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Li S, Wuyun TN, Wang L, Zhang J, Tian H, Zhang Y, Wang S, Xia Y, Liu X, Wang N, Lv F, Xu J, Tang Z. Genome-wide and functional analysis of late embryogenesis abundant (LEA) genes during dormancy and sprouting periods of kernel consumption apricots (P. armeniaca L. × P. sibirica L.). Int J Biol Macromol 2024:133245. [PMID: 38977045 DOI: 10.1016/j.ijbiomac.2024.133245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/05/2024] [Accepted: 06/16/2024] [Indexed: 07/10/2024]
Abstract
Late embryogenesis abundant (LEA) proteins play a crucial role in protecting cells from stress, making them potential contributors to abiotic stress tolerance. This study focuses on apricot (P. armeniaca L. × P. sibirica L.), where a comprehensive genome-wide analysis identified 54 LEA genes, categorized into eight subgroups based on phylogenetic relationships. Synteny analysis revealed 14 collinear blocks containing LEA genes between P. armeniaca × P. sibirica and Arabidopsis thaliana, with an additional 9 collinear blocks identified between P. armeniaca × P. sibirica and poplar. Examination of gene structure and conserved motifs indicated that these subgroups exhibit consistent exon-intron patterns and shared motifs. The expansion and duplication of LEA genes in P. armeniaca × P. sibirica were driven by whole-genome duplication (WGD), segmental duplication, and tandem duplication events. Expression analysis, utilizing RNA-seq data and quantitative real-time RT-PCR (qRT-PCR), indicated induction of PasLEA2-20, PasLEA3-2, PasLEA6-1, Pasdehydrin-3, and Pasdehydrin-5 in flower buds during dormancy and sprouting phases. Coexpression network analysis linked LEA genes with 15 cold-resistance genes. Remarkably, during the four developmental stages of flower buds in P. armeniaca × P. sibirica - physiological dormancy, ecological dormancy, sprouting period, and germination stage - the expression patterns of all PasLEAs coexpressed with cold stress-related genes remained consistent. Protein-protein interaction networks, established using Arabidopsis orthologs, emphasized connections between PasLEA proteins and cold resistance pathways. Overexpression of certain LEA genes in yeast and Arabidopsis conferred advantages under cold stress, including increased pod length, reduced bolting time and flowering time, improved survival and seed setting rates, elevated proline accumulation, and enhanced antioxidative enzymatic activities. Furthermore, these overexpressed plants exhibited upregulation of genes related to flower development and cold resistance. The Y1H assay confirmed that PasGBF4 and PasDOF3.5 act as upstream regulatory factors by binding to the promoter region of PasLEA3-2. PasDOF2.4, PasDnaJ2, and PasAP2 were also found to bind to the promoter of Pasdehydrin-3, regulating the expression levels of downstream genes. This comprehensive study explores the evolutionary relationships among PasLEA genes, protein interactions, and functional analyses during various stages of dormancy and sprouting in P. armeniaca × P. sibirica. It offers potential targets for enhancing cold resistance and manipulating flower bud dormancy in this apricot hybrid.
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Affiliation(s)
- Shaofeng Li
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Ta-Na Wuyun
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, PR China.
| | - Lin Wang
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, PR China.
| | - Jianhui Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hua Tian
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Yaodan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Shaoli Wang
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Yongxiu Xia
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Xue Liu
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Ning Wang
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Fenni Lv
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences (Nanjing Botany Garden Mem. Sun Yat-Sen), Nanjing 210014, Jiangsu Province, PR China.
| | - Jihuang Xu
- Experimental Center of Tropical Forestry, Chinese Academy of Forestry, Pingxiang 532600, PR China.
| | - Zhimin Tang
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100093, PR China.
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Hamid R, Jacob F, Ghorbanzadeh Z, Khayam Nekouei M, Zeinalabedini M, Mardi M, Sadeghi A, Kumar S, Ghaffari MR. Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses. PeerJ 2024; 12:e17462. [PMID: 38827302 PMCID: PMC11144395 DOI: 10.7717/peerj.17462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/05/2024] [Indexed: 06/04/2024] Open
Abstract
Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Golestan, Iran
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, Kerala, India
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
| | | | - Mehrshad Zeinalabedini
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
| | - Mohsen Mardi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
| | - Akram Sadeghi
- Department of Microbial Biotechnology and Biosafety, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborrz, Iran
| | - Sushil Kumar
- Agricultural Biotechnology, Anand agricultural University, Anand, Gujarat, India
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
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Blume-Werry G, Semenchuk P, Ljung K, Milbau A, Novak O, Olofsson J, Brunoni F. In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge. THE NEW PHYTOLOGIST 2024; 242:988-999. [PMID: 38375943 DOI: 10.1111/nph.19616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/04/2024] [Indexed: 02/21/2024]
Abstract
Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.
