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Mishra P, Roggen A, Ljung K, Albani MC, Vayssières A. Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials. FRONTIERS IN PLANT SCIENCE 2024; 15:1352830. [PMID: 38693930 PMCID: PMC11062184 DOI: 10.3389/fpls.2024.1352830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.
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Affiliation(s)
- Priyanka Mishra
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, India
| | - Adrian Roggen
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Maria C. Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Rijk Zwaan, De Lier, Netherlands
| | - Alice Vayssières
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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Lin W, Wu S, Wei M. Ubiquitylome analysis reveals the involvement of ubiquitination in the cold responses of banana seedling leaves. J Proteomics 2023; 288:104994. [PMID: 37598917 DOI: 10.1016/j.jprot.2023.104994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Low temperature is a crucial environmental factor limiting the productivity and distribution of banana. Ubiquitination (Kub) is one of the main posttranslational modifications (PTMs) involved in plant responses to abiotic stresses. However, little information is available on the effects of Kub on banana under cold stress. In this study, we used label-free quantification (LFQ) to identify changes in the protein expression and Kub levels in banana seedling leaves after chilling treatment. In total, 4156 proteins, 1089 ubiquitinated proteins and 2636 Kub sites were quantified. Western blot assays showed that Kub was abundant in leaves after low-temperature treatment. Our results show that the proteome and ubiquitylome were negatively correlated, indicating that Kub could be involved in the degradation of proteins in banana after chilling treatment. Based on bioinformatics analysis, low-temperature stress-related signals and metabolic pathways such as cold acclimation, glutathione metabolism, calcium signaling, and photosynthesis signaling were identified. In addition, we found that transcription factors and chromatin remodeling factors related to low-temperature stress were ubiquitinated. Overall, our work presents the first systematic analysis of the Kub proteome in banana under cold stress and provides support for future studies on the regulatory mechanisms of Kub during the cold stress response in plants. SIGNIFICANCE: Banana is a typical tropical fruit tree with poor low-temperature tolerance,however, the role of PTMs such as Kub in the cold response of banana remains unclear. This study highlights the fact that the effects of low-temperature on proteome and ubiquitylome in the banana seedling leaves, we discussed the correlation between transcriptome and proteome, ubiquitylome and proteome, and we analyzed the expression and the changes of ubiquitination levels of low-temperature related proteins and pathway after chilling treatment, and we found that transcription factors and chromatin remodeling factors related to low-temperature stress were ubiquitinated. This study provides new insights into the ubiquitination pathway of banana under cold stress.
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Affiliation(s)
- Wei Lin
- Subtropical Agriculture Research Institute, Fujian Academy of Agricultural Sciences, Zhangzhou, Fujian 363005, People's Republic of China.
| | - Shuijin Wu
- Subtropical Agriculture Research Institute, Fujian Academy of Agricultural Sciences, Zhangzhou, Fujian 363005, People's Republic of China
| | - Mi Wei
- Academy of Sericulture Sciences, Nanning, Guangxi 530007, People's Republic of China
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Wang YJ, Wu LL, Sun MH, Li Z, Tan XF, Li JA. Transcriptomic and metabolomic insights on the molecular mechanisms of flower buds in responses to cold stress in two Camellia oleifera cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1126660. [PMID: 36968351 PMCID: PMC10037702 DOI: 10.3389/fpls.2023.1126660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION The Camellia oleifera (C. oleifera) cultivars 'Huashuo' (HS) and 'Huaxin' (HX) are new high-yielding and economically valuable cultivars that frequently encounter prolonged cold weather during the flowering period, resulting in decreased yields and quality. The flower buds of HS sometimes fail to open or open incompletely under cold stress, whereas the flower buds of HX exhibit delayed opening but the flowers and fruits rarely drop. METHODS In this study, flower buds at the same development stage of two C. oleifera cultivars were used as test materials for a combination of physiological, transcriptomic and metabolomic analyses, to unravel the different cold regulatory mechanisms between two cultivars of C. oleifera. RESULTS AND DISCUSSION Key differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) involved in sugar metabolism, phenylpropanoid biosynthesis, and hormone signal transduction were significantly higher in HX than in HS, which is consistent with phenotypic observations from a previous study. The results indicate that the flower buds of HX are less affected by long-term cold stress than those of HS, and that cold resistance in C. oleifera cultivars varies among tissues or organs.This study will provide a basis for molecular markers and molecular breeding of C. oleifera.
