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Wang Z, Zhang W, Ding C, Xia Y, Yuan Z, Guo J, Yu J, Zhang B, Su X. RNA-seq reveals the gene expression in patterns in Populus × euramericana 'Neva' plantation under different precision water and fertilizer-intensive management. BMC PLANT BIOLOGY 2024; 24:759. [PMID: 39118015 PMCID: PMC11312740 DOI: 10.1186/s12870-024-05427-4] [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: 02/07/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Populus spp. is a crucial fast-growing and productive tree species extensively cultivated in the mid-latitude plains of the world. However, the impact of intensive cultivation management on gene expression in plantation remains largely unexplored. RESULTS Precision water and fertilizer-intensive management substantially increased key enzyme activities of nitrogen transport, assimilation, and photosynthesis (1.12-2.63 times than CK) in Populus × euramericana 'Neva' plantation. Meanwhile, this management approach had a significant regulatory effect on the gene expression of poplar plantations. 1554 differential expression genes (DEGs)were identified in drip irrigation (ND) compared with conventional irrigation. Relative to ND, 2761-4116 DEGs, predominantly up-regulated, were identified under three drip fertilization combinations, among which 202 DEGs were mainly regulated by fertilization. Moreover, drip irrigation reduced the expression of cell wall synthesis-related genes to reduce unnecessary water transport. Precision drip and fertilizer-intensive management promotes the synergistic regulation of carbon and nitrogen metabolism and up-regulates the expression of major genes in nitrogen transport and assimilation processes (5 DEGs), photosynthesis (15 DEGs), and plant hormone signal transduction (11 DEGs). The incorporation of trace elements further enhanced the up-regulation of secondary metabolic process genes. In addition, the co-expression network identified nine hub genes regulated by precision water and fertilizer-intensive management, suggesting a pivotal role in regulating the growth of poplar. CONCLUSION Precision water and fertilizer-intensive management demonstrated the ability to regulate the expression of key genes and transcription factor genes involved in carbon and nitrogen metabolism pathways, plant hormone signal transduