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Gao H, Wu F. Physiological and transcriptomic analysis of tomato in response to sub-optimal temperature stress. PLANT SIGNALING & BEHAVIOR 2024; 19:2332018. [PMID: 38511566 PMCID: PMC10962623 DOI: 10.1080/15592324.2024.2332018] [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: 11/16/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Tomato (Solanum lycopersicum L.) is one of the most important economic crops in China. However, its quality and yield are susceptible to the adverse effects of low temperatures. In our study, two tomato cultivars, showing different tolerance to low temperatures, namely the cold-sensitive tomato cultivar (S708) and cold-tolerant tomato cultivar (T722), were grown at optimal (25/18°C) and sub-optimal (15/10°C) temperature conditions for 5 days. Our study aimed to explore the effect of sub-optimal temperature on fresh weight, chlorophyll content and chlorophyll fluorescence, soluble sugars and proline content of two tomato cultivars. Moreover, we employed RNA-Seq to analyze the transcriptomic response of tomato roots to sub-optimal temperature. The results revealed that S708 showed a more significant reduction in fresh weight, chlorophyll content, photochemical efficiency of PSII (YII), maximum quantum yield of PSII (Fv/Fm), photochemical quenching (qP) and electron transport rate (ETR) compared to T722 under the sub-optimal temperature condition. Notably, T722 maintained higher level of soluble sugars and proline in comparison to S708 uner sub-optimal temperature. RNA-seq data showed that up-regulated DEGs in both tomato cultivars were involved in "plant-pathogen interaction", "MAPK signaling pathway", "plant hormone signal transduction", and "phosphatidylinositol signaling system". Furthermore, "Amino sugar and nucleotide sugar metabolism" pathway was enriched only in T722. Moreover, under sub-optimal temperature, transcription factor genes and osmoregulation genes showed varying degrees of response in both tomato cultivars. Conclusion: In summary, our results offer detailed insights into the response characteristics of tomato to sub-optimal temperature, providing valuable references for the practical management of tomato crops under sub-optimal temperature condition.
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Affiliation(s)
- Huan Gao
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Fengzhi Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China
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2
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Yue H, Chen G, Zhang Z, Guo Z, Zhang Z, Zhang S, Turlings TCJ, Zhou X, Peng J, Gao Y, Zhang D, Shi X, Liu Y. Single-cell transcriptome landscape elucidates the cellular and developmental responses to tomato chlorosis virus infection in tomato leaf. PLANT, CELL & ENVIRONMENT 2024; 47:2660-2674. [PMID: 38619176 DOI: 10.1111/pce.14906] [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: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/23/2024] [Indexed: 04/16/2024]
Abstract
Plant viral diseases compromise the growth and yield of the crop globally, and they tend to be more serious under extreme temperatures and drought climate changes. Currently, regulatory dynamics during plant development and in response to virus infection at the plant cell level remain largely unknown. In this study, single-cell RNA sequencing on 23 226 individual cells from healthy and tomato chlorosis virus-infected leaves was established. The specific expression and epigenetic landscape of each cell type during the viral infection stage were depicted. Notably, the mesophyll cells showed a rapid function transition in virus-infected leaves, which is consistent with the pathological changes such as thinner leaves and decreased chloroplast lamella in virus-infected samples. Interestingly, the F-box protein SKIP2 was identified to play a pivotal role in chlorophyll maintenance during virus infection in tomato plants. Knockout of the SlSKIP2 showed a greener leaf state before and after virus infection. Moreover, we further demonstrated that SlSKIP2 was located in the cytomembrane and nucleus and directly regulated by ERF4. In conclusion, with detailed insights into the plant responses to viral infections at the cellular level, our study provides a genetic framework and gene reference in plant-virus interaction and breeding in the future research.
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Affiliation(s)
- Hao Yue
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Gong Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Zhuo Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhaojiang Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanhong Zhang
- Institute of Vegetable, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Songbai Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ted C J Turlings
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Jing Peng
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yang Gao
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Deyong Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Xiaobin Shi
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Yong Liu
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
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3
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Zhou L, Cao H, Zeng X, Wu Q, Li Q, Martin JJJ, Fu D, Liu X, Li X, Li R, Ye J. Oil Palm AP2 Subfamily Gene EgAP2.25 Improves Salt Stress Tolerance in Transgenic Tobacco Plants. Int J Mol Sci 2024; 25:5621. [PMID: 38891808 PMCID: PMC11171577 DOI: 10.3390/ijms25115621] [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: 04/11/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
AP2/ERF transcription factor genes play an important role in regulating the responses of plants to various abiotic stresses, such as cold, drought, high salinity, and high temperature. However, less is known about the function of oil palm AP2/ERF genes. We previously obtained 172 AP2/ERF genes of oil palm and found that the expression of EgAP2.25 was significantly up-regulated under salinity, cold, or drought stress conditions. In the present study, the sequence characterization and expression analysis for EgAP2.25 were conducted, showing that it was transiently over-expressed in Nicotiana tabacum L. The results indicated that transgenic tobacco plants over-expressing EgAP2.25 could have a stronger tolerance to salinity stress than wild-type tobacco plants. Compared with wild-type plants, the over-expression lines showed a significantly higher germination rate, better plant growth, and less chlorophyll damage. In addition, the improved salinity tolerance of EgAP2.25 transgenic plants was mainly attributed to higher antioxidant enzyme activities, increased proline and soluble sugar content, reduced H2O2 production, and lower MDA accumulation. Furthermore, several stress-related marker genes, including NtSOD, NtPOD, NtCAT, NtERD10B, NtDREB2B, NtERD10C, and NtP5CS, were significantly up-regulated in EgAP2.25 transgenic tobacco plants subjected to salinity stress. Overall, over-expression of the EgAP2.25 gene significantly enhanced salinity stress tolerance in transgenic tobacco plants. This study lays a foundation for further exploration of the regulatory mechanism of the EgAP2.25 gene in conferring salinity tolerance in oil palm.
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Affiliation(s)
- Lixia Zhou
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Hongxing Cao
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xianhai Zeng
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Qiufei Wu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Qihong Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Jerome Jeyakumar John Martin
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Dengqiang Fu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xiaoyu Liu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xinyu Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Rui Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Jianqiu Ye
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
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4
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Li Y, Zhu J, Xu J, Zhang X, Xie Z, Li Z. Effect of cold stress on photosynthetic physiological characteristics and molecular mechanism analysis in cold-resistant cotton (ZM36) seedlings. FRONTIERS IN PLANT SCIENCE 2024; 15:1396666. [PMID: 38803600 PMCID: PMC11128660 DOI: 10.3389/fpls.2024.1396666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024]
Abstract
Low temperature and cold damage seriously hinder the growth, development, and morphogenesis of cotton seedlings. However, the response mechanism of cotton seedlings under cold stress still lacks research. In this study, transcriptome sequencing, gas exchange parameters, and rapid chlorophyll fluorescence parameters were analyzed in leaves of cold-tolerant upland cotton variety "ZM36" under different temperature stress [25°C (T25, CK), 15°C (T15), 10°C (T10), and 4°C (T4)]. The results showed that the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), PSII potential maximum photochemical efficiency (Fv/Fm), and performance index (PIabs) of cotton leaves significantly decreased, and the intercellular CO2 concentration (Ci) and Fo/Fm significantly increased under cold stress. The transcriptome sequencing analysis showed that a total of 13,183 DEGs were involved in the response of cotton seedlings at each temperature point (T25, T15, T10, and T4), mainly involving five metabolic pathways-the phosphatidylinositol signaling system, photosynthesis, photosynthesis antenna protein, carbon fixation in photosynthetic organisms, and carotenoid synthesis. The 1,119 transcription factors were discovered among all the DEGs. These transcription factors involve 59 families, of which 15.8% of genes in the NAC family are upregulated. Through network regulatory analysis, the five candidate genes GhUVR8 (GH_A05G3668), GhPLATZ (GH_A09G2161), GhFAD4-1 (GH_A01G0758), GhNFYA1 (GH_A02G1336), and GhFAD4-2 (GH_D01G0766) were identified in response to cold stress. Furthermore, suppressing the expression level of GhPLATZ by virus-induced gene silencing led to the reduction of low temperature resistance, implying GhPLATZ as a positive regulator of low temperature tolerance. The findings of the study revealed a piece of the complex response mechanism of the cold-tolerant variety "ZM36" to different cold stresses and excavated key candidate genes for low temperature response, which provided support for accelerating the selection and breeding of cotton varieties with low temperature tolerance.
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Affiliation(s)
- Youzhong Li
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shihezi, Xinjiang, China
| | - Jincheng Zhu
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang, China
| | - Jianwei Xu
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Xianliang Zhang
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji, China
| | - Zongming Xie
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shihezi, Xinjiang, China
| | - Zhibo Li
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
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5
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Zhou D, Ding M, Wen S, Tian Q, Zhang X, Fang Y, Xue D. Characterization of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Its Response to Abiotic Stress in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1010. [PMID: 38611539 PMCID: PMC11013768 DOI: 10.3390/plants13071010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/30/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024]
Abstract
Fatty acyl-CoA reductase (FAR) is an important NADPH-dependent enzyme that can produce primary alcohol from fatty acyl-CoA or fatty acyl-carrier proteins as substrates. It plays a pivotal role in plant growth, development, and stress resistance. Herein, we performed genome-wide identification and expression analysis of FAR members in rice using bioinformatics methods. A total of eight OsFAR genes were identified, and the OsFARs were comprehensively analyzed in terms of phylogenetic relationships, duplication events, protein motifs, etc. The cis-elements of the OsFARs were predicted to respond to growth and development, light, hormones, and abiotic stresses. Gene ontology annotation analysis revealed that OsFAR proteins participate in biological processes as fatty acyl-CoA reductase during lipid metabolism. Numerous microRNA target sites were present in OsFARs mRNAs. The expression analysis showed that OsFARs were expressed at different levels during different developmental periods and in various tissues. Furthermore, the expression levels of OsFARs were altered under abiotic stresses, suggesting that FARs may be involved in abiotic stress tolerance in rice. The findings presented here serve as a solid basis for further exploring the functions of OsFARs.