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Affiliation(s)
- Ya-Jun Wang
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, and the Key Laboratory of Non-Wood Forest Products, Forestry Ministry, Central South University of Forestry and Technology, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, China
- Camellia Oil Tree Research Institute of Central South University of Forestry and Technology, Changsha, China
- The Belt and Road International Union Research Center for Tropical Arid Non-wood Forest in Hunan Province, Changsha, China
| | - Ling-Li Wu
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, and the Key Laboratory of Non-Wood Forest Products, Forestry Ministry, Central South University of Forestry and Technology, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, China
- Camellia Oil Tree Research Institute of Central South University of Forestry and Technology, Changsha, China
- The Belt and Road International Union Research Center for Tropical Arid Non-wood Forest in Hunan Province, Changsha, China
| | - Min-hong Sun
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, and the Key Laboratory of Non-Wood Forest Products, Forestry Ministry, Central South University of Forestry and Technology, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, China
| | - Ze Li
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, and the Key Laboratory of Non-Wood Forest Products, Forestry Ministry, Central South University of Forestry and Technology, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, China
- Camellia Oil Tree Research Institute of Central South University of Forestry and Technology, Changsha, China
- The Belt and Road International Union Research Center for Tropical Arid Non-wood Forest in Hunan Province, Changsha, China
| | - Xiao-Feng Tan
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, and the Key Laboratory of Non-Wood Forest Products, Forestry Ministry, Central South University of Forestry and Technology, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, China
- Camellia Oil Tree Research Institute of Central South University of Forestry and Technology, Changsha, China
- The Belt and Road International Union Research Center for Tropical Arid Non-wood Forest in Hunan Province, Changsha, China
| | - Jian-An Li
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, and the Key Laboratory of Non-Wood Forest Products, Forestry Ministry, Central South University of Forestry and Technology, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, China
- Camellia Oil Tree Research Institute of Central South University of Forestry and Technology, Changsha, China
- The Belt and Road International Union Research Center for Tropical Arid Non-wood Forest in Hunan Province, Changsha, China
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Hussain MA, Luo D, Zeng L, Ding X, Cheng Y, Zou X, Lv Y, Lu G. Genome-wide transcriptome profiling revealed biological macromolecules respond to low temperature stress in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2022; 13:1050995. [PMID: 36452101 PMCID: PMC9702069 DOI: 10.3389/fpls.2022.1050995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/14/2022] [Indexed: 06/12/2023]
Abstract
Brassica napus L. (B. napus) is a vital oilseed crop cultivated worldwide; low temperature (LT) is one of the major stress factors that limit its growth, development, distribution, and production. Even though processes have been developed to characterize LT-responsive genes, only limited studies have exploited the molecular response mechanisms in B. napus. Here the transcriptome data of an elite B. napus variety with LT adaptability was acquired and applied to investigate the gene expression profiles of B. napus in response to LT stress. The bioinformatics study revealed a total of 79,061 unigenes, of which 3,703 genes were differentially expressed genes (DEGs), with 2,129 upregulated and 1,574 downregulated. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis pinpointed that the DEGs were enriched in LT-stress-responsive biological functions and metabolic pathways, which included sugar metabolism, antioxidant defense system, plant hormone signal transduction, and photosynthesis. Moreover, a group of LT-stress-responsive transcription factors with divergent expression patterns under LT was summarized. A combined protein interaction suggested that a complex interconnected regulatory network existed in all detected pathways. RNA-seq data was verified using real-time quantitative polymerase chain reaction analysis. Based on these findings, we presented a hypothesis model illustrating valuable information for understanding the LT response mechanisms in B. napus.
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Affiliation(s)
- Muhammad Azhar Hussain
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Dan Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Liu Zeng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiaoyu Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yong Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiling Zou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yan Lv
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Guangyuan Lu
- School of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
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Wang H, Zhong L, Fu X, Huang S, Fu H, Shi X, Hu L, Cai Y, He H, Chen X. Physiological and Transcriptomic Analyses Reveal the Mechanisms of Compensatory Growth Ability for Early Rice after Low Temperature and Weak Light Stress. PLANTS 2022; 11:plants11192523. [PMID: 36235390 PMCID: PMC9570567 DOI: 10.3390/plants11192523] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
“Late spring coldness” (T) is a frequent meteorological disaster in the spring in southern China, often causing severe yield losses of direct-seeded early rice. In this study, we investigated the mechanisms underlying the differences in the compensatory growth ability of different rice genotypes by focusing on agronomic traits, physiological indicators, and transcriptome. The results showed that there were significant differences in the compensatory growth recovery ability of different genotypes after a combination of four days of low temperature and weak light stress. Only the strong compensatory growth genotype B116 was able to grow rapidly and reduce soluble protein and H2O2 concentrations rapidly after stress. By analyzing enzyme activity as well as endogenous hormone concentration, we found that the high superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities and high levels of abscisic acid (ABA) could reduce the damage of B116 during stress. Meanwhile, higher glutamine synthetase (GS) and nitrate reductase (NR) activity and higher levels of gibberellin A3(GA3), indoleacetic acid (IAA), and zeatin nucleoside (ZR) could enable B116 to grow rapidly after stress. The identified differentially expressed genes (DEGs) indicated that there were large differences in POD-related genes and gibberellin metabolism between B116 and B144 after stress; RT-PCR quantification also showed a trend consistent with RNA-seq, which may be an important reason for the differences in compensatory growth ability.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lei Zhong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoquan Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shiying Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
| | - Haihui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiang Shi
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lifang Hu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yicong Cai
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Super Rice Engineering Technology Center, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Correspondence:
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Transcriptome Analysis of the Responses of Rice Leaves to Chilling and Subsequent Recovery. Int J Mol Sci 2022; 23:ijms231810739. [PMID: 36142652 PMCID: PMC9502032 DOI: 10.3390/ijms231810739] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Improving chilling tolerance at the seedling stage in rice is essential for agricultural research. We combined a physiological analysis with transcriptomics in a variety Dular subjected to chilling followed by recovery at normal temperature to better understand the chilling tolerance mechanisms of rice. Chilling inhibited the synthesis of chlorophyll and non-structural carbohydrate (NSC) and disrupted the ion balance of the plant, resulting in the impaired function of rice leaves. The recovery treatment can effectively reverse the chilling-related injury. Transcriptome results displayed that 21,970 genes were identified at three different temperatures, and 11,732 genes were differentially expressed. According to KEGG analysis, functional categories for differentially expressed genes (DEGs) mainly included ribosome (8.72%), photosynthesis–antenna proteins (7.38%), phenylpropanoid biosynthesis (11.41%), and linoleic acid metabolism (10.07%). The subcellular localization demonstrated that most proteins were located in the chloroplasts (29.30%), cytosol (10.19%), and nucleus (10.19%). We proposed that some genes involved in photosynthesis, ribosome, phenylpropanoid biosynthesis, and linoleic acid metabolism may play key roles in enhancing rice adaptation to chilling stress and their recovery capacity. These findings provide a foundation for future research into rice chilling tolerance mechanisms.