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Affiliation(s)
- Gesche Blume-Werry
- Department of Ecology and Environmental Science, Umeå University, 901 87, Umeå, Sweden
| | - Philipp Semenchuk
- Department of Arctic Biology, UNIS - The University Centre in Svalbard, 9171, Longyearbyen, Norway
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Ann Milbau
- Department of Ecology and Environmental Science, Umeå University, 901 87, Umeå, Sweden
| | - Ondrej Novak
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Johan Olofsson
- Department of Ecology and Environmental Science, Umeå University, 901 87, Umeå, Sweden
| | - Federica Brunoni
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
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Chen M, Dai Y, Liao J, Wu H, Lv Q, Huang Y, Liu L, Feng Y, Lv H, Zhou B, Peng D. TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2214-2234. [PMID: 38195092 DOI: 10.1093/jxb/erae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.
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Affiliation(s)
- Min Chen
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yani Dai
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Jiamin Liao
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Huan Wu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Qiang Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Huang
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Lichang Liu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Feng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Hongxuan Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Bo Zhou
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, 410004, Changsha, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
| | - Dan Peng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
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Liu J, Xuan L, Yu C, Hua J, Wang Z, Yin Y, Wang Z. Molecular Mechanism of Different Rooting Capacity between Two Clones of Taxodium hybrid 'Zhongshanshan'. Int J Mol Sci 2024; 25:2427. [PMID: 38397108 PMCID: PMC10889566 DOI: 10.3390/ijms25042427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
The conifer Taxodium hybrid 'Zhongshanshan' (T. hybrid 'Zhongshanshan') is characterized by rapid growth, strong stress resistance, and high ornamental value and has significant potential for use in afforestation, landscaping, and wood production. The main method of propagating T. hybrid 'Zhongshanshan' is tender branch cutting, but the cutting rooting abilities of different T. hybrid 'Zhongshanshan' clones differ significantly. To explore the causes of rooting ability differences at a molecular level, we analyzed the transcriptome data of cutting base and root tissues of T. hybrid 'Zhongshanshan 149' with a rooting rate of less than 5% and T. hybrid 'Zhongshanshan 118' with rooting rate greater than 60%, at the developmental time points in this study. The results indicated that differentially expressed genes between the two clones were mainly associated with copper ion binding, peroxidase, and oxidoreductase activity, response to oxidative stress, phenylpropanoid and flavonoid biosynthesis, and plant hormone signal transduction, among others. The expression pattern of ThAP2 was different throughout the development of the adventitive roots of the two clone cuttings. Therefore, this gene was selected for further study. It was shown that ThAP2 was a nuclear-localized transcription factor and demonstrated a positive feedback effect on rooting in transgenic Nicotiana benthamiana cuttings. Thus, the results of this study explain the molecular mechanism of cutting rooting and provide candidate gene resources for developing genetic breeding strategies for optimizing superior clones of T. hybrid 'Zhongshanshan'.
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Affiliation(s)
- Jiaqi Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (J.L.); (L.X.); (C.Y.); (J.H.); (Z.W.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Lei Xuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (J.L.); (L.X.); (C.Y.); (J.H.); (Z.W.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (J.L.); (L.X.); (C.Y.); (J.H.); (Z.W.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (J.L.); (L.X.); (C.Y.); (J.H.); (Z.W.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Ziyang Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (J.L.); (L.X.); (C.Y.); (J.H.); (Z.W.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (J.L.); (L.X.); (C.Y.); (J.H.); (Z.W.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (J.L.); (L.X.); (C.Y.); (J.H.); (Z.W.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
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Jensen CNG, Pang JKY, Hahn CM, Gottardi M, Husted S, Moelbak L, Kovács ÁT, Fimognari L, Schulz A. Differential influence of Bacillus subtilis strains on Arabidopsis root architecture through common and distinct plant hormonal pathways. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111936. [PMID: 38042415 DOI: 10.1016/j.plantsci.2023.111936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/28/2023] [Indexed: 12/04/2023]
Abstract
Plant growth-promoting microbes (PGPM) can enhance crop yield and health, but knowledge of their mode-of-action is limited. We studied the influence of two Bacillus subtilis strains, the natural isolate ALC_02 and the domesticated 168 Gö, on Arabidopsis and hypothesized that they modify the root architecture by modulating hormone transport or signaling. Both bacteria promoted increase of shoot and root surface area in vitro, but through different root anatomical traits. Mutant plants deficient in auxin transport or signaling responded less to the bacterial strains than the wild-type, and application of the auxin transport inhibitor NPA strongly reduced the influence of the strains. Both bacteria produced auxin and enhanced shoot auxin levels in DR5::GUS reporter plants. Accordingly, most of the beneficial effects of the strains were dependent on functional auxin transport and signaling, while only 168 Gö depended on functional ethylene signaling. As expected, only ALC_02 stimulated plant growth in soil, unlike 168 Gö that was previously reported to have reduced biofilms. Collectively, the results highlight that B. subtilis strains can have strikingly different plant growth-promoting properties, dependent on what experimental setup they are tested in, and the importance of choosing the right PGPM for a desired root phenotype.
