - Ali Movahedi
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
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Paes de Melo B, Carpinetti PDA, Fraga OT, Rodrigues-Silva PL, Fioresi VS, de Camargos LF, Ferreira MFDS. Abiotic Stresses in Plants and Their Markers: A Practice View of Plant Stress Responses and Programmed Cell Death Mechanisms. PLANTS (BASEL, SWITZERLAND) 2022; 11:1100. [PMID: 35567101 PMCID: PMC9103730 DOI: 10.3390/plants11091100] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 05/12/2023]
Abstract
Understanding how plants cope with stress and the intricate mechanisms thereby used to adapt and survive environmental imbalances comprise one of the most powerful tools for modern agriculture. Interdisciplinary studies suggest that knowledge in how plants perceive, transduce and respond to abiotic stresses are a meaningful way to design engineered crops since the manipulation of basic characteristics leads to physiological remodeling for plant adaption to different environments. Herein, we discussed the main pathways involved in stress-sensing, signal transduction and plant adaption, highlighting biochemical, physiological and genetic events involved in abiotic stress responses. Finally, we have proposed a list of practice markers for studying plant responses to multiple stresses, highlighting how plant molecular biology, phenotyping and genetic engineering interconnect for creating superior crops.
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Affiliation(s)
- Bruno Paes de Melo
- Trait Development Department, LongPing HighTech, Cravinhos 14140-000, SP, Brazil
| | - Paola de Avelar Carpinetti
- Genetics and Breeding Program, Universidade Federal do Espírito Santo, Alegre 29500-000, ES, Brazil; (P.d.A.C.); (V.S.F.); (M.F.d.S.F.)
| | - Otto Teixeira Fraga
- Applied Biochemistry Program, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil;
| | | | - Vinícius Sartori Fioresi
- Genetics and Breeding Program, Universidade Federal do Espírito Santo, Alegre 29500-000, ES, Brazil; (P.d.A.C.); (V.S.F.); (M.F.d.S.F.)
| | | | - Marcia Flores da Silva Ferreira
- Genetics and Breeding Program, Universidade Federal do Espírito Santo, Alegre 29500-000, ES, Brazil; (P.d.A.C.); (V.S.F.); (M.F.d.S.F.)
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Xiong J, Chen D, Su T, Shen Q, Wu D, Zhang G. Genome-Wide Identification, Expression Pattern and Sequence Variation Analysis of SnRK Family Genes in Barley. PLANTS 2022; 11:plants11070975. [PMID: 35406955 PMCID: PMC9002700 DOI: 10.3390/plants11070975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/02/2023]
Abstract
Sucrose non-fermenting 1 (SNF1)-related protein kinase (SnRK) is a large family of protein kinases that play a significant role in plant stress responses. Although intensive studies have been conducted on SnRK members in some crops, little is known about the SnRK in barley. Using phylogenetic and conserved motif analyses, we discovered 46 SnRK members scattered across barley’s 7 chromosomes and classified them into 3 sub-families. The gene structures of HvSnRKs showed the divergence among three subfamilies. Gene duplication and synteny analyses on the genomes of barley and rice revealed the evolutionary features of HvSnRKs. The promoter regions of HvSnRK family genes contained many ABRE, MBS and LTR elements responding to abiotic stresses, and their expression patterns varied with different plant tissues and abiotic stresses. HvSnRKs could interact with the components of ABA signaling pathway to respond to abiotic stress. Moreover, the haplotypes of HvSnRK2.5 closely associated with drought tolerance were detected in a barley core collection. The current results could be helpful for further exploration of the HvSnRK genes responding to abiotic stress tolerance in barley.
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Affiliation(s)
- Jiangyan Xiong
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
| | - Danyi Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
| | - Tingting Su
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
| | - Qiufang Shen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
| | - Dezhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Correspondence: (D.W.); (G.Z.)
| | - Guoping Zhang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
- Linyi Institute of Agricultural Sciences, Zhejiang University, Linyi 276000, China
- Correspondence: (D.W.); (G.Z.)