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Affiliation(s)
- Danni Zhou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
| | - Mingyu Ding
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
| | - Shuting Wen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
| | - Quanxiang Tian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
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6
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Hu C, Wang M, Zhu C, Wu S, Li J, Yu J, Hu Z. A transcriptional regulation of ERF15 contributes to ABA-mediated cold tolerance in tomato. PLANT, CELL & ENVIRONMENT 2024; 47:1334-1347. [PMID: 38221812 DOI: 10.1111/pce.14816] [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: 06/05/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
Cold stress is a major meteorological threat to crop growth and yield. Abscisic acid (ABA) plays important roles in plant cold tolerance by activating the expression of cold-responsive genes; however, the underlying transcriptional regulatory module remains unknown. Here, we demonstrated that the cold- and ABA-responsive transcription factor ETHYLENE RESPONSE FACTOR 15 (ERF15) positively regulates ABA-mediated cold tolerance in tomato. Exogenous ABA treatment significantly enhanced cold tolerance in wild-type tomato plants but failed to rescue erf15 mutants from cold stress. Transcriptome analysis showed that ERF15 was associated with the expression of cold-responsive transcription factors such as CBF1 and WRKY6. Further RT-qPCR assays confirmed that the ABA-induced increased in CBF1 and WRKY6 transcripts was suppressed in erf15 mutants when the plants were subjected to cold treatment. Moreover, yeast one-hybrid assays, dual-luciferase assays and electrophoretic mobility shift assays demonstrated that ERF15 activated the transcription of CBF1 and WRKY6 by binding their promoters. Silencing CBF1 or WRKY6 significantly decreased cold tolerance. Overall, our study identified the role of ERF15 in conferring ABA-mediated cold tolerance in tomato plants by activating CBF1 and WRKY6 expression. This study not only broadens our knowledge of the mechanism of ABA-mediated cold tolerance in plants but also highlights ERF15 as an ideal target gene for cold-tolerant crop breeding.
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Affiliation(s)
- Chaoyi Hu
- Hainan Institute, Zhejiang University, Sanya, China
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Mengqi Wang
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Changan Zhu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Shaofang Wu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Jiajia Li
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Jingquan Yu
- Hainan Institute, Zhejiang University, Sanya, China
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Zhangjian Hu
- Hainan Institute, Zhejiang University, Sanya, China
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
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7
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Zhong S, Zhu H, Li W, Wu D, Miao Y, Dong B, Wang Y, Xiao Z, Fang Q, Deng J, Zhao H. DNA methylome analysis reveals novel insights into active hypomethylated regulatory mechanisms of temperature-dependent flower opening in Osmanthus fragrans. HORTICULTURE RESEARCH 2024; 11:uhae010. [PMID: 38464472 PMCID: PMC10923647 DOI: 10.1093/hr/uhae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/01/2024] [Indexed: 03/12/2024]
Abstract
Short-term ambient low temperature (ALT) stimulation is necessary for Osmanthus fragrans to facilitate continued flower opening after floral bud development reaches maturity. DNA methylation, a vital epigenetic modification, regulates various biological processes in response to temperature fluctuations. However, its role in temperature-driven flower opening remains elusive. In this study, we identified the pivotal timeframe during which O. fragrans promptly detected temperature cues. Using whole-genome bisulfite sequencing, we explored global DNA hypomethylation during this phase, with the most significant changes occurring in CHH sequence contexts. Auxin transport inhibitor (TIBA) application revealed that ALT-induced endogenous auxin accumulation promoted peduncle elongation. In our mRNA-seq analysis, we discovered that the differentially expressed genes (DEGs) with hypo-differentially methylated regions (hypo-DMRs) were mainly enriched in auxin and temperature response, RNA processing, and carbohydrate and lipid metabolism. Transcripts of three DNA demethylase genes (OfROS1a, OfDML3, OfDME) showed upregulation. Furthermore, all DNA methylase genes, except OfCMT2b, also displayed increased expression, specifically with two of them, OfCMT3a and OfCMT1, being associated with hypo-DMRs. Promoter assays showed that OfROS1a, with promoters containing low-temperature- and auxin-responsive elements, were activated by ALT and exogenous IAA at low concentrations but inhibited at high concentrations. Overexpression of OfROS1 reduced endogenous auxin levels but enhanced the expression of genes related to auxin response and spliceosome in petunia. Furthermore, OfROS1 promoted sucrose synthesis in petunia corollas. Our data characterized the rapid response of active DNA hypomethylation to ALT and suggested a possible epiregulation of temperature-dependent flower opening in O. fragrans. This study revealed the pivotal role of DNA hypomethylation in O. fragrans during the ALT-responsive phase before flower opening, involving dynamic DNA demethylation, auxin signaling modulation, and a potential feedback loop between hypomethylation and methylation.
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Affiliation(s)
- Shiwei Zhong
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Huijun Zhu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
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8
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Tang Q, Wei S, Zheng X, Tu P, Tao F. APETALA2/ethylene-responsive factors in higher plant and their roles in regulation of plant stress response. Crit Rev Biotechnol 2024:1-19. [PMID: 38267262 DOI: 10.1080/07388551.2023.2299769] [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: 08/18/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024]
Abstract
Plants, anchored throughout their life cycles, face a unique set of challenges from fluctuating environments and pathogenic assaults. Central to their adaptative mechanisms are transcription factors (TFs), particularly the AP2/ERF superfamily-one of the most extensive TF families unique to plants. This family plays instrumental roles in orchestrating diverse biological processes ranging from growth and development to secondary metabolism, and notably, responses to both biotic and abiotic stresses. Distinguished by the presence of the signature AP2 domain or its responsiveness to ethylene signals, the AP2/ERF superfamily has become a nexus of research focus, with increasing literature elucidating its multifaceted roles. This review provides a synoptic overview of the latest research advancements on the AP2/ERF family, spanning its taxonomy, structural nuances, prevalence in higher plants, transcriptional and post-transcriptional dynamics, and the intricate interplay in DNA-binding and target gene regulation. Special attention is accorded to the ethylene response factor B3 subgroup protein Pti5 and its role in stress response, with speculative insights into its functionalities and interaction matrix in tomatoes. The overarching goal is to pave the way for harnessing these TFs in the realms of plant genetic enhancement and novel germplasm development.
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Affiliation(s)
- Qiong Tang
- College of Standardization, China Jiliang University, Hangzhou, China
| | - Sishan Wei
- College of Standardization, China Jiliang University, Hangzhou, China
| | - Xiaodong Zheng
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Pengcheng Tu
- Department of Environmental Health, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Fei Tao
- College of Standardization, China Jiliang University, Hangzhou, China
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9
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Ma Z, Hu L, Jiang W. Understanding AP2/ERF Transcription Factor Responses and Tolerance to Various Abiotic Stresses in Plants: A Comprehensive Review. Int J Mol Sci 2024; 25:893. [PMID: 38255967 PMCID: PMC10815832 DOI: 10.3390/ijms25020893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Abiotic stress is an adverse environmental factor that severely affects plant growth and development, and plants have developed complex regulatory mechanisms to adapt to these unfavourable conditions through long-term evolution. In recent years, many transcription factor families of genes have been identified to regulate the ability of plants to respond to abiotic stresses. Among them, the AP2/ERF (APETALA2/ethylene responsive factor) family is a large class of plant-specific proteins that regulate plant response to abiotic stresses and can also play a role in regulating plant growth and development. This paper reviews the structural features and classification of AP2/ERF transcription factors that are involved in transcriptional regulation, reciprocal proteins, downstream genes, and hormone-dependent signalling and hormone-independent signalling pathways in response to abiotic stress. The AP2/ERF transcription factors can synergise with hormone signalling to form cross-regulatory networks in response to and tolerance of abiotic stresses. Many of the AP2/ERF transcription factors activate the expression of abiotic stress-responsive genes that are dependent or independent of abscisic acid and ethylene in response to abscisic acid and ethylene. In addition, the AP2/ERF transcription factors are involved in gibberellin, auxin, brassinosteroid, and cytokinin-mediated abiotic stress responses. The study of AP2/ERF transcription factors and interacting proteins, as well as the identification of their downstream target genes, can provide us with a more comprehensive understanding of the mechanism of plant action in response to abiotic stress, which can improve plants' ability to tolerate abiotic stress and provide a more theoretical basis for increasing plant yield under abiotic stress.
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Affiliation(s)
- Ziming Ma
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China;
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Lanjuan Hu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China;
| | - Wenzhu Jiang
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China;
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Cui T, Zang S, Sun X, Zhang J, Su Y, Wang D, Wu G, Chen R, Que Y, Lin Q, You C. Molecular identification and functional characterization of a transcription factor GeRAV1 from Gelsemium elegans. BMC Genomics 2024; 25:22. [PMID: 38166591 PMCID: PMC10759518 DOI: 10.1186/s12864-023-09919-9] [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: 08/25/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Gelsemium elegans is a traditional Chinese medicinal plant and temperature is one of the key factors affecting its growth. RAV (related to ABI3/VP1) transcription factor plays multiple roles in higher plants, including the regulation of plant growth, development, and stress response. However, RAV transcription factor in G. elegans has not been reported. RESULTS In this study, three novel GeRAV genes (GeRAV1-GeRAV3) were identified from the transcriptome of G. elegans under low temperature stress. Phylogenetic analysis showed that GeRAV1-GeRAV3 proteins were clustered into groups II, IV, and V, respectively. RNA-sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) analyses indicated that the expression of GeRAV1 and GeRAV2 was increased in response to cold stress. Furthermore, the GeRAV1 gene was successfully cloned from G. elegans leaf. It encoded a hydrophilic, unstable, and non-secretory protein that contained both AP2 and B3 domains. The amino acid sequence of GeRAV1 protein shared a high similarity of 81.97% with Camptotheca acuminata CaRAV. Subcellular localization and transcriptional self-activation experiments demonstrated that GeRAV1 was a nucleoprotein without self-activating activity. The GeRAV1 gene was constitutively expressed in the leaves, stems, and roots of the G. elegans, with the highest expression levels in roots. In addition, the expression of the GeRAV1 gene was rapidly up-regulated under abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA) stresses, suggesting that it may be involved in hormonal signaling pathways. Moreover, GeRAV1 conferred improved cold and sodium chloride tolerance in Escherichia coli Rosetta cells. CONCLUSIONS These findings provided a foundation for further understanding on the function and regulatory mechanism of the GeRAV1 gene in response to low-temperature stress in G. elegans.
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Affiliation(s)
- Tianzhen Cui
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinlu Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guran Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruiqi Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qing Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- The Second People's Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350003, China.
| | - Chuihuai You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- The Second People's Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350003, China.