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Affiliation(s)
- Camilla Niketa Gadomska Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark; Plant Health Innovation, Chr-Hansen A/S, Taastrup, Denmark
| | - Janet Ka Yan Pang
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Charlotte Marie Hahn
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Søren Husted
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lars Moelbak
- Plant Health Innovation, Chr-Hansen A/S, Taastrup, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Alexander Schulz
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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Hua Z, Zhang T, Luo J, Bai H, Ma S, Qiang H, Guo X. Internalization, physiological responses and molecular mechanisms of lettuce to polystyrene microplastics of different sizes: Validation of simulated soilless culture. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132710. [PMID: 37832437 DOI: 10.1016/j.jhazmat.2023.132710] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/12/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
Microplastics (MPs) exists widely in the environment, and the resulting pollution of MPs has become a global environmental problem. Plants can absorb MPs through their roots. However, studies on the mechanism of the effect of root exposure to different size MPs on vegetables are limited. Here, we use Polystyrene (PS) MPs with different particle sizes to investigate the internalization, physiological response and molecular mechanism of lettuce to MPs. MPs may accumulate in large amounts in lettuce roots and migrate to the aboveground part through the vascular bundle, while small particle size MPs (SMPs, 100 nm) have stronger translocation ability than large particle size MPs (LMPs, 500 nm). MPs can cause physiological and biochemical responses and transcriptome changes in lettuce. SMPs and LMPs resulted in reduced biomass (38.27 % and 48.22 % reduction in fresh weight); caused oxidative stress (59.33 % and 47.74 % upregulation of SOD activity in roots) and differential gene expression (605 and 907 DEGs). Signal transduction, membrane transport and alteration of synthetic and metabolic pathways may be the main causes of physiological toxicity of lettuce. Our study provides important information for understanding the behavior and fate of MPs in edible vegetables, especially the physiological toxicity of MPs to edible vegetables, in order to assess the potential threat of MPs to food safety and agricultural sustainable development.
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Affiliation(s)
- Zhengdong Hua
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Tianli Zhang
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Junqi Luo
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Haoduo Bai
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Sirui Ma
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Hong Qiang
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China; Key Laboratory of Plant Nutrition and the Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Xuetao Guo
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China; Key Laboratory of Plant Nutrition and the Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, China.
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Meng Q, Zhang R, Wang Y, Zhi H, Tang S, Jia G, Diao X. Genome-Wide Characterization and Haplotypic Variation Analysis of the YUC Gene Family in Foxtail Millet ( Setaria italica). Int J Mol Sci 2023; 24:15637. [PMID: 37958621 PMCID: PMC10648439 DOI: 10.3390/ijms242115637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023] Open
Abstract
Panicle development and grain production in crop species are essential breeding characteristics affected by the synthesis of auxin, which is influenced by flavin monooxygenase-encoding genes such as YUC (YUCCA) family members. In this trial, fourteen YUCs were identified and named uniformly in foxtail millet, an ancient crop species cultivated across the world. The phylogenetic analysis revealed that the SiYUCs were clustered into four subgroups; protein motif and gene structure analyses suggested that the closely clustered SiYUC genes were relatively conserved within each subgroup; while genome mapping analysis indicated that the SiYUC genes were unevenly distributed on foxtail millet chromosomes and colinear with other grass species. Transcription analysis revealed that the SiYUC genes differed greatly in expression pattern in different tissues and contained hormonal/light/stress-responding cis-elements. The haplotype characterization of SiYUC genes indicated many superior haplotypes of SiYUCs correlated with higher panicle and grain weight could be favorably selected by breeding. These results will be useful for the further study of the functional characteristics of SiYUC genes, particularly with regard to the marker-assisted pyramiding of beneficial haplotypes in foxtail millet breeding programs.
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Affiliation(s)
| | | | | | | | | | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Q.M.); (R.Z.); (Y.W.); (H.Z.); (S.T.)
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Q.M.); (R.Z.); (Y.W.); (H.Z.); (S.T.)