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Khatab AA, Li J, Hu L, Yang J, Fan C, Wang L, Xie G. Global identification of quantitative trait loci and candidate genes for cold stress and chilling acclimation in rice through GWAS and RNA-seq. PLANTA 2022; 256:82. [PMID: 36103054 DOI: 10.1007/s00425-022-03995-z] [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: 08/16/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
Associated analysis of GWAS with RNA-seq had detected candidate genes responsible for cold stress and chilling acclimation in rice. Haplotypes of two candidate genes and geographic distribution were analyzed. To explore new candidate genes and genetic resources for cold tolerance improvement in rice, genome-wide association study (GWAS) mapping experiments with 351 rice core germplasms was performed for three traits (survival rate, shoot length and chlorophyll content) under three temperature conditions (normal temperature, cold stress and chilling acclimation), yielding a total of 134 QTLs, of which 54, 59 and 21 QTLs were responsible for normal temperature, cold stress and chilling acclimation conditions, respectively. Integrated analysis of significant SNPs in 134 QTLs further identified 116 QTLs for three temperature treatments, 53, 43 and 18 QTLs responsible for normal temperature, cold stress and chilling acclimation, respectively, and 2 QTLs were responsible for both cold stress and chilling acclimation. Matching differentially expressed genes from RNA-seq to 43 and 18 QTLs for cold stress and chilling acclimation, we identified 69 and 44 trait-associated candidate genes, respectively, to be classified into six and five groups, particularly involved in metabolisms, reactive oxygen species scavenging and hormone signaling. Interestingly, two candidate genes LOC_Os01g04814, encoding a vacuolar protein sorting-associating protein 4B, and LOC_Os01g48440, encoding glycosyltransferase family 43 protein, showed the highest expression levels under chilling acclimation. Haplotype analysis revealed that both genes had a distinctive differentiation with subpopulation. Haplotypes of both genes with more japonica accessions have higher latitude distribution and higher chilling tolerance than the chilling sensitive indica accessions. These findings reveal the new insight into the molecular mechanism and candidate genes for cold stress and chilling acclimation in rice.
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Affiliation(s)
- Ahmed Adel Khatab
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jiangyi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Chuchuan Fan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lingqiang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China.
| | - Guosheng Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice. PLANTS 2022; 11:plants11182329. [PMID: 36145730 PMCID: PMC9506393 DOI: 10.3390/plants11182329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022]
Abstract
Rice, a cold-sensitive crop, is a staple food for more than 50% of the world’s population. Low temperature severely compromises the growth of rice and challenges China’s food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the genetic basis of its cold tolerance is still unclear. Here, we report quantitative trait loci (QTLs) analysis for seedling cold tolerance (SCT) using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 10 putative QTLs were identified for SCT under 4 °C cold treatment, each explaining 2.0–6.8% of the phenotypic variation in this population. Furthermore, transcriptome sequencing of DXWR seedlings before and after cold treatment was performed, and 898 and 3413 differentially expressed genes (DEGs) relative to 0 h in cold-tolerant for 4 h and 12 h were identified, respectively. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these DEGs. Using transcriptome data and genetic linkage analysis, combined with qRT-PCR, sequence comparison, and bioinformatics, LOC_Os08g04840 was putatively identified as a candidate gene for the major effect locus qSCT8. These findings provided insights into the genetic basis of SCT for the improvement of cold stress potential in rice breeding programs.
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Ma NL, Lam SD, Che Lah WA, Ahmad A, Rinklebe J, Sonne C, Peng W. Integration of environmental metabolomics and physiological approach for evaluation of saline pollution to rice plant. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117214. [PMID: 33971466 DOI: 10.1016/j.envpol.2021.117214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 04/03/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Salinisation of soil is associated with urban pollution, industrial development and rising sea level. Understanding how high salinity is managed at the plant cellular level is vital to increase sustainable farming output. Previous studies focus on plant stress responses under salinity tolerance. Yet, there is limited knowledge about the mechanisms involved from stress state until the recovery state; our research aims to close this gap. By using the most tolerance genotype (SS1-14) and the most susceptible genotype (SS2-18), comparative physiological, metabolome and post-harvest assessments were performed to identify the underlying mechanisms for salinity stress recovery in plant cells. The up-regulation of glutamine, asparagine and malonic acid were found in recovered-tolerant genotype, suggesting a role in the regulation of panicle branching and spikelet formation for survival. Rice could survive up to 150 mM NaCl (∼15 ds/m) with declined of production rate 5-20% ranged from tolerance to susceptible genotype. This show that rice farming may still be viable on the high saline affected area with the right selection of salt-tolerant species, including glycophytes. The salt recovery biomarkers identified in this study and the adaption underlined could be empowered to address salinity problem in rice field.
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Affiliation(s)
- Nyuk Ling Ma
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.
| | - Su Datt Lam
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, United Kingdom; Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Wan Afifudeen Che Lah
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Aziz Ahmad
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285, Wuppertal, Germany; Department of Environment, Energy, And Geoinformatics Sejong University, Seoul, 05006, Republic of Korea.
| | - Christian Sonne
- Department of Bioscience, Aarhus University, Arctic Research Center (ARC), Frederiksborgvej 399, PO Box 358, 4000, Roskilde, Denmark
| | - Wanxi Peng
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
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Marzec M, Situmorang A, Brewer PB, Brąszewska A. Diverse Roles of MAX1 Homologues in Rice. Genes (Basel) 2020; 11:E1348. [PMID: 33202900 PMCID: PMC7709044 DOI: 10.3390/genes11111348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.
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Affiliation(s)
- Marek Marzec
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Philip B. Brewer
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Agnieszka Brąszewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
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11
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Aslam M, Sugita K, Qin Y, Rahman A. Aux/IAA14 Regulates microRNA-Mediated Cold Stress Response in Arabidopsis Roots. Int J Mol Sci 2020; 21:E8441. [PMID: 33182739 PMCID: PMC7697755 DOI: 10.3390/ijms21228441] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators of plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA (miR) in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4 °C revealed that the auxin signaling mutant, solitary root 1 (slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRs in the wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26-31 nt small RNA population in slr1 compared with wild type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRs in slr1 at 4 °C compared with wild type. Target gene expression analysis of the members from one potential candidate miR, miR169, revealed the possible involvement of miR169/NF-YA module in the Aux/IAA14-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRs in auxin and cold responses.
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Affiliation(s)
- Mohammad Aslam
- Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan; (M.A.); (K.S.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China;
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kenji Sugita
- Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan; (M.A.); (K.S.)
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China;
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Abidur Rahman
- Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan; (M.A.); (K.S.)