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Kumari A, Sharma P, Rani M, Laxmi V, Sahil, Sahi C, Satturu V, Katiyar-Agarwal S, Agarwal M. Meta-QTL and ortho analysis unravels the genetic architecture and key candidate genes for cold tolerance at seedling stage in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:93-108. [PMID: 38435852 PMCID: PMC10902255 DOI: 10.1007/s12298-024-01412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/13/2023] [Accepted: 01/10/2024] [Indexed: 03/05/2024]
Abstract
Rice, a critical cereal crop, grapples with productivity challenges due to its inherent sensitivity to low temperatures, primarily during the seedling and booting stages. Recognizing the polygenic complexity of cold stress signaling in rice, a meta-analysis was undertaken, focusing on 20 physiological traits integral to cold tolerance. This initiative allowed the consolidation of genetic data from 242 QTLs into 58 meta-QTLs, thereby significantly constricting the genetic and physical intervals, with 84% of meta-QTLs (MQTLs) being reduced to less than 2 Mb. The list of 10,505 genes within these MQTLs, was further refined utilizing expression datasets to pinpoint 46 pivotal genes exhibiting noteworthy differential regulation during cold stress. The study underscored the presence of several TFs such as WRKY, NAC, CBF/DREB, MYB, and bHLH, known for their roles in cold stress response. Further, ortho-analysis involving maize, barley, and Arabidopsis identified OsWRKY71, among others, as a prospective candidate for enhancing cold tolerance in diverse crop plants. In conclusion, our study delineates the intricate genetic architecture underpinning cold tolerance in rice and propounds significant candidate genes, offering crucial insights for further research and breeding strategies focused on fortifying crops against cold stress, thereby bolstering global food resilience. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01412-1.
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Affiliation(s)
- Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Mamta Rani
- Department of Botany, University of Delhi, Delhi, India
| | - Vijay Laxmi
- Department of Botany, University of Delhi, Delhi, India
| | - Sahil
- Department of Botany, University of Delhi, Delhi, India
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066 India
| | - Vanisree Satturu
- Professor Jayashankar, Telangana State Agricultural University, Hyderabad, India
| | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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Zhang J, Zhao H, Chen L, Lin J, Wang Z, Pan J, Yang F, Ni X, Wang Y, Wang Y, Li R, Pi E, Wang S. Multifaceted roles of WRKY transcription factors in abiotic stress and flavonoid biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1303667. [PMID: 38169626 PMCID: PMC10758500 DOI: 10.3389/fpls.2023.1303667] [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: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Increasing biotic and abiotic stresses are seriously impeding the growth and yield of staple crops and threatening global food security. As one of the largest classes of regulators in vascular plants, WRKY transcription factors play critical roles governing flavonoid biosynthesis during stress responses. By binding major W-box cis-elements (TGACCA/T) in target promoters, WRKYs modulate diverse signaling pathways. In this review, we optimized existing WRKY phylogenetic trees by incorporating additional plant species with WRKY proteins implicated in stress tolerance and flavonoid regulation. Based on the improved frameworks and documented results, we aim to deduce unifying themes of distinct WRKY subfamilies governing specific stress responses and flavonoid metabolism. These analyses will generate experimentally testable hypotheses regarding the putative functions of uncharacterized WRKY homologs in tuning flavonoid accumulation to enhance stress resilience.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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13
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Cai X, Chen Y, Wang Y, Shen Y, Yang J, Jia B, Sun X, Sun M. A comprehensive investigation of the regulatory roles of OsERF096, an AP2/ERF transcription factor, in rice cold stress response. PLANT CELL REPORTS 2023; 42:2011-2022. [PMID: 37812280 DOI: 10.1007/s00299-023-03079-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
KEY MESSAGE OsERF096 negatively regulates rice cold tolerance and mediates IAA biosynthesis and signaling under cold stress. The APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors play important roles in regulating plant tolerance to abiotic stress. OsERF096 was previously identified as a direct target of miR1320, and was suggested to negatively regulate rice cold tolerance. In this study, we performed RNA-sequencing and targeted metabolomics assays to reveal the regulatory roles of OsERF096 in cold stress response. GO and KEGG analysis of differentially expressed genes showed that the starch and sucrose metabolism, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly enriched. Quantification analysis confirmed a significant difference in sugar contents among WT and OsERF096 transgenic lines under cold treatment. Targeted metabolomics analysis uncovered that IAA accumulation and signaling were modified by OsERF096 in response to cold stress. Expectedly, qRT-PCR assays confirmed significant OsIAAs and OsARFs expression changes in OsERF096 transgenic lines. Finally, we identified three targets of OsERF096 based on RNA-seq, qRT-PCR, and dual-LUC assays. In summary, these results revealed the multiple regulatory roles of OsERF096 in cold stress response.
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Affiliation(s)
- Xiaoxi Cai
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yue Chen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yan Wang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yang Shen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Junkai Yang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Bowei Jia
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| | - Mingzhe Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
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Xu C, Gui Z, Huang Y, Yang H, Luo J, Zeng X. Integrated Transcriptomics and Metabolomics Analyses Provide Insights into Qingke in Response to Cold Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18345-18358. [PMID: 37966343 DOI: 10.1021/acs.jafc.3c07005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The survival and productivity of qingke in high altitude (>4300 m, average yearly temperature <0 °C) of the Tibetan Plateau are significantly impacted by low-temperature stress. Uncovering the mechanisms underlying low-temperature stress response in cold-tolerant qingke varieties is crucial for qingke breeding. Herein, we conducted a comprehensive transcriptomic and metabolomic analysis on cold-sensitive (ZQ) and cold-tolerant (XL) qingke varieties under chilling and freezing treatments and identified lipid metabolism pathways as enriched in response to freezing treatment. Additionally, a significant positive correlation was observed between the expression of C-repeat (CRT) binding factor 10A (HvCBF10A) and Gly-Asp-Ser-Leu-motif lipase (HvGDSL) and the accumulation of multiple lipids. Functional analysis confirmed that HvCBF10A directly binds to HvGDSL, and silencing HvCBF10A resulted in a significant decrease in both HvGDSL and lipid levels, consequently impairing the cold tolerance. Overall, HvCBF10A and HvGDSL are functional units in actively regulating lipid metabolism to enhance freezing stress tolerance in qingke.
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Affiliation(s)
- Congping Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory of Barley Biology and Genetic Improvement on QingHai-Tibet Plateau, Ministry of Agriculture, Lhasa 850002, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850002, China
| | - Zihao Gui
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yuxiao Huang
- Hainan Yazhou Bay grain Laboratory, Sanya 572025, China
| | - Haizhen Yang
- Key Laboratory of Barley Biology and Genetic Improvement on QingHai-Tibet Plateau, Ministry of Agriculture, Lhasa 850002, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850002, China
| | - Jie Luo
- Hainan Yazhou Bay grain Laboratory, Sanya 572025, China
| | - Xingquan Zeng
- Key Laboratory of Barley Biology and Genetic Improvement on QingHai-Tibet Plateau, Ministry of Agriculture, Lhasa 850002, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850002, China
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Rao X, Qian Z, Xie L, Wu H, Luo Q, Zhang Q, He L, Li F. Genome-Wide Identification and Expression Pattern of MYB Family Transcription Factors in Erianthus fulvus. Genes (Basel) 2023; 14:2128. [PMID: 38136950 PMCID: PMC10743048 DOI: 10.3390/genes14122128] [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: 10/24/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
MYB family genes have many functions and are widely involved in plant abiotic-stress responses. Erianthus fulvus is an important donor material for stress-resistance genes in sugarcane breeding. However, the MYB family genes in E. fulvus have not been systematically investigated. In this study, 133 EfMYB genes, including 48 Ef1R-MYB, 84 EfR2R3-MYB and 1 Ef3R-MYB genes, were identified in the E. fulvus genome. Among them, the EfR2R3-MYB genes were classified into 20 subgroups. In addition, these EfMYB genes were unevenly distributed across 10 chromosomes. A total of 4 pairs of tandemly duplicated EfMYB genes and 21 pairs of segmentally duplicated EfMYB genes were identified in the E. fulvus genome. Protein-interaction analysis predicted that 24 EfMYB proteins had potential interactions with 14 other family proteins. The EfMYB promoter mainly contains cis-acting elements related to the hormone response, stress response, and light response. Expression analysis showed that EfMYB39, EfMYB84, and EfMYB124 could be significantly induced using low-temperature stress. EfMYB30, EfMYB70, EfMYB81, and EfMYB101 responded positively to drought stress. ABA treatment significantly induced EfMYB1, EfMYB30, EfMYB39, EfMYB84, and EfMYB130. All nine genes were induced using MeJA treatment. These results provide comprehensive information on EfMYB genes and can serve as a reference for further studies of gene function.
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Affiliation(s)
- Xibing Rao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Zhenfeng Qian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Linyan Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Huaying Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Quan Luo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Qiyue Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Lilian He
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Fusheng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
- The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Kunming 650201, China
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming 650201, China
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Pandey P, Tripathi A, Dwivedi S, Lal K, Jhang T. Deciphering the mechanisms, hormonal signaling, and potential applications of endophytic microbes to mediate stress tolerance in medicinal plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1250020. [PMID: 38034581 PMCID: PMC10684941 DOI: 10.3389/fpls.2023.1250020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
The global healthcare market in the post-pandemic era emphasizes a constant pursuit of therapeutic, adaptogenic, and immune booster drugs. Medicinal plants are the only natural resource to meet this by supplying an array of bioactive secondary metabolites in an economic, greener and sustainable manner. Driven by the thrust in demand for natural immunity imparting nutraceutical and life-saving plant-derived drugs, the acreage for commercial cultivation of medicinal plants has dramatically increased in recent years. Limited resources of land and water, low productivity, poor soil fertility coupled with climate change, and biotic (bacteria, fungi, insects, viruses, nematodes) and abiotic (temperature, drought, salinity, waterlogging, and metal toxicity) stress necessitate medicinal plant productivity enhancement through sustainable strategies. Plants evolved intricate physiological (membrane integrity, organelle structural changes, osmotic adjustments, cell and tissue survival, reclamation, increased root-shoot ratio, antibiosis, hypersensitivity, etc.), biochemical (phytohormones synthesis, proline, protein levels, antioxidant enzymes accumulation, ion exclusion, generation of heat-shock proteins, synthesis of allelochemicals. etc.), and cellular (sensing of stress signals, signaling pathways, modulating expression of stress-responsive genes and proteins, etc.) mechanisms to combat stresses. Endophytes, colonizing in different plant tissues, synthesize novel bioactive compounds that medicinal plants can harness to mitigate environmental cues, thus making the agroecosystems self-sufficient toward green and sustainable approaches. Medicinal plants with a host set of metabolites and endophytes with another set of secondary metabolites interact in a highly complex manner involving adaptive mechanisms, including appropriate cellular responses triggered by stimuli received from the sensors situated on the cytoplasm and transmitting signals to the transcriptional machinery in the nucleus to withstand a stressful environment effectively. Signaling pathways serve as a crucial nexus for sensing stress and establishing plants' proper molecular and cellular responses. However, the underlying mechanisms and critical signaling pathways triggered by endophytic microbes are meager. This review comprehends the diversity of endophytes in medicinal plants and endophyte-mediated plant-microbe interactions for biotic and abiotic stress tolerance in medicinal plants by understanding complex adaptive physiological mechanisms and signaling cascades involving defined molecular and cellular responses. Leveraging this knowledge, researchers can design specific microbial formulations that optimize plant health, increase nutrient uptake, boost crop yields, and support a resilient, sustainable agricultural system.
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Affiliation(s)
- Praveen Pandey
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Division of Plant Breeding and Genetic Resource Conservation, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Arpita Tripathi
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Faculty of Education, Teerthanker Mahaveer University, Moradabad, India
| | - Shweta Dwivedi
- Division of Plant Breeding and Genetic Resource Conservation, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kanhaiya Lal
- Division of Plant Breeding and Genetic Resource Conservation, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Tripta Jhang
- Division of Plant Breeding and Genetic Resource Conservation, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
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Wang S, Shen Y, Deng D, Guo L, Zhang Y, Nie Y, Du Y, Zhao X, Ye X, Huang J, Huang H, Zhu JK, Wu W. Orthogroup and phylotranscriptomic analyses identify transcription factors involved in the plant cold response: A case study of Arabidopsis BBX29. PLANT COMMUNICATIONS 2023; 4:100684. [PMID: 37674317 PMCID: PMC10721519 DOI: 10.1016/j.xplc.2023.100684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/08/2023]
Abstract
C-repeat binding factors (CBFs) are well-known transcription factors (TFs) that regulate plant cold acclimation. RNA sequencing (RNA-seq) data from diverse plant species provide opportunities to identify other TFs involved in the cold response. However, this task is challenging because gene gain and loss has led to an intertwined community of co-orthologs and in-paralogs between and within species. Using orthogroup (closely related homologs) analysis, we identified 10,549 orthogroups in five representative eudicots. A phylotranscriptomic analysis of cold-treated seedlings from eudicots identified 35 high-confidence conserved cold-responsive transcription factor orthogroups (CoCoFos). These 35 CoCoFos included the well-known cold-responsive regulators CBFs, HSFC1, ZAT6/10, and CZF1 among others. We used Arabidopsis BBX29 for experimental validation. Expression and genetic analyses showed that cold-induction of BBX29 is CBF- and abscisic acid-independent, and BBX29 is a negative regulator of cold tolerance. Integrative RNA-seq and Cleavage Under Targets and Tagmentation followed by sequencing analyses revealed that BBX29 represses a set of cold-induced TFs (ZAT12, PRR9, RVE1, MYB96, etc.). Altogether, our analysis yielded a library of eudicot CoCoFos and demonstrated that BBX29 is a negative regulator of cold tolerance in Arabidopsis.
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Affiliation(s)
- Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China
| | - Yirong Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China
| | - Yixian Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China
| | - Yuqi Nie
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China
| | - Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China
| | - Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China
| | - Xiaoxue Ye
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China
| | - Huahong Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China.
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an 311300, Hangzhou, China.
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Yang S, Zhou J, Li Y, Wu J, Ma C, Chen Y, Sun X, Wu L, Liang X, Fu Q, Xu Z, Li L, Huang Z, Zhu J, Jia X, Ye X, Chen R. AP2/EREBP Pathway Plays an Important Role in Chaling Wild Rice Tolerance to Cold Stress. Int J Mol Sci 2023; 24:14441. [PMID: 37833888 PMCID: PMC10572191 DOI: 10.3390/ijms241914441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Cold stress is the main factor limiting rice production and distribution. Chaling wild rice can survive in cold winters. AP2/EREBP is a known transcription factor family associated with abiotic stress. We identified the members of the AP2/EREBP transcription factor family in rice, maize, and Arabidopsis, and conducted collinearity analysis and gene family analysis. We used Affymetrix array technology to analyze the expression of AP2/EREBP family genes in Chaling wild rice and cultivated rice cultivar Pei'ai64S, which is sensitive to cold. According to the GeneChip results, the expression levels of AP2/EREBP genes in Chaling wild rice were different from those in Pei'ai64S; and the increase rate of 36 AP2/EREBP genes in Chaling wild rice was higher than that in Pei'ai64S. Meanwhile, the MYC elements in cultivated rice and Chaling wild rice for the Os01g49830, Os03g08470, and Os03g64260 genes had different promoter sequences, resulting in the high expression of these genes in Chaling wild rice under low-temperature conditions. Furthermore, we analyzed the upstream and downstream genes of the AP2/EREBP transcription factor family and studied the conservation of these genes. We found that the upstream transcription factors were more conserved, indicating that these upstream transcription factors may be more important in regulating cold stress. Meanwhile, we found the expression of AP2/EREBP pathway genes was significantly increased in recombinant inbred lines from Nipponbare crossing with Chaling wild rice, These results suggest that the AP2/EREBP signaling pathway plays an important role in Chaling wild rice tolerance to cold stress.
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Affiliation(s)
- Songjin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Jingming Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Yaqi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Jiacheng Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Chuan Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Yulin Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Xingzhuo Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Lingli Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Xin Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Qiuping Fu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Zhengjun Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Lihua Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Zhengjian Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Jianqing Zhu
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
| | - Xiaomei Jia
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
| | - Xiaoying Ye
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
| | - Rongjun Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
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Ding H, Yang Z, Zai Z, Feng K, Wang L, Yue Y, Yang X. Genome-Wide Analysis of ZAT Gene Family in Osmanthus fragrans and the Function Exploration of OfZAT35 in Cold Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2346. [PMID: 37375971 DOI: 10.3390/plants12122346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/04/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Osmanthus fragrans is a popular ornamental and odorant plant with high commercial value, but its cultivation and exploitation are limited by low temperature. The ZAT (zinc finger of Arabidopsis thaliana) genes as a subclass of the C2H2-type zinc finger proteins (C2H2-ZFP) family play essential roles in various abiotic stresses. However, their roles in cold stress response in O. fragrans remain unclear. This study identified 38 OfZATs, which could be divided into 5 subgroups based on the phylogenetic tree, with OfZATs in the same subgroup harboring similar gene structures and motif patterns. In addition, 49 segmental and 5 tandem duplication events were detected among OfZAT genes, while some OfZAT genes exhibited specific expression patterns in different tissues. Furthermore, two OfZATs were induced in salt stress and eight OfZATs responded to cold stress. Interestingly, OfZAT35 showed a continuously increasing expression trend under cold stress, while its protein showed nucleus localization with no transcriptional activation activity. Transiently transformed tobacco overexpressing OfZAT35 exhibited a significantly higher relative electrolyte leakage (REL) level and increased activities of superoxide dismutase (SOD), peroxidase (POD), and Ascorbate peroxidase (APX), while there was significantly decreased activity of catalase (CAT). Moreover, CAT, DREB3, and LEA5, which are associated with cold stress, were dramatically decreased after cold treatment in transiently transformed tobacco, suggesting that overexpression of OfZAT35 negatively regulated cold stress. This study provides a basis for exploring the roles of ZAT genes and contributes to uncovering the mechanism of ZAT-mediated cold stress response in O. fragrans.
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Affiliation(s)
- Huifen Ding
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhandong Yang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhouying Zai
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Keyi Feng
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Lianggui Wang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuanzheng Yue
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiulian Yang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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20
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Edrisi Maryan K, Farrokhi N, Samizadeh Lahiji H. Cold-responsive transcription factors in Arabidopsis and rice: A regulatory network analysis using array data and gene co-expression network. PLoS One 2023; 18:e0286324. [PMID: 37289769 PMCID: PMC10249815 DOI: 10.1371/journal.pone.0286324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
Plant growth and development can be influenced by cold stress. Responses of plants to cold are regulated in part by transcription factors (TFs) and microRNAs, which their determination would be necessary in comprehension of the corresponding molecular cues. Here, transcriptomes of Arabidopsis and rice were analyzed to computationally determine TFs and microRNAs that are differentially responsive to cold treatment, and their co-expression networks were established. Among 181 Arabidopsis and 168 rice differentially expressed TF genes, 37 (26 novel) were up- and 16 (8 novel) were downregulated. Common TF encoding genes were from ERF, MYB, bHLH, NFY, bZIP, GATA, HSF and WRKY families. NFY A4/C2/A10 were the significant hub TFs in both plants. Phytohormone responsive cis-elements such as ABRE, TGA, TCA and LTR were the common cis-elements in TF promoters. Arabidopsis had more responsive TFs compared to rice possibly due to its greater adaptation to ranges geographical latitudes. Rice had more relevant miRNAs probably because of its bigger genome size. The interacting partners and co-expressed genes were different for the common TFs so that of the downstream regulatory networks and the corresponding metabolic pathways. Identified cold-responsive TFs in (A + R) seemed to be more engaged in energy metabolism esp. photosynthesis, and signal transduction, respectively. At post-transcriptional level, miR5075 showed to target many identified TFs in rice. In comparison, the predictions showed that identified TFs are being targeted by diverse groups of miRNAs in Arabidopsis. Novel TFs, miRNAs and co-expressed genes were introduced as cold-responsive markers that can be harnessed in future studies and development of crop tolerant varieties.
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Affiliation(s)
- Khazar Edrisi Maryan
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
- Department of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran
| | - Naser Farrokhi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
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21
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Wu H, He Q, Wang Q. Advances in Rice Seed Shattering. Int J Mol Sci 2023; 24:ijms24108889. [PMID: 37240235 DOI: 10.3390/ijms24108889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Seed shattering is an important trait that wild rice uses to adapt to the natural environment and maintain population reproduction, and weedy rice also uses it to compete with the rice crop. The loss of shattering is a key event in rice domestication. The degree of shattering is not only one of the main reasons for rice yield reduction but also affects its adaptability to modern mechanical harvesting methods. Therefore, it is important to cultivate rice varieties with a moderate shattering degree. In this paper, the research progress on rice seed shattering in recent years is reviewed, including the physiological basis, morphological and anatomical characteristics of rice seed shattering, inheritance and QTL/gene mapping of rice seed shattering, the molecular mechanism regulating rice seed shattering, the application of seed-shattering genes, and the relationship between seed-shattering genes and domestication.