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Shu Y, Zhang W, Tang L, Li Z, Liu X, Liu X, Liu W, Li G, Ying J, Huang J, Tong X, Hu H, Zhang J, Wang Y. ABF1 Positively Regulates Rice Chilling Tolerance via Inducing Trehalose Biosynthesis. Int J Mol Sci 2023; 24:11082. [PMID: 37446259 DOI: 10.3390/ijms241311082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Chilling stress seriously limits grain yield and quality worldwide. However, the genes and the underlying mechanisms that respond to chilling stress remain elusive. This study identified ABF1, a cold-induced transcription factor of the bZIP family. Disruption of ABF1 impaired chilling tolerance with increased ion leakage and reduced proline contents, while ABF1 over-expression lines exhibited the opposite tendency, suggesting that ABF1 positively regulated chilling tolerance in rice. Moreover, SnRK2 protein kinase SAPK10 could phosphorylate ABF1, and strengthen the DNA-binding ability of ABF1 to the G-box cis-element of the promoter of TPS2, a positive regulator of trehalose biosynthesis, consequently elevating the TPS2 transcription and the endogenous trehalose contents. Meanwhile, applying exogenous trehalose enhanced the chilling tolerance of abf1 mutant lines. In summary, this study provides a novel pathway 'SAPK10-ABF1-TPS2' involved in rice chilling tolerance through regulating trehalose homeostasis.
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Affiliation(s)
- Yazhou Shu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wensheng Zhang
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Liqun Tang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhiyong Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Xinyong Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Xixi Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Wanning Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Guanghao Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Jiezheng Ying
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Jie Huang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Xiaohong Tong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Honghong Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Yifeng Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
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10
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Meng S, Xiang H, Yang X, Ye Y, Han L, Xu T, Liu Y, Wang F, Tan C, Qi M, Li T. Effects of Low Temperature on Pedicel Abscission and Auxin Synthesis Key Genes of Tomato. Int J Mol Sci 2023; 24:ijms24119186. [PMID: 37298137 DOI: 10.3390/ijms24119186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Cold stress usually causes the abscission of floral organs and a decline in fruit setting rate, seriously reducing tomato yield. Auxin is one of the key hormones that affects the abscission of plant floral organs; the YUCCA (YUC) family is a key gene in the auxin biosynthesis pathway, but there are few research reports on the abscission of tomato flower organs. This experiment found that, under low temperature stress, the expression of auxin synthesis genes increased in stamens but decreased in pistils. Low temperature treatment decreased pollen vigor and pollen germination rate. Low night temperature reduced the tomato fruit setting rate and led to parthenocarpy, and the treatment effect was most obvious in the early stage of tomato pollen development. The abscission rate of tomato pTRV-Slfzy3 and pTRV-Slfzy5 silenced plants was higher than that of the control, which is the key auxin synthesis gene affecting the abscission rate. The expression of Solyc07g043580 was down-regulated after low night temperature treatment. Solyc07g043580 encodes the bHLH-type transcription factor SlPIF4. It has been reported that PIF4 regulates the expression of auxin synthesis and synthesis genes, and is a key protein in the interaction between low temperature stress and light in regulating plant development.
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Affiliation(s)
- Sida Meng
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Hengzuo Xiang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Xiaoru Yang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Yunzhu Ye
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Leilei Han
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Yufeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Feng Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Changhua Tan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticulture Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Shenyang 110866, China
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11
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Luo P, Di DW. Precise Regulation of the TAA1/TAR-YUCCA Auxin Biosynthesis Pathway in Plants. Int J Mol Sci 2023; 24:ijms24108514. [PMID: 37239863 DOI: 10.3390/ijms24108514] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The indole-3-pyruvic acid (IPA) pathway is the main auxin biosynthesis pathway in the plant kingdom. Local control of auxin biosynthesis through this pathway regulates plant growth and development and the responses to biotic and abiotic stresses. During the past decades, genetic, physiological, biochemical, and molecular studies have greatly advanced our understanding of tryptophan-dependent auxin biosynthesis. The IPA pathway includes two steps: Trp is converted to IPA by TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS/TRYPTOPHAN AMINOTRANSFERASE RELATED PROTEINs (TAA1/TARs), and then IPA is converted to IAA by the flavin monooxygenases (YUCCAs). The IPA pathway is regulated at multiple levels, including transcriptional and post-transcriptional regulation, protein modification, and feedback regulation, resulting in changes in gene transcription, enzyme activity and protein localization. Ongoing research indicates that tissue-specific DNA methylation and miRNA-directed regulation of transcription factors may also play key roles in the precise regulation of IPA-dependent auxin biosynthesis in plants. This review will mainly summarize the regulatory mechanisms of the IPA pathway and address the many unresolved questions regarding this auxin biosynthesis pathway in plants.
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Affiliation(s)
- Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Dong-Wei Di
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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