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
- Agri-Innovation Center, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
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12
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Zhang Z, Xiao W, Qiu J, Xin Y, Liu Q, Chen H, Fu Y, Ma H, Chen W, Huang Y, Ruan S, Yan J. Nystose regulates the response of rice roots to cold stress via multiple signaling pathways: A comparative proteomics analysis. PLoS One 2020; 15:e0238381. [PMID: 32881942 PMCID: PMC7470417 DOI: 10.1371/journal.pone.0238381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/15/2020] [Indexed: 11/18/2022] Open
Abstract
Small fructans improve plant tolerance for cold stress. However, the underlying molecular mechanisms are poorly understood. Here, we have demonstrated that the small fructan tetrasaccharide nystose improves the cold stress tolerance of primary rice roots. Roots developed from seeds soaked in nystose showed lower browning rate, higher root activity, and faster growth compared to seeds soaked in water under chilling stress. Comparative proteomics analysis of nystose-treated and control roots identified a total of 497 differentially expressed proteins. GO classification and KEGG pathway analysis documented that some of the upregulated differentially expressed proteins were implicated in the regulation of serine/threonine protein phosphatase activity, abscisic acid-activated signaling, removal of superoxide radicals, and the response to oxidative stress and defense responses. Western blot analysis indicated that nystose promotes the growth of primary rice roots by increasing the level of RSOsPR10, and the cold stress-induced change in RSOsPR10levelis regulated by jasmonate, salicylic acid, and abscisic acid signaling pathways in rice roots. Furthermore, OsMKK4-dependentmitogen-activated protein kinase signaling cascades may be involved in the nystose-induced cold tolerance of primary rice roots. Together, these results indicate that nystose acts as an immunostimulator of the response to cold stress by multiple signaling pathways.
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Affiliation(s)
- Zijie Zhang
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture and Food Science, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Wenfei Xiao
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jieren Qiu
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Ya Xin
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qinpo Liu
- College of Agriculture and Food Science, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Huizhe Chen
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yaping Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Huasheng Ma
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Wenyue Chen
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yuqin Huang
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Songlin Ruan
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture and Food Science, Zhejiang Agriculture & Forestry University, Hangzhou, China
- * E-mail: (SR); (JY)
| | - Jianli Yan
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (SR); (JY)
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13
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Niu Y, Liu Z, He H, Han X, Qi Z, Yang Y. Gene expression and metabolic changes of Momordica charantia L. seedlings in response to low temperature stress. PLoS One 2020; 15:e0233130. [PMID: 32469892 PMCID: PMC7259686 DOI: 10.1371/journal.pone.0233130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/28/2020] [Indexed: 11/19/2022] Open
Abstract
Low temperature is one of the abiotic factors limiting germination, growth and distribution of the plant in current plant-products industry, especially for the tropical vegetables in non-tropical area or other fields under cold temperature. Screening the plant with ability against cold temperature captured worldwide attention and exerted great importance. In our previous work, the anti-cold specie of Momordica Charantia L. seedlings was screened out. Yet, the molecular and physiological mechanisms underlying this adaptive process still remain unknown. This study was aimed to investigate adaption mechanism of anti-cold species of Momordica Charantia L. seedlings in genetical and metabolomics levels. Two species, cold-susceptible group (Y17) and cold-resistant group (Y54), were evaluated containing the indexes of malondialdehyde (MDA), hydrogen peroxide (H2O2), proline content, activities of antioxidant enzymes, metabolites changes and genes differentiation in plant tissues after cold treatment. It found that low temperature stress resulted in increased accumulation of MDA, H2O2 and proline content in two species, but less expressions in cold-resistant species Y54. As compared to Y17, cold-resistant species Y54 presented significantly enhanced antioxidant enzyme activities of POD (peroxidase), CAT (cataalase) and SOD (superoxide dismutase). Meanwhile, higher expressed genes encoded antioxidant enzymes and transcription factors when exposure to the low temperature were found in cold-resistant species Y54, and core genes were explored by Q-PCR validation, including McSOD1, McPDC1 and McCHS1. Moreover, plant metabolites containing amino acid, sugar, fatty acid and organic acid in Y54 were higher than Y17, indicating their important roles in cold acclimation. Meanwhile, initial metabolites, including amimo acids, polypeptides, sugars, organic acids and nucleobases, were apparently increased in cold resistant species Y54 than cold susceptible species Y17. Our results demonstrated that the Momordica Charantia L. seedlings achieved cold tolerance might be went through mobilization of antioxidant systems, adjustment of the transcription factors and accumulation of osmoregulation substance. This work presented meaning information for revealing the anti-cold mechanism of the Momordica Charantia L. seedlings and newsight for further screening of anti-cold species in other plant.
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Affiliation(s)
- Yu Niu
- Tropical Crops Genetic Resources Research Institute, CATAS, Danzhou Hainan, China
| | - Ziji Liu
- Tropical Crops Genetic Resources Research Institute, CATAS, Danzhou Hainan, China
| | - Huang He
- Tropical Crops Genetic Resources Research Institute, CATAS, Danzhou Hainan, China
| | - Xu Han
- Tropical Crops Genetic Resources Research Institute, CATAS, Danzhou Hainan, China
| | - Zhiqiang Qi
- Tropical Crops Genetic Resources Research Institute, CATAS, Danzhou Hainan, China
- * E-mail: (YY); (ZQ)
| | - Yan Yang
- Tropical Crops Genetic Resources Research Institute, CATAS, Danzhou Hainan, China
- * E-mail: (YY); (ZQ)
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14
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Yu P, Jiang N, Fu W, Zheng G, Li G, Feng B, Chen T, Ma J, Li H, Tao L, Fu G. ATP Hydrolysis Determines Cold Tolerance by Regulating Available Energy for Glutathione Synthesis in Rice Seedling Plants. RICE (NEW YORK, N.Y.) 2020; 13:23. [PMID: 32274603 PMCID: PMC7145886 DOI: 10.1186/s12284-020-00383-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/23/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Glutathione (GSH) is important for plants to resist abiotic stress, and a large amount of energy is required in the process. However, it is not clear how the energy status affects the accumulation of GSH in plants under cold stress. RESULTS Two rice pure lines, Zhongzao39 (ZZ39) and its recombinant inbred line 82 (RIL82) were subjected to cold stress for 48 h. Under cold stress, RIL82 suffered more damages than ZZ39 plants, in which higher increases in APX activity and GSH content were showed in the latter than the former compared with their respective controls. This indicated that GSH was mainly responsible for the different cold tolerance between these two rice plants. Interestingly, under cold stress, greater increases in contents of carbohydrate, NAD(H), NADP(H) and ATP as well as the expression levels of GSH1 and GSH2 were showed in RIL82 than ZZ39 plants. In contrast, ATPase content in RIL82 plants was adversely inhibited by cold stress while it increased significantly in ZZ39 plants. This indicated that cold stress reduced the accumulation of GSH in RIL82 plants mainly due to the inhibition on ATP hydrolysis rather than energy deficit. CONCLUSION We inferred that the energy status determined by ATP hydrolysis involved in regulating the cold tolerance of plants by controlling GSH synthesis.
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Affiliation(s)
- Pinghui Yu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Ning Jiang
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Weimeng Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Guangjie Zheng
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Guangyan Li
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Baohua Feng
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Tingting Chen
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Jiaying Ma
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Hubo Li
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Longxing Tao
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Guanfu Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
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15
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Buti M, Baldoni E, Formentin E, Milc J, Frugis G, Lo Schiavo F, Genga A, Francia E. A Meta-Analysis of Comparative Transcriptomic Data Reveals a Set of Key Genes Involved in the Tolerance to Abiotic Stresses in Rice. Int J Mol Sci 2019; 20:E5662. [PMID: 31726733 PMCID: PMC6888222 DOI: 10.3390/ijms20225662] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 12/16/2022] Open
Abstract
Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the "Drought and Salt Tolerance" TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.
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Affiliation(s)
- Matteo Buti
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola 2, 42124 Reggio Emilia, Italy; (M.B.); (J.M.); (E.F.)
- Present address: Department of Agriculture, Food, Environment and Forestry, University of Florence, 50144 Florence, Italy
| | - Elena Baldoni
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133 Milano, Italy;
- CNR-IBBA, Rome Unit, via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy;
| | - Elide Formentin
- Department of Biology, University of Padova, 35131 Padova, Italy; (E.F.); (F.L.S.)
- Botanical Garden, University of Padova, 35123 Padova, Italy
| | - Justyna Milc
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola 2, 42124 Reggio Emilia, Italy; (M.B.); (J.M.); (E.F.)
| | - Giovanna Frugis
- CNR-IBBA, Rome Unit, via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy;
| | - Fiorella Lo Schiavo
- Department of Biology, University of Padova, 35131 Padova, Italy; (E.F.); (F.L.S.)
- Botanical Garden, University of Padova, 35123 Padova, Italy
| | - Annamaria Genga
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133 Milano, Italy;
| | - Enrico Francia
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola 2, 42124 Reggio Emilia, Italy; (M.B.); (J.M.); (E.F.)
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16
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Zheng D, Wang L, Chen L, Pan X, Lin K, Fang Y, Wang XE, Zhang W. Salt-Responsive Genes are Differentially Regulated at the Chromatin Levels Between Seedlings and Roots in Rice. PLANT & CELL PHYSIOLOGY 2019; 60:1790-1803. [PMID: 31111914 DOI: 10.1093/pcp/pcz095] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
The elucidation of epigenetic responses of salt-responsive genes facilitates understanding of the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms are associated with the expression of salt-responsive genes in rice and other crops. In this study, we reported tissue-specific gene expression and tissue-specific changes in chromatin modifications or signatures between seedlings and roots in response to salt treatment. Our study indicated that among six of individual mark examined (H3K4me3, H3K27me3, H4K12ac, H3K9ac, H3K27ac and H3K36me3), a positive association between salt-related changes in histone marks and the expression of differentially expressed genes (DEGs) was observed only for H3K9ac and H4K12ac in seedlings and H3K36me3 in roots. In contrast, chromatin states (CSs) with combinations of six histone modification marks played crucial roles in the differential expression of salt-responsive genes between seedlings and roots. Most importantly, CS7 containing the bivalent marks H3K4me3 and H3K27me3, with a mutual exclusion of functions with each other, displayed distinct functions in the expression of DEGs in both tissues. Specifically, H3K27me3 in CS7 mainly suppressed the expression of DEGs in roots, while H3K4me3 affected the expression of down- and up-regulated genes, possibly by antagonizing the repressive role of H3K27me3 in seedlings. Our findings indicate distinct impacts of the CSs on the differential expression of salt-responsive genes between seedlings and roots in rice, which provides an important background for understanding chromatin-based epigenetic mechanisms that might confer salt tolerance in plants.
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Affiliation(s)
- Dongyang Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Lei Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Lifen Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Xiucai Pan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Kande Lin
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Yuan Fang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Xiu-E Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
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17
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Dong J, Zhao J, Zhang S, Yang T, Liu Q, Mao X, Fu H, Yang W, Liu B. Physiological and genome-wide gene expression analyses of cold-induced leaf rolling at the seedling stage in rice (Oryza sativa L.). ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2019.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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18
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Yang G, Chen S, Li D, Gao X, Su L, Peng S, Zhai M. Multiple transcriptional regulation of walnut JrGSTTau1 gene in response to osmotic stress. PHYSIOLOGIA PLANTARUM 2019; 166:748-761. [PMID: 30187482 DOI: 10.1111/ppl.12833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 05/26/2023]
Abstract
Glutathione S-transferases (GSTs) are important plant proteins involved in biotic and abiotic stress responses. A gene from Juglans regia, JrGSTTau1 was previously cloned and functionally characterized as an enzyme involved in improving cold tolerance in plants. To clarify the functional mechanism of JrGSTTau1 and its role in stress response, here, the JrGSTTau1 promoter including the up-stream regulators was examined using yeast one-hybrid together with transient expression assays, and the osmotic stress response ability was confirmed by comparing with wild-type plants. The 1500 bp JrGSTTau1 promoter displayed high GUS expression activity and was enhanced by mannitol stress. The promoter is composed of abundant cis-elements, some of which were osmotic stress response-related motifs, such as ABRE, DRE and MYB, indicating that the expression of JrGSTTau1 is regulated by potential up-stream regulators under abiotic stress. The transcription factors (TFs) of JrDREB2A, JrMYC2, JrMYB44, JrDof1 and JrWRKY7 were identified, which shared a similar response with JrGSTTau1 when exposed to PEG6000 in walnut leaf and root. These results implied that JrDREB2A, JrMYC2, JrMYB44, JrDof1 and JrWRKY7 may act as up-stream regulators of JrGSTTau1 to regulate or combine functionality with JrGSTTau1 in osmotic stress response. Furthermore, compared with the WT plants, the transgenic tobacco plants that overexpress JrGSTTau1 showed improved tolerance to drought induced by osmotic stress, in which antioxidant enzymes, proline and reactive oxygen species (ROS) are involved. Our results demonstrated the positive role played by JrGSTTau1 in osmotic tolerance, which is regulated by multiple up-stream regulators.