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Affiliation(s)
- Hao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qi He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Quan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Agricultural Sciences, Nankai University, Tianjin 300071, China
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22
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Akbari A, Ismaili A, Amirbakhtiar N, Pouresmael M, Shobbar ZS. Genome-wide transcriptional profiling provides clues to molecular mechanisms underlying cold tolerance in chickpea. Sci Rep 2023; 13:6279. [PMID: 37072529 PMCID: PMC10113226 DOI: 10.1038/s41598-023-33398-3] [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: 11/29/2022] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
Chickpea is an important food legume cultivated in several countries. A sudden drop in autumn temperature, freezing winter temperature, and late spring cold events result in significant losses in chickpea production. The current study used RNA sequencing of two cold tolerant (Saral) and sensitive (ILC533) Kabuli chickpea genotypes to identify cold tolerance-associated genes/pathways. A total of 200.85 million raw reads were acquired from the leaf samples by Illumina sequencing, and around 86% of the clean reads (199 million) were mapped to the chickpea reference genome. The results indicated that 3710 (1980 up- and 1730 down-regulated) and 3473 (1972 up- and 1501 down-regulated) genes were expressed differentially under cold stress in the tolerant and sensitive genotypes, respectively. According to the GO enrichment analysis of uniquely down-regulated genes under cold stress in ILC533, photosynthetic membrane, photosystem II, chloroplast part, and photosystem processes were enriched, revealing that the photosynthesis is severely sensitive to cold stress in this sensitive genotype. Many remarkable transcription factors (CaDREB1E, CaMYB4, CaNAC47, CaTCP4, and CaWRKY33), signaling/regulatory genes (CaCDPK4, CaPP2C6, CaMKK2, and CaHSFA3), and protective genes (CaCOR47, CaLEA3, and CaGST) were identified among the cold-responsive genes of the tolerant genotype. These findings would help improve cold tolerance across chickpea genotypes by molecular breeding or genetic engineering.
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Affiliation(s)
- Alireza Akbari
- 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.
| | - Nazanin Amirbakhtiar
- Genetic Research Department, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Masoumeh Pouresmael
- Genetic Research Department, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization, Karaj, Iran.
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Gusain S, Joshi S, Joshi R. Sensing, signalling, and regulatory mechanism of cold-stress tolerance in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107646. [PMID: 36958153 DOI: 10.1016/j.plaphy.2023.107646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Cold stress is a crucial environmental factor influencing growth and distribution and possessing yield penalties. To survive in the cold, plants have evolved to use a range of molecular mechanisms. The major regulatory pathway under low-temperature stress involves the conversion of external stimulus into an internal signal that triggers a defence mechanism through a transcriptional cascade to counter stress. Cold-receptive mechanism and cell signalling involve cold-related signalling molecules, sensors, calcium signals, MAPK cascade, and ICE-COR-CBF pathway that modulate signal transduction in plants. Of these, the ICE-CBF-COR signalling is considered to be an important regulator for cold-stress acclimation. ICE stimulates acclimation to cold and plays a pivotal role in regulating CBF-mediated cold-tolerance mechanism. Thus, CBFs regulate COR gene expression by binding to its promoter. Similarly, the C-repeat binding factor-dependent signalling cascade also stimulates osmotic stress-regulatory gene expression. This review elucidates the regulatory mechanism underlying cold stress, i.e., signal molecules, cold receptors, signal-transduction pathways, metabolic regulation under cold stress, and crosstalk of regulatory pathways with other abiotic stresses in plants. The results may pave the way for crop improvement in low-temperature environments.
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Affiliation(s)
- Suman Gusain
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India
| | - Shubham Joshi
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India
| | - Rohit Joshi
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India.
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24
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Advances of Apetala2/Ethylene Response Factors in Regulating Development and Stress Response in Maize. Int J Mol Sci 2023; 24:ijms24065416. [PMID: 36982510 PMCID: PMC10049130 DOI: 10.3390/ijms24065416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/28/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Apetala2/ethylene response factor (AP2/ERF) is one of the largest families of transcription factors, regulating growth, development, and stress response in plants. Several studies have been conducted to clarify their roles in Arabidopsis and rice. However, less research has been carried out on maize. In this review, we systematically identified the AP2/ERFs in the maize genome and summarized the research progress related to AP2/ERF genes. The potential roles were predicted from rice homologs based on phylogenetic and collinear analysis. The putative regulatory interactions mediated by maize AP2/ERFs were discovered according to integrated data sources, implying that they involved complex networks in biological activities. This will facilitate the functional assignment of AP2/ERFs and their applications in breeding strategy.
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Li C, Mao B, Wang K, Xu L, Fan L, Wang Y, Li Y, Ma Y, Wang L, Liu L. RsERF40 contributes to cold stress tolerance and cell expansion of taproot in radish ( Raphanus sativus L.). HORTICULTURE RESEARCH 2023; 10:uhad013. [PMID: 36968181 PMCID: PMC10031735 DOI: 10.1093/hr/uhad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of taproots are inhibited by cold stress in radish (Raphanus sativus L.). Ethylene-responsive element binding factors (ERF) are key participators in the cold stress response and growth regulation of plants. However, the function of ERF genes in cold tolerance and root development in radish remains elusive. Here, we showed that the secondary growth of radish taproots was inhibited by cold stress. Comparative transcriptome analysis demonstrated that the RsERF40 gene is an important regulator of the cold stress response and root growth regulation. The cold tolerance of transgenic Arabidopsis plants overexpressing the RsERF40 gene was significantly improved. Overexpressing RsERF40 in the cold-sensitive radish genotype and silencing RsERF40 in the cold-tolerant radish genotype indicated that RsERF40 was beneficial for alleviating oxidative damage under cold stress in radish. Transgenic Arabidopsis seedlings showed an increase in the elongation and radial growth of dark-grown roots. RT-qPCR analysis showed that the expression of the cold-related genes (CORs) RsCOR78 and RsCOR413PM1 and the cell wall strengthening-related genes RsCESA6 and RsEXPB3 was upregulated in transgenic Arabidopsis seedlings. Yeast one-hybrid (Y1H) and dual-luciferase reporter assays (DLA) revealed that RsERF40 directly regulates RsCOR78, RsCOR413PM1, RsCESA6 and RsEXPB3 expression, illustrating that RsERF40 enhances cold tolerance and taproot growth by modulating osmotic adjustment and cell wall mechanical strength in radish. In this study, the RsERF40-regulon was firstly found to be a new cold response pathway independent of the CBF-COR pathway conferring cold stress tolerance with increasing radish taproot growth. These results provided novel insight into the molecular mechanism underlying cold stress response and would facilitate the genetic improvement of cold tolerance in radish and other root vegetable crops.
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Affiliation(s)
- Cui Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Baozhen Mao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yinbo Ma
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Lun Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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Chen N, Pan L, Yang Z, Su M, Xu J, Jiang X, Yin X, Wang T, Wan F, Chi X. A MYB-related transcription factor from peanut, AhMYB30, improves freezing and salt stress tolerance in transgenic Arabidopsis through both DREB/CBF and ABA-signaling pathways. FRONTIERS IN PLANT SCIENCE 2023; 14:1136626. [PMID: 36925750 PMCID: PMC10013196 DOI: 10.3389/fpls.2023.1136626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/14/2023] [Indexed: 06/12/2023]
Abstract
Abiotic stresses such as salinity and low temperature have serious impact on peanut growth and yield. The present work investigated the function of a MYB-related transcription factor gene AhMYB30 obtained from peanut under salt and low temperature stresses by transgenic methods. The results indicated that the overexpression of AhMYB30 in Arabidopsis could enhance the resistance of transgenic plants to freezing and salt stresses. The expression of stress-response genes RD29A (Response-to-Dehydration 29A), COR15A (Cold-Regulated 15A), KIN1 (Kinesin 1) and ABI2 (Abscisic acid Insensitive 2) increased in transgenic plants compared with in wild-type. Subcellular localization and transcriptional autoactivation validation demonstrated that AhMYB30 has essential features of transcription factors. Therefore, AhMYB30 may increase salt and freezing stress tolerance as the transcription factor (TF) in Arabidopsis through both DREB/CBF and ABA-signaling pathways. Our results lay the theoretical foundation for exploring stress resistance mechanisms of peanut and offering novel genetic resources for molecular breeding.
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Affiliation(s)
- Na Chen
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Lijuan Pan
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Zhen Yang
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Maowen Su
- Department of Animal and Plant Quarantine, Qingdao Customs, Qingdao, China
| | - Jing Xu
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Xiao Jiang
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Xiangzhen Yin
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Tong Wang
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Feifei Wan
- Division for Guidance of Cooperative Economy, Binzhou Agricultural Technology Extension Center, Binzhou, China
| | - Xiaoyuan Chi
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
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Ren C, Fan P, Li S, Liang Z. Advances in understanding cold tolerance in grapevine. PLANT PHYSIOLOGY 2023:kiad092. [PMID: 36789447 DOI: 10.1093/plphys/kiad092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/06/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely low temperatures, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
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Kaushal P, Ali N, Saini S, Pati PK, Pati AM. Physiological and molecular insight of microbial biostimulants for sustainable agriculture. FRONTIERS IN PLANT SCIENCE 2023; 14:1041413. [PMID: 36794211 PMCID: PMC9923114 DOI: 10.3389/fpls.2023.1041413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Increased food production to cater the need of growing population is one of the major global challenges. Currently, agro-productivity is under threat due to shrinking arable land, increased anthropogenic activities and changes in the climate leading to frequent flash floods, prolonged droughts and sudden fluctuation of temperature. Further, warm climatic conditions increase disease and pest incidences, ultimately reducing crop yield. Hence, collaborated global efforts are required to adopt environmentally safe and sustainable agro practices to boost crop growth and productivity. Biostimulants appear as a promising means to improve growth of plants even under stressful conditions. Among various categories of biostimulants, microbial biostimulants are composed of microorganisms such as plant growth-promoting rhizobacteria (PGPR) and/or microbes which stimulate nutrient uptake, produce secondary metabolites, siderophores, hormones and organic acids, participate in nitrogen fixation, imparts stress tolerance, enhance crop quality and yield when applied to the plants. Though numerous studies convincingly elucidate the positive effects of PGPR-based biostimulants on plants, yet information is meagre regarding the mechanism of action and the key signaling pathways (plant hormone modulations, expression of pathogenesis-related proteins, antioxidants, osmolytes etc.) triggered by these biostimulants in plants. Hence, the present review focuses on the molecular pathways activated by PGPR based biostimulants in plants facing abiotic and biotic challenges. The review also analyses the common mechanisms modulated by these biostimulants in plants to combat abiotic and biotic stresses. Further, the review highlights the traits that have been modified through transgenic approach leading to physiological responses akin to the application of PGPR in the target plants.