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9
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Gu BJ, Tong YK, Wang YY, Zhang ML, Ma GJ, Wu XQ, Zhang JF, Xu F, Li J, Ren F. Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp. PeerJ 2022; 10:e12882. [PMID: 35237467 PMCID: PMC8884064 DOI: 10.7717/peerj.12882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 01/13/2022] [Indexed: 01/11/2023] Open
Abstract
The MYB-CC family is a subtype within the MYB superfamily. This family contains an MYB domain and a predicted coiled-coil (CC) domain. Several MYB-CC transcription factors are involved in the plant's adaptability to low phosphate (Pi) stress. We identified 30, 34, and 55 MYB-CC genes in Brassica rapa, Brassica oleracea, and Brassica napus, respectively. The MYB-CC genes were divided into nine groups based on phylogenetic analysis. The analysis of the chromosome distribution and gene structure revealed that most MYB-CC genes retained the same relative position on the chromosomes and had similar gene structures during allotetraploidy. Evolutionary analysis showed that the ancestral whole-genome triplication (WGT) and the recent allopolyploidy are critical for the expansion of the MYB-CC gene family. The expression patterns of MYB-CC genes were found to be diverse in different tissues of the three Brassica species. Furthermore, the gene expression analysis under low Pi stress revealed that MYB-CC genes may be related to low Pi stress responses. These results may increase our understanding of MYB-CC gene family diversification and provide the basis for further analysis of the specific functions of MYB-CC genes in Brassica species.
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Affiliation(s)
- Bin-Jie Gu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Yi-Kai Tong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - You-Yi Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Mei-Li Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Guang-Jing Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Qin Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Jian-Feng Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Fan Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
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10
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Chen Z, Zhou L, Jiang P, Lu R, Halford NG, Liu C. Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment. BMC Genomics 2021; 22:300. [PMID: 33902444 PMCID: PMC8074225 DOI: 10.1186/s12864-021-07601-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/11/2021] [Indexed: 01/21/2023] Open
Abstract
Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07601-6.
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Affiliation(s)
- Zhiwei Chen
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China
| | - Longhua Zhou
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China
| | - Panpan Jiang
- Shenzhen RealOm ics (Biotech) Co., Ltd., Shenzhen, 518081, China
| | - Ruiju Lu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China
| | - Nigel G Halford
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Chenghong Liu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China. .,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China.
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11
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Wang Y, Liu A. Genomic Characterization and Expression Analysis of the SnRK Family Genes in Dendrobium officinale Kimura et Migo (Orchidaceae). PLANTS 2021; 10:plants10030479. [PMID: 33802577 PMCID: PMC8000535 DOI: 10.3390/plants10030479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 11/16/2022]
Abstract
Sucrose non-fermenting1-related protein kinases (SnRKs) are a type of Ser/Thr protein kinases, and they play an important role in plant life, especially in metabolism and responses to environmental stresses. However, there is limited information on SnRK genes in Dendrobium officinale. In the present research, a total of 36 DoSnRK genes were identified based on genomic data. These DoSnRKs could be grouped into three subfamilies, including 1 member of DoSnRK1, 7 of DoSnRK2, and 28 of DoSnRK3. The gene structure analysis of DoSnRK genes showed that 17 members had no introns, while 16 members contained six or more introns. The conserved domains and motifs were found in the same subfamily. The various cis-elements present in the promoter regions showed that DoSnRK genes could respond to stresses and hormones. Furthermore, the expression patterns of DoSnRK genes in eight tissues were investigated according to RNA sequencing data, indicating that multiple DoSnRK genes were ubiquitously expressed in these tissues. The transcript levels of DoSnRK genes after drought, MeJA, and ABA treatments were analyzed by quantitative real-time PCR and showed that most DoSnRK genes could respond to these stresses. Therefore, genomic characterization and expression analyses provide valuable information on DoSnRK genes for further understanding the functions of SnRKs in plants.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- Bio-Innovation Center of DR PLANT, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
- Correspondence: ; Tel.: +86-87165223125
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