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Affiliation(s)
- Guiyan Yang
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
- Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - Shuwen Chen
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
- Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - Dapei Li
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - Xiangqian Gao
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - Liyuan Su
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - Shaobing Peng
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - MeiZhi Zhai
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
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19
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Abstract
Abnormal environmental temperature affects plant growth and threatens crop production. Understanding temperature signal sensing and the balance between defense and development in plants lays the foundation for improvement of temperature resilience. Here, we summarize the current understanding of cold signal perception/transduction as well as heat stress response. Dissection of plant responses to different levels of cold stresses (chilling and freezing) illustrates their common and distinct signaling pathways. Axillary bud differentiation in response to chilling is presented as an example of the trade-off between defense and development. Vernalization is a cold-dependent development adjustment mediated by O-GlcNAcylation and phosphorylation to sense long-term cold. Recent progress on major quantitative trait loci genes for heat tolerance has been summarized. Molecular mechanisms in utilizing temperature-sensitive sterility in super hybrid breeding in China are revealed. The way to improve crop temperature resilience using integrative knowledge of omics as well as systemic and synthetic biology, especially the molecular module program, is summarized.
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Affiliation(s)
- Jingyu Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Xin-Min Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100093, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
- University of Chinese Academy of Sciences, Beijing 100093, China
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20
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Filiz E, Ozyigit II, Saracoglu IA, Uras ME, Sen U, Yalcin B. Abiotic stress-induced regulation of antioxidant genes in different Arabidopsis ecotypes: microarray data evaluation. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2018.1556120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Ertugrul Filiz
- Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, Cilimli, Duzce, Turkey
| | - Ibrahim Ilker Ozyigit
- Department of Biology, Faculty of Science and Arts, Marmara University, Goztepe, Istanbul, Turkey
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Ibrahim Adnan Saracoglu
- Department of Chemistry, Faculty of Science and Arts, Marmara University, Goztepe, Istanbul, Turkey
| | - Mehmet Emin Uras
- Department of Biology, Faculty of Science and Arts, Marmara University, Goztepe, Istanbul, Turkey
| | - Ugur Sen
- Department of Biology, Faculty of Science and Arts, Marmara University, Goztepe, Istanbul, Turkey
| | - Bahattin Yalcin
- Department of Chemistry, Faculty of Science and Arts, Marmara University, Goztepe, Istanbul, Turkey
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21
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Ma NL, Che Lah WA, Abd. Kadir N, Mustaqim M, Rahmat Z, Ahmad A, Lam SD, Ismail MR. Susceptibility and tolerance of rice crop to salt threat: Physiological and metabolic inspections. PLoS One 2018; 13:e0192732. [PMID: 29489838 PMCID: PMC5831039 DOI: 10.1371/journal.pone.0192732] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/29/2018] [Indexed: 01/07/2023] Open
Abstract
Salinity threat is estimated to reduce global rice production by 50%. Comprehensive analysis of the physiological and metabolite changes in rice plants from salinity stress (i.e. tolerant versus susceptible plants) is important to combat higher salinity conditions. In this study, we screened a total of 92 genotypes and selected the most salinity tolerant line (SS1-14) and most susceptible line (SS2-18) to conduct comparative physiological and metabolome inspections. We demonstrated that the tolerant line managed to maintain their water and chlorophyll content with lower incidence of sodium ion accumulation. We also examined the antioxidant activities of these lines: production of ascorbate peroxidase (APX) and catalase (CAT) were significantly higher in the sensitive line while superoxide dismutase (SOD) was higher in the tolerant line. Partial least squares discriminant analysis (PLS-DA) score plots show significantly different response for both lines after the exposure to salinity stress. In the tolerant line, there was an upregulation of non-polar metabolites and production of sucrose, GABA and acetic acid, suggesting an important role in salinity adaptation. In contrast, glutamine and putrescine were noticeably high in the susceptible rice. Coordination of different strategies in tolerant and susceptible lines show that they responded differently after exposure to salt stress. These findings can assist crop development in terms of developing tolerance mechanisms for rice crops.
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Affiliation(s)
- Nyuk Ling Ma
- School of Fundamental Science, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
- * E-mail:
| | - Wan Afifudeen Che Lah
- School of Fundamental Science, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Nisrin Abd. Kadir
- School of Fundamental Science, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Mohamad Mustaqim
- School of Fundamental Science, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Zaidah Rahmat
- Department of Biotechnology and Medical Engineering, University Technology Malaysia, Skudai, Johor, Malaysia
| | - Aziz Ahmad
- School of Fundamental Science, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Su Datt Lam
- School of Biosciences and Biotechnology, Faculty of Science and Technology, University Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, United Kingdom
| | - Mohd Razi Ismail
- Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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22
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Wan T, Liu ZM, Li LF, Leitch AR, Leitch IJ, Lohaus R, Liu ZJ, Xin HP, Gong YB, Liu Y, Wang WC, Chen LY, Yang Y, Kelly LJ, Yang J, Huang JL, Li Z, Liu P, Zhang L, Liu HM, Wang H, Deng SH, Liu M, Li J, Ma L, Liu Y, Lei Y, Xu W, Wu LQ, Liu F, Ma Q, Yu XR, Jiang Z, Zhang GQ, Li SH, Li RQ, Zhang SZ, Wang QF, Van de Peer Y, Zhang JB, Wang XM. A genome for gnetophytes and early evolution of seed plants. NATURE PLANTS 2018; 4:82-89. [PMID: 29379155 DOI: 10.1038/s41477-017-0097-2] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 12/27/2017] [Indexed: 05/07/2023]
Abstract
Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms.