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Affiliation(s)
- Priya Kaushal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP, India
| | - Nilofer Ali
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shivani Saini
- Department of Botany, Goswami Ganesh Dutta Sanatan Dharma College, Chandigarh, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Aparna Maitra Pati
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Dong R, Luo B, Tang L, Wang QX, Lu ZJ, Chen C, Yang F, Wang S, He J. A comparative transcriptomic analysis reveals a coordinated mechanism activated in response to cold acclimation in common vetch (Vicia sativa L.). BMC Genomics 2022; 23:814. [PMID: 36482290 PMCID: PMC9733113 DOI: 10.1186/s12864-022-09039-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Due to its strong abiotic stress tolerance, common vetch is widely cultivated as a green manure and forage crop in grass and crop rotation systems. The comprehensive molecular mechanisms activated in common vetch during cold adaptation remain unknown. RESULTS We investigated physiological responses and transcriptome profiles of cold-sensitive (Lanjian No. 1) and cold-tolerant (Lanjian No. 3) cultivars during cold acclimation to explore the molecular mechanisms of cold acclimation. In total, 2681 and 2352 differentially expressed genes (DEGs) were identified in Lanjian No. 1 and Lanjian No. 3, respectively; 7532 DEGs were identified in both lines. DEGs involved in "plant hormone signal transduction" were significantly enriched during cold treatment, and 115 DEGs involved in cold-processed hormone signal transduction were identified. Common vetch increased the level of indoleacetic acid (IAA) by upregulating the transcriptional regulator Aux/IAA and downregulating GH3, endowing it with stronger cold tolerance. An auxin-related DEG was overexpressed in yeast and shown to possess a biological function conferring cold tolerance. CONCLUSION This study identifies specific genes involved in Ca2+ signaling, redox regulation, circadian clock, plant hormones, and transcription factors whose transcriptional differentiation during cold acclimation may improve cold tolerance and contributes to the understanding of common and unique molecular mechanisms of cold acclimation in common vetch. The candidate genes identified here also provide valuable resources for further functional genomic and breeding studies.
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Affiliation(s)
- Rui Dong
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Ben Luo
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Li Tang
- grid.428986.90000 0001 0373 6302School of Tropical Crops, Hainan University, Haikou, China
| | - Qiu-xia Wang
- grid.32566.340000 0000 8571 0482State Key Laboratory of Grassland Agro-ecosystems, China, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhong-Jie Lu
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Chao Chen
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Feng Yang
- Grassland Technology Experiment and Extension Station, Guiyang, China
| | - Song Wang
- Grassland Technology Experiment and Extension Station, Guiyang, China
| | - Jin He
- grid.443382.a0000 0004 1804 268XCollege of Agriculture, Guizhou University, Guiyang, China
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Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie ( Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development. Int J Mol Sci 2022; 23:ijms232315117. [PMID: 36499437 PMCID: PMC9736067 DOI: 10.3390/ijms232315117] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
AP2/ERF transcription factors (TFs) are one of the largest superfamilies in plants, and play vital roles in growth and response to biotic/abiotic stresses. Although the AP2/ERF family has been extensively characterized in many species, very little is known about this family in ramie (Boehmeria nivea L.). In this study, 138 AP2/ERF TFs were identified from the ramie genome and were grouped into five subfamilies, including the AP2 (19), RAV (5), Soloist (1), ERF (77), and DREB (36). Unique motifs were found in the DREB/ERF subfamily members, implying significance to the AP2/ERF TF functions in these evolutionary branches. Segmental duplication events were found to play predominant roles in the BnAP2/ERF TF family expansion. Light-, stress-, and phytohormone-responsive elements were identified in the promoter region of BnAP2/ERF genes, with abscisic acid response elements (ABRE), methyl jasmonate response elements, and the dehydration response element (DRE) being dominant. The integrated transcriptome and quantitative real-time PCR (qPCR) revealed 12 key BnAP2/ERF genes positively responding to waterlogging. Five of the genes are also involved in ramet development, with two (BnERF-30 and BnERF-32) further showing multifunctional roles. The protein interaction prediction analysis further verified their crosstalk mechanism in coordinating waterlogging resistance and ramet development. Our study provides new insights into the presence of AP2/ERF TFs in ramie, and provides candidate AP2/ERF TFs for further studies on breeding varieties with coupling between water stress tolerance and high yield.
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Khoso MA, Hussain A, Ritonga FN, Ali Q, Channa MM, Alshegaihi RM, Meng Q, Ali M, Zaman W, Brohi RD, Liu F, Manghwar H. WRKY transcription factors (TFs): Molecular switches to regulate drought, temperature, and salinity stresses in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1039329. [PMID: 36426143 PMCID: PMC9679293 DOI: 10.3389/fpls.2022.1039329] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 06/01/2023]
Abstract
The WRKY transcription factor (TF) belongs to one of the major plant protein superfamilies. The WRKY TF gene family plays an important role in the regulation of transcriptional reprogramming associated with plant stress responses. Change in the expression patterns of WRKY genes or the modifications in their action; participate in the elaboration of numerous signaling pathways and regulatory networks. WRKY proteins contribute to plant growth, for example, gamete formation, seed germination, post-germination growth, stem elongation, root hair growth, leaf senescence, flowering time, and plant height. Moreover, they play a key role in many types of environmental signals, including drought, temperature, salinity, cold, and biotic stresses. This review summarizes the current progress made in unraveling the functions of numerous WRKY TFs under drought, salinity, temperature, and cold stresses as well as their role in plant growth and development.
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Affiliation(s)
- Muneer Ahmed Khoso
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
- Department of Life Science, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Amjad Hussain
- College of Plant Science and Technology, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | | | - Qurban Ali
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | | | - Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Qinglin Meng
- Department of Biology and Food Engineering, Bozhou University, Bozhou, China
| | - Musrat Ali
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad Pakistan, Islamabad, Pakistan
| | - Wajid Zaman
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Rahim Dad Brohi
- Department of Animal Reproduction/Theriogenology, Faculty of Veterinary Science, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Pakistan
| | - Fen Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
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Li C, Sun Y, Li J, Zhang T, Zhou F, Song Q, Liu Y, Brestic M, Chen TH, Yang X. ScCBF1 plays a stronger role in cold, salt and drought tolerance than StCBF1 in potato (Solanum tuberosum). JOURNAL OF PLANT PHYSIOLOGY 2022; 278:153806. [PMID: 36115270 DOI: 10.1016/j.jplph.2022.153806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Solanum tuberosum (St) and Solanum commersonii (Sc) are two potato varieties with different freezing tolerance. Among them, St is a freezing-sensitive variety and. Sc is a cold-resistant wild potato. CBF/DREB family members mainly function in response to freezing stress. In order to explore the different roles of St C-Repeat Binding Factor1 (StCBF1) and Sc C-Repeat Binding Factor1 (ScCBF1) in potato plants (Solanum tuberosum) under stress conditions, two kinds of potato lines were obtained with ScCBF1 and StCBF1 overexpressing respectively. Phenotypes analysis showed that both overexpressing ScCBF1 and StCBF1 caused smaller leaves, and reduced tuber yield. While the limited phenotypes of StCBF1 lines were more severe than that of ScCBF lines. After freezing treatment, StCBF1 over expression plants grown better than WT plants and worse than ScCBF1 over expression plants. Specifically, compared with wild-type lines, overexpressing ScCBF1 could up-regulate fatty acid desaturase genes, key enzyme of Calvin cycle genes, and antioxidant enzyme genes. Both ScCBF1 and StCBF1 lines showed higher PSII activity, thus maintaining a higher photosynthetic rate under cold stress. In addition, we also found that overexpression ScCBF1 and StCBF1 could also enhance the drought and salt tolerance in potato. In summary, ScCBF1 plays a stronger role in cold, salt, and drought tolerance than StCBF1 in potato (Solanum tuberosum).
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Affiliation(s)
- Chongyang Li
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, China
| | - Yalu Sun
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, China
| | - Jian Li
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, China
| | - Tianpeng Zhang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, China
| | - Fengli Zhou
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, China
| | - Qiping Song
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, China
| | - Yang Liu
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, China
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, A. Hlinku 2, Nitra, 94976, Slovak Republic
| | - Tony Hh Chen
- Department of Horticulture, ALS 4017, Oregon State University, Corvallis, OR, 97331, USA
| | - Xinghong Yang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, China.
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Guo Z, Ma W, Cai L, Guo T, Liu H, Wang L, Liu J, Ma B, Feng Y, Liu C, Pan G. Comparison of anther transcriptomes in response to cold stress at the reproductive stage between susceptible and resistant Japonica rice varieties. BMC PLANT BIOLOGY 2022; 22:500. [PMID: 36284279 PMCID: PMC9597962 DOI: 10.1186/s12870-022-03873-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Rice is one of the most important cereal crops in the world but is susceptible to cold stress (CS). In this study, we carried out parallel transcriptomic analysis at the reproductive stage on the anthers of two Japonica rice varieties with contrasting CS resistance: cold susceptible Longjing11 (LJ11) and cold resistant Longjing25 (LJ25). RESULTS According to the obtained results, a total of 16,762 differentially expressed genes (DEGs) were identified under CS, including 7,050 and 14,531 DEGs in LJ25 and LJ11, respectively. Examining gene ontology (GO) enrichment identified 35 up- and 39 down-regulated biological process BP GO terms were significantly enriched in the two varieties, with 'response to heat' and 'response to cold' being the most enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 33 significantly enriched pathways. Only the carbon metabolism and amino acid biosynthesis pathways with down-regulated DEGs were enriched considerably in LJ11, while the plant hormone signal transduction pathway (containing 153 DEGs) was dramatically improved. Eight kinds of plant hormones were detected in the pathway, while auxin, abscisic acid (ABA), salicylic acid (SA), and ethylene (ETH) signaling pathways were found to be the top four pathways with the most DEGs. Furthermore, the protein-protein interaction (PPI) network analysis identified ten hub genes (co-expressed gene number ≥ 30), including six ABA-related genes. Various DEGs (such as OsDREB1A, OsICE1, OsMYB2, OsABF1, OsbZIP23, OsCATC, and so on) revealed distinct expression patterns among rice types when the DEGs between LJ11 and LJ25 were compared, indicating that they are likely responsible for CS resistance of rice in cold region. CONCLUSION Collectively, our findings provide comprehensive insights into complex molecular mechanisms of CS response and can aid in CS resistant molecular breeding of rice in cold regions.