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Affiliation(s)
- Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
| | - Zhi-Ming Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ling-Fei Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China
| | - Hai-Ping Xin
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Wen-Cai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ling-Yun Chen
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ji Yang
- Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Jin-Ling Huang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ping Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Li Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Hong-Mei Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Hui Wang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Shu-Han Deng
- Novogene Bioinformatics Institute, Beijing, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ji Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yan Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yang Lei
- Novogene Bioinformatics Institute, Beijing, China
| | - Wei Xu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ling-Qing Wu
- Novogene Bioinformatics Institute, Beijing, China
| | - Fan Liu
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
| | - Qian Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xin-Ran Yu
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui-Qiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China.
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Centre for Plant Systems Biology, VIB, Ghent, Belgium.
- Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
| | - Jin-Bo Zhang
- Novogene Bioinformatics Institute, Beijing, China.
| | - Xiao-Ming Wang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
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Wang W, Wang X, Huang M, Cai J, Zhou Q, Dai T, Cao W, Jiang D. Hydrogen Peroxide and Abscisic Acid Mediate Salicylic Acid-Induced Freezing Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1137. [PMID: 30123235 PMCID: PMC6085453 DOI: 10.3389/fpls.2018.01137] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/13/2018] [Indexed: 05/02/2023]
Abstract
Salicylic acid (SA) can induce plant resistance to biotic and abiotic stresses through cross talk with other signaling molecules, whereas the interaction between hydrogen peroxide (H2O2) and abscisic acid (ABA) in response to SA signal is far from clear. Here, we focused on the roles and interactions of H2O2 and ABA in SA-induced freezing tolerance in wheat plants. Exogenous SA pretreatment significantly induced freezing tolerance of wheat via maintaining relatively higher dark-adapted maximum photosystem II quantum yield, electron transport rates, less cell membrane damage. Exogenous SA induced the accumulation of endogenous H2O2 and ABA. Endogenous H2O2 accumulation in the apoplast was triggered by both cell wall peroxidase and membrane-linked NADPH oxidase. The pharmacological study indicated that pretreatment with dimethylthiourea (H2O2 scavenger) completely abolished SA-induced freezing tolerance and ABA synthesis, while pretreatment with fluridone (ABA biosynthesis inhibitor) reduced H2O2 accumulation by inhibiting NADPH oxidase encoding genes expression and partially counteracted SA-induced freezing tolerance. These findings demonstrate that endogenous H2O2 and ABA signaling may form a positive feedback loop to mediate SA-induced freezing tolerance in wheat.
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Affiliation(s)
| | - Xiao Wang
- *Correspondence: Xiao Wang, ; Dong Jiang,
| | | | | | | | | | | | - Dong Jiang
- *Correspondence: Xiao Wang, ; Dong Jiang,
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24
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Wang W, Wang X, Huang M, Cai J, Zhou Q, Dai T, Cao W, Jiang D. Hydrogen Peroxide and Abscisic Acid Mediate Salicylic Acid-Induced Freezing Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1137. [PMID: 30123235 DOI: 10.3389/fpls.2018.01137/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/13/2018] [Indexed: 05/20/2023]
Abstract
Salicylic acid (SA) can induce plant resistance to biotic and abiotic stresses through cross talk with other signaling molecules, whereas the interaction between hydrogen peroxide (H2O2) and abscisic acid (ABA) in response to SA signal is far from clear. Here, we focused on the roles and interactions of H2O2 and ABA in SA-induced freezing tolerance in wheat plants. Exogenous SA pretreatment significantly induced freezing tolerance of wheat via maintaining relatively higher dark-adapted maximum photosystem II quantum yield, electron transport rates, less cell membrane damage. Exogenous SA induced the accumulation of endogenous H2O2 and ABA. Endogenous H2O2 accumulation in the apoplast was triggered by both cell wall peroxidase and membrane-linked NADPH oxidase. The pharmacological study indicated that pretreatment with dimethylthiourea (H2O2 scavenger) completely abolished SA-induced freezing tolerance and ABA synthesis, while pretreatment with fluridone (ABA biosynthesis inhibitor) reduced H2O2 accumulation by inhibiting NADPH oxidase encoding genes expression and partially counteracted SA-induced freezing tolerance. These findings demonstrate that endogenous H2O2 and ABA signaling may form a positive feedback loop to mediate SA-induced freezing tolerance in wheat.
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Affiliation(s)
- Weiling Wang
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Xiao Wang
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Mei Huang
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jian Cai
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Qin Zhou
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Tingbo Dai
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Weixing Cao
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, China
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25
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Zhao J, Zhang S, Dong J, Yang T, Mao X, Liu Q, Wang X, Liu B. A novel functional gene associated with cold tolerance at the seedling stage in rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1141-1148. [PMID: 28173633 PMCID: PMC5552475 DOI: 10.1111/pbi.12704] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 01/11/2017] [Accepted: 02/02/2017] [Indexed: 05/24/2023]
Abstract
Identification and cloning of cold-tolerant genes that can stably express under different cold environments are crucial for molecular rice breeding for cold tolerance. In the previous study, we identified a cold-tolerant QTL at the seedling stage, qCTS-9 which could be detected under different cold environments using a recombinant inbred line (RIL) population derived from a cold-tolerant variety Lijiangxintuanheigu (LTH) and a cold-sensitive variety Shanhuangzhan 2 (SHZ-2). In this study, eight candidate genes within the qCTS-9 interval were identified through integrated analysis of QTL mapping with genomewide differential expression profiling of LTH. The qRT-PCR assay showed that only Os09g0410300 exhibited different expression patterns between LTH and SHZ-2 during cold stress, and significantly positive correlation was found between cold induction of Os09g0410300 and seedling cold tolerance in the RI lines. Five SNPs and one InDel in the promoters of Os09g0410300 were detected between LTH and SHZ-2, and the InDel marker ID410300 designed based on the insertion-deletion polymorphism in the promoter was significantly associated with seedling cold tolerance in RIL population. Further, Os09g0410300 over-expression plants exhibited enhanced cold tolerance at the seedling stage compared with the wild-type plants. Thus, our results suggest that Os09g0410300 is the functional gene underlying qCTS-9. To our knowledge, it is a novel gene contributed to enhance cold tolerance at the seedling stage in rice. Identification of the functional gene underlying qCTS-9 and development of the gene-specific marker will facilitate molecular breeding for cold tolerance at the seedling stage in rice through transgenic approach and marker-assisted selection (MAS).