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Affiliation(s)
- Zhenhua Guo
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Wendong Ma
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China
| | - Lijun Cai
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, 154007, Jiamusi, Heilongjiang, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Linan Wang
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China
| | - Junliang Liu
- Jiamusi Longjing Seed Industry Co., LTD, 154026, Jiamusi, Heilongjiang, China
| | - Bo Ma
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, 161006, Qiqihar, Heilongjiang, China
| | - Yanjiang Feng
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China.
| | - Chuanxue Liu
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China.
| | - Guojun Pan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China.
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Physiological and Proteomic Responses of Cassava to Short-Term Extreme Cool and Hot Temperature. PLANTS 2022; 11:plants11172307. [PMID: 36079689 PMCID: PMC9460903 DOI: 10.3390/plants11172307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Temperature is one of the most critical factors affecting cassava metabolism and growth. This research was conducted to investigate the effects of short-term exposure to extreme cool (15 °C) and hot (45 °C) temperature on photosynthesis, biochemical and proteomics changes in potted plants of two cassava cultivars, namely Rayong 9 and Kasetsart 50. One-month-old plants were exposed to 15, 30, and 45 °C for 60 min in a temperature chamber under light intensity of 700 μmol m−2 s−1. Compared to the optimum temperature (30 °C), exposure to 15 °C resulted in 28% reduction in stomatal conductance (gs) and 62% reduction in net photosynthesis rate (Pn). In contrast, gs under 45 °C increased 2.61 folds, while Pn was reduced by 50%. The lower Pn but higher electron transport rate (ETR) of the cold-stressed plants indicated that a greater proportion of electrons was transported via alternative pathways to protect chloroplast from being damaged by reactive oxygen species (ROS). Moreover, malondialdehyde (MDA) contents, a marker related to the amount of ROS, were significantly higher at low temperature. Proteomics analysis revealed some interesting differentially expressed proteins (DEPs) including annexin, a multi-functional protein functioning in early events of heat stress signaling. In response to low-temperature stress, AP2/ERF domain-containing protein (a cold-related transcription factor) and glutaredoxin domain-containing protein (a component of redox signaling network under cold stress) were detected. Taken together, both cultivars were more sensitive to low than high temperature. Moreover, Rayong 9 displayed higher Pn under both temperature stresses, and was more efficient in controlling ROS under cold stress than Kasetsart 50.
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Tang X, Li J, Liu L, Jing H, Zuo W, Zeng Y. Transcriptome Analysis Provides Insights into Potentilla bifurca Adaptation to High Altitude. Life (Basel) 2022; 12:life12091337. [PMID: 36143374 PMCID: PMC9503701 DOI: 10.3390/life12091337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Potentilla bifurca is widely distributed in Eurasia, including the Tibetan Plateau. It is a valuable medicinal plant in the Tibetan traditional medicine system, especially for the treatment of diabetes. This study investigated the functional gene profile of Potentilla bifurca at different altitudes by RNA-sequencing technology, including de novo assembly of 222,619 unigenes from 405 million clean reads, 57.64% of which were annotated in Nr, GO, KEGG, Pfam, and Swiss-Prot databases. The most significantly differentially expressed top 50 genes in the high-altitude samples were derived from plants that responded to abiotic stress, such as peroxidase, superoxide dismutase protein, and the ubiquitin-conjugating enzyme. Pathway analysis revealed that a large number of DEGs encode key enzymes involved in secondary metabolites, including phenylpropane and flavonoids. In addition, a total of 298 potential genomic SSRs were identified in this study, which provides information on the development of functional molecular markers for genetic diversity assessment. In conclusion, this study provides the first comprehensive assessment of the Potentilla bifurca transcriptome. This provides new insights into coping mechanisms for non-model organisms surviving in harsh environments at high altitudes, as well as molecular evidence for the selection of superior medicinal plants.
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Affiliation(s)
- Xun Tang
- College of Life Sciences, Qinghai Normal University, Xining 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jinping Li
- College of Life Sciences, Qinghai Normal University, Xining 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Likuan Liu
- College of Life Sciences, Qinghai Normal University, Xining 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Hui Jing
- Qinghai Agricultural Technology Extension Station, Xining 810007, China
| | - Wenming Zuo
- College of Life Sciences, Qinghai Normal University, Xining 810008, China
| | - Yang Zeng
- College of Life Sciences, Qinghai Normal University, Xining 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
- Correspondence:
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Zhou Y, Wen L, Liao L, Lin S, Zheng E, Li Y, Zhang Y. Comparative transcriptome analysis unveiling reactive oxygen species scavenging system of Sonneratia caseolaris under salinity stress. FRONTIERS IN PLANT SCIENCE 2022; 13:953450. [PMID: 35958196 PMCID: PMC9358527 DOI: 10.3389/fpls.2022.953450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Many mangrove forests have undergone major changes as a result of human activity and global climate change. Sonneratia caseolaris is a common tree located in inner mangroves, and its range extends inland along tidal creeks, as far as the influence of salinity extends. This study investigated the physiological and molecular response mechanisms of S. caseolaris by analyzing its antioxidant defense capacity, including its differentially expressed genes (DEGs) under similar salt stress conditions. Salt treatment significantly affected the osmoprotectants and lipid peroxidation in S. caseolaris seedlings, which increased proline (Pro) content by 31.01-54.90% during all sample periods and decreased malonaldehyde (MDA) content by 12.81 and 18.17% at 25 and 40 days under 3.0% NaCl treatment. Antioxidant enzyme activities increased significantly following 3.0% NaCl treatment. Transcriptome analysis following De novo assembly showed 26,498 matched unigenes. The results showed that 1,263 DEGs responded to transcription factors (TFs) and plant phytohormones and mediated oxidoreductase activity to scavenge reactive oxygen species (ROS) in the control vs. 3.0% NaCl comparison. In addition, the transcription levels of genes associated with auxin and ethylene signal transduction also changed. Under salt stress, ROS scavenging genes (POD, CAT, and APX) and part of AP2, MYB, NAC, C2C2, bHLH, and WRKY TFs were upregulated. This study identified important pathways and candidate genes involved in S. caseolaris salinity tolerance and provided suggestions for further research into the mechanisms of salt tolerance in S. caseolaris.
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Shafi KM, Sowdhamini R. Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members. BMC Genomics 2022; 23:516. [PMID: 35842574 PMCID: PMC9288012 DOI: 10.1186/s12864-022-08751-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/07/2022] [Indexed: 11/25/2022] Open
Abstract
Background Plant species from Rosaceae family are economically important. One of the major environmental factors impacting those species is cold stress. Although several Rosaceae plant genomes have recently been sequenced, there have been very few research conducted on cold upregulated genes and their promoter binding sites. In this study, we used computational approaches to identify and analyse potential cold stress response genes across ten Rosaceae family members. Results Cold stress upregulated gene data from apple and strawberry were used to identify syntelogs in other Rosaceae species. Gene duplication analysis was carried out to better understand the distribution of these syntelog genes in different Rosaceae members. A total of 11,145 popular abiotic stress transcription factor-binding sites were identified in the upstream region of these potential cold-responsive genes, which were subsequently categorised into distinct transcription factor (TF) classes. MYB classes of transcription factor binding site (TFBS) were abundant, followed by bHLH, WRKY, and AP2/ERF. TFBS patterns in the promoter regions were compared among these species and gene families, found to be quite different even amongst functionally related syntelogs. A case study on important cold stress responsive transcription factor family, AP2/ERF showed less conservation in TFBS patterns in the promoter regions. This indicates that syntelogs from the same group may be comparable at the gene level but not at the level of cis-regulatory elements. Therefore, for such genes from the same family, different repertoire of TFs could be recruited for regulation and expression. Duplication events must have played a significant role in the similarity of TFBS patterns amongst few syntelogs of closely related species. Conclusions Our study overall suggests that, despite being from the same gene family, different combinations of TFs may play a role in their regulation and expression. The findings of this study will provide information about potential genes involved in the cold stress response, which will aid future functional research of these gene families involved in many important biological processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08751-x.
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Affiliation(s)
- K Mohamed Shafi
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.,The University of Trans-Disciplinary Health Sciences & Technology (TDU), Yelahanka, Bangalore, Karnataka, 560064, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India. .,Molecular BIophysics Unit, Indian Institute of Science, 560012, Bangalore, India.
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Wan R, Song J, Lv Z, Qi X, Han X, Guo Q, Wang S, Shi J, Jian Z, Hu Q, Chen Y. Genome-Wide Identification and Comprehensive Analysis of the AP2/ERF Gene Family in Pomegranate Fruit Development and Postharvest Preservation. Genes (Basel) 2022; 13:genes13050895. [PMID: 35627280 PMCID: PMC9141937 DOI: 10.3390/genes13050895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/13/2022] [Indexed: 02/07/2023] Open
Abstract
Pomegranate (Punica granatum L.) is a kind of fruit with significant economic, ecological and health values. AP2/ERF transcription factors belong to a large group of factors mainly found in plants and play key roles in plant growth and development. However, AP2/ERF genes in pomegranate and their implication in development and postharvest preservation have been little described. In this study, 116 PgAP2/ERF genes in pomegranate were identified and renamed based on their chromosomal distributions. Phylogenetic relationship with genes from other species, structures, duplications, annotations, cis-elements in promoter sequences, and protein-protein interaction networks among PgAP2/ERF proteins were comprehensively explored. Expression analysis revealed several PgAP2/ERFs associated with the phenotypes of pomegranate seed hardness, including PgAP2/ERF5, PgAP2/ERF36, PgAP2/ERF58, and PgAP2/ERF86. Subsequent analysis indicated that many differentially expressed PgAP2/ERF genes are potentially important regulators of pomegranate fruit development. Furthermore, expression of more than one-half of PgAP2/ERFs was repressed in ‘Tunisian soft seed’ pomegranate fruit under low-temperature cold storage. The results showed that 1-MCP implicated in promoting postharvest preservation of ‘Tunisian soft seed’ pomegranate upregulated the PgAP2/ERF4, PgAP2/ERF15, PgAP2/ERF26, PgAP2/ERF30, PgAP2/ERF35 and PgAP2/ERF45 genes compared to those under low-temperature cold storage. This indicates that these genes are important candidate genes involved in pomegranate postharvest preservation. In summary, the findings of the present study provide an important basis for characterizing the PgAP2/ERF family genes and provide information on the candidate genes involved in pomegranate fruit development and postharvest preservation.
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Affiliation(s)
- Ran Wan
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Jinhui Song
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Zhenyang Lv
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Xingcheng Qi
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Xuemeng Han
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Qiang Guo
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Sa Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Jiangli Shi
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Zaihai Jian
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Qingxia Hu
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
- Correspondence:
| | - Yanhui Chen
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
- Henan Key Laboratory of Fruit and Cucurbit Biology, College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
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Overexpression of LT, an Oncoprotein Derived from the Polyomavirus SV40, Promotes Somatic Embryogenesis in Cotton. Genes (Basel) 2022; 13:genes13050853. [PMID: 35627238 PMCID: PMC9140353 DOI: 10.3390/genes13050853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/21/2022] [Accepted: 04/21/2022] [Indexed: 12/04/2022] Open
Abstract
Although genetic transformation has opened up a new era for cotton molecular breeding, it still suffers from the limitation problem of long transformation periods, which slows down the generation of new cotton germplasms. In this study, LT gene (SV40 large T antigen), which promotes the transformation efficiency of animal cells, was codon-optimized. Its overexpression vector was transformed into cotton. It was observed that EC (embryogenic callus) formation period was 33% shorter and transformation efficiency was slightly higher in the LT T0 generation than that of control. RNA-seq data of NEC (non-embryonic callus) and EC from LT and control revealed that more DEGs (differential expression genes) in NEC were identified than that of EC, indicating LT mainly functioned in NEC. Further KEGG, GO, and transcription factor analyses showed that DEGs were significantly enriched in brassinosteroid biosynthesis pathways and that bHLH, MYB, and AP2/ERF were the top three gene families, which are involved in EC formation. In addition, the key genes related to the auxin pathway were differentially expressed only in LT overexpression NEC, which caused early response, biosynthesis, and transportation of the hormone, resulting in EC earlier formation. In summary, the results demonstrated that LT can promote somatic embryogenesis in cotton, which provides a new strategy for improving cotton transformation and shortening EC formation time.
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Wang S, Zhang S. Selection of the Reference Gene for Expression Normalization in Salsola ferganica under Abiotic Stress. Genes (Basel) 2022; 13:genes13040571. [PMID: 35456377 PMCID: PMC9029158 DOI: 10.3390/genes13040571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/01/2023] Open
Abstract
Salsola ferganica is a natural desert herbaceous plant in the arid area of western and northwestern China. Because of its salt tolerance and drought resistance, it is of great significance in desert afforestation and sand-fixing capacity. There has been much research on the genes involved in plants under desert stresses in recent years. The application of the best internal reference genes for standardization was a critical procedure in analyzing the gene expression under different types. Even so, the reference gene has not been reported in the application of gene expression normalization of S. ferganica. In this study, nine reference genes (TUA-1726, TUA-1760, TUB, GAPDH, ACT, 50S, HSC70, APT, and U-box) in S. ferganica were adopted and analyzed under six different treatments (ABA, heat, cold, NaCl, methyl viologen (MV), and PEG). The applicability of candidate genes was evaluated by statistical software, including geNorm, NormFinder, BestKeeper, and RefFinder, based on their stability values in all the treatments. These results indicated that the simultaneous selection of two stable reference genes would fully standardize the optimization of the normalization research. To verify the feasibility of the above internal reference genes, the CT values of AP2/ERF transcription factor family genes were standardized using the most (ACT) and least (GAPDH) stable reference genes in S. ferganica seedlings under six abiotic stresses. The research showed that HSC70 and U-box were the most appropriate reference genes in ABA stressed samples, and ACT and U-box genes were the optimal references for heat-stressed samples. TUA-1726 and U-box showed the smallest value in gene expression levels of cold treatment. The internal reference groups of the best applicability for the other samples were U-box and ACT under NaCl treatment, ACT and TUA-1726 under MV stress, HSC70 and TUB under PEG treatment, and ACT in all samples. ACT and U-box showed higher stability than the other genes based on the comprehensive stability ranking of RefFinder, as determined by the geometric mean in this study. These results will contribute to later gene expression studies in other closely related species and provide an important foundation for gene expression analysis in S. ferganica.
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Affiliation(s)
- Shuran Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
| | - Sheng Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
- College of Forestry, Northwest A&F University, Xianyang 712100, China
- Correspondence:
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The Caucasian Clover Gene TaMYC2 Responds to Abiotic Stress and Improves Tolerance by Increasing the Activity of Antioxidant Enzymes. Genes (Basel) 2022; 13:genes13020329. [PMID: 35205373 PMCID: PMC8871790 DOI: 10.3390/genes13020329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 02/06/2023] Open
Abstract
Abiotic stress affects metabolic processes in plants and restricts plant growth and development. In this experiment, Caucasian clover (Trifolium ambiguum M. Bieb.) was used as a material, and the CDS of TaMYC2, which is involved in regulating the response to abiotic stress, was cloned. The CDS of TaMYC2 was 726 bp in length and encoded 241 amino acids. The protein encoded by TaMYC2 was determined to be unstable, be highly hydrophilic, and contain 23 phosphorylation sites. Subcellular localization results showed that TaMYC2 was localized in the nucleus. TaMYC2 responded to salt, alkali, cold, and drought stress and could be induced by IAA, GA3, and MeJA. By analyzing the gene expression and antioxidant enzyme activity in plants before and after stress, we found that drought and cold stress could induce the expression of TaMYC2 and increase the antioxidant enzyme activity. TaMYC2 could also induce the expression of ROS scavenging-related and stress-responsive genes and increase the activity of antioxidant enzymes, thus improving the ability of plants to resist stress. The results of this experiment provide references for subsequent in-depth exploration of both the function of TaMYC2 in and the molecular mechanism underlying the resistance of Caucasian clover.
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Bashir SS, Hussain A, Hussain SJ, Wani OA, Zahid Nabi S, Dar NA, Baloch FS, Mansoor S. Plant drought stress tolerance: understanding its physiological, biochemical and molecular mechanisms. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2021.2020161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Sheikh Shanawaz Bashir
- Department of Botany, School of Chemical and Life Science, Jamia Hamdard University, New Delhi, India
| | - Anjuman Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Sofi Javed Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Owais Ali Wani
- Department of Soil Science, FoA, Wadura, Sopore, Sher-e-Kashmir University of Agricultural Sciences & Technology Shalimar Kashmir, Srinagar, Jammu and Kashmir, India
| | - Sheikh Zahid Nabi
- Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Niyaz A. Dar
- ARSSSS Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology, Shalimar Kashmir, Srinagar, Jammu and Kashmir, India
| | - Faheem Shehzad Baloch
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Sheikh Mansoor
- Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
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Qu Z, Jia Y, Duan Y, Chen H, Wang X, Zheng H, Liu H, Wang J, Zou D, Zhao H. Integrated Isoform Sequencing and Dynamic Transcriptome Analysis Reveals Diverse Transcripts Responsible for Low Temperature Stress at Anther Meiosis Stage in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:795834. [PMID: 34975985 PMCID: PMC8718874 DOI: 10.3389/fpls.2021.795834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Low temperatures stress is one of the important factors limiting rice yield, especially during rice anther development, and can cause pollen sterility and decrease grain yield. In our study, low-temperature stress decreased pollen viability and spikelet fertility by affecting the sugar, nitrogen and amino acid contents of anthers. We performed RNA-seq and ISO-seq experiments to study the genome-wide transcript expression profiles in low-temperature anthers. A total of 4,859 differentially expressed transcripts were detected between the low-temperature and control groups. Gene ontology enrichment analysis revealed significant terms related to cold tolerance. Hexokinase and glutamate decarboxylase participating in starch and sucrose metabolism may play important roles in the response to cold stress. Using weighted gene co-expression network analysis, nine hub transcripts were found that could improve cold tolerance throughout the meiosis period of rice: Os02t0219000-01 (interferon-related developmental regulator protein), Os01t0218350-00 (tetratricopeptide repeat-containing thioredoxin), Os08t0197700-00 (luminal-binding protein 5), Os11t0200000-01 (histone deacetylase 19), Os03t0758700-01 (WD40 repeat domain-containing protein), Os06t0220500-01 (7-deoxyloganetin glucosyltransferase), Pacbio.T01382 (sucrose synthase 1), Os01t0172400-01 (phospholipase D alpha 1), and Os01t0261200-01 (NAC domain-containing protein 74). In the PPI network, the protein minichromosome maintenance 4 (MCM4) may play an important role in DNA replication induced by cold stress.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
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Wang H, Bi Y, Gao Y, Yan Y, Yuan X, Xiong X, Wang J, Liang J, Li D, Song F. A Pathogen-Inducible Rice NAC Transcription Factor ONAC096 Contributes to Immunity Against Magnaprothe oryzae and Xanthomonas oryzae pv. oryzae by Direct Binding to the Promoters of OsRap2.6, OsWRKY62, and OsPAL1. FRONTIERS IN PLANT SCIENCE 2021; 12:802758. [PMID: 34956298 PMCID: PMC8702954 DOI: 10.3389/fpls.2021.802758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The rice NAC transcriptional factor family harbors 151 members, and some of them play important roles in rice immunity. Here, we report the function and molecular mechanism of a pathogen-inducible NAC transcription factor, ONAC096, in rice immunity against Magnaprothe oryzae and Xanthomonas oryzae pv. oryzae. Expression of ONAC096 was induced by M. oryzae and by abscisic acid and methyl jasmonate. ONAC096 had the DNA binding ability to NAC recognition sequence and was found to be a nucleus-localized transcriptional activator whose activity depended on its C-terminal. CRISPR/Cas9-mediated knockout of ONAC096 attenuated rice immunity against M. oryzae and X. oryzae pv. oryzae as well as suppressed chitin- and flg22-induced reactive oxygen species burst and expression of PTI marker genes OsWRKY45 and OsPAL4; by contrast, overexpression of ONAC096 enhanced rice immunity against these two pathogens and strengthened chitin- or flg22-induced PTI. RNA-seq transcriptomic profiling and qRT-PCR analysis identified a small set of defense and signaling genes that are putatively regulated by ONAC096, and further biochemical analysis validated that ONAC096 could directly bind to the promoters of OsRap2.6, OsWRKY62, and OsPAL1, three known defense and signaling genes that regulate rice immunity. ONAC096 interacts with ONAC066, which is a positive regulator of rice immunity. These results demonstrate that ONAC096 positively contributes to rice immunity against M. oryzae and X. oryzae pv. oryzae through direct binding to the promoters of downstream target genes including OsRap2.6, OsWRKY62, and OsPAL1.
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Affiliation(s)
- Hui Wang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Bi
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yizhou Gao
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuqing Yan
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xi Yuan
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Xiaohui Xiong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiajing Wang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiayu Liang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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