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Affiliation(s)
- Junliang Zhao
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Shaohong Zhang
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Jingfang Dong
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Tifeng Yang
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Xingxue Mao
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Qing Liu
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Xiaofei Wang
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Bin Liu
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangdong Academy of Agricultural SciencesGuangzhouChina
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26
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Jha UC, Bohra A, Jha R. Breeding approaches and genomics technologies to increase crop yield under low-temperature stress. PLANT CELL REPORTS 2017; 36:1-35. [PMID: 27878342 DOI: 10.1007/s00299-016-2073-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/04/2016] [Indexed: 05/11/2023]
Abstract
Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research, Kanpur, 208024, India.
| | - Abhishek Bohra
- Indian Institute of Pulses Research, Kanpur, 208024, India.
| | - Rintu Jha
- Indian Institute of Pulses Research, Kanpur, 208024, India
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27
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Kumar M, Gho YS, Jung KH, Kim SR. Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage. FRONTIERS IN PLANT SCIENCE 2017; 8:1120. [PMID: 28713404 PMCID: PMC5491850 DOI: 10.3389/fpls.2017.01120] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/09/2017] [Indexed: 05/14/2023]
Abstract
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in 'Dongjin,' the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the 'L-phenylalanine catabolic process,' within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified 'Major Metabolic' processes and 'Regulatory Gene Modules' as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.
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Affiliation(s)
- Manu Kumar
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
| | - Yun-Shil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
| | - Seong-Ryong Kim
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
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28
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Yang G, Xu Z, Peng S, Sun Y, Jia C, Zhai M. In planta characterization of a tau class glutathione S-transferase gene from Juglans regia (JrGSTTau1) involved in chilling tolerance. PLANT CELL REPORTS 2016; 35:681-92. [PMID: 26687965 DOI: 10.1007/s00299-015-1912-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/11/2015] [Accepted: 11/26/2015] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE JrGSTTau1 is an important candidate gene for plant chilling tolerance regulation. A tau subfamily glutathione S-transferase (GST) gene from Juglans regia (JrGSTTau1, GeneBank No.: KT351091) was cloned and functionally characterized. JrGSTTau1 was induced by 16, 12, 10, 8, and 6 °C stresses. The transiently transformed J. regia showed much greater GST, glutathione peroxidase (GPX), superoxide dismutase (SOD), and peroxidase (POD) activities and lower H2O2, malondialdehyde (MDA), reactive oxygen species (ROS), and electrolyte leakage (EL) rate than prokII (empty vector control) and RNAi::JrGSTTau1 under cold stress, indicating that JrGSTTau1 may be involved in chilling tolerance. To further confirm the role of JrGSTTau1, JrGSTTau1 was heterologously expressed in tobacco, transgenic Line5, Line9, and Line12 were chosen for analysis. The germinations of WT, Line5, Line9, and Line12 were similar, but the fresh weight, primary root length, and total chlorophyll content (tcc) of the transgenic lines were significantly higher than those of WT under cold stress. When cultivated in soil, the GST and SOD activities of transgenic tobacco were significantly higher than those of WT; however, the MDA and H2O2 contents of WT were on average 1.47- and 1.96-fold higher than those of Line5, Line9, and Line12 under 16 °C. The DAB, Evans blue, and PI staining further confirmed these results. Furthermore, the abundances of NtGST, MnSOD, NtMAPK9, and CDPK15 were elevated in 35S::JrGSTTau1 tobacco compared with WT. These results suggested that JrGSTTau1 improves the plant chilling tolerance involved in protecting enzymes, ROS scavenging, and stress-related genes, indicating that JrGSTTau1 is a candidate gene for the potential application in molecular breeding to enhance plant abiotic stress tolerance.
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Affiliation(s)
- Guiyan Yang
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Zhenggang Xu
- College of Life Science and Technology, Central South University of Forestry and Technology, 498 Shaoshan South Road, Changsha, 410004, Hunan Province, People's Republic of China
| | - Shaobing Peng
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yudong Sun
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Caixia Jia
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Meizhi Zhai
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China.
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Genome-wide identification and expression profiling analysis of ZmPIN, ZmPILS, ZmLAX and ZmABCB auxin transporter gene families in maize (Zea mays L.) under various abiotic stresses. PLoS One 2015; 10:e0118751. [PMID: 25742625 PMCID: PMC4351008 DOI: 10.1371/journal.pone.0118751] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/06/2015] [Indexed: 11/30/2022] Open
Abstract
The auxin influx carriers auxin resistant 1/like aux 1 (AUX/LAX), efflux carriers pin-formed (PIN) (together with PIN-like proteins) and efflux/conditional P-glycoprotein (ABCB) are major protein families involved in auxin polar transport. However, how they function in responses to exogenous auxin and abiotic stresses in maize is largely unknown. In this work, the latest updated maize (Zea mays L.) reference genome sequence was used to characterize and analyze the ZmLAX, ZmPIN, ZmPILS and ZmABCB family genes from maize. The results showed that five ZmLAXs, fifteen ZmPINs, nine ZmPILSs and thirty-five ZmABCBs were mapped on all ten maize chromosomes. Highly diversified gene structures, nonconservative transmembrane helices and tissue-specific expression patterns suggested the possibility of function diversification for these genes. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze the expression patterns of ZmLAX, ZmPIN, ZmPILS and ZmABCB genes under exogenous auxin and different environmental stresses. The expression levels of most ZmPIN, ZmPILS, ZmLAX and ZmABCB genes were induced in shoots and were reduced in roots by various abiotic stresses (drought, salt and cold stresses). The opposite expression response patterns indicated the dynamic auxin transport between shoots and roots under abiotic stresses. Analysis of the expression patterns of ZmPIN, ZmPILS, ZmLAX and ZmABCB genes under drought, salt and cold treatment may help us to understand the possible roles of maize auxin transporter genes in responses and tolerance to environmental stresses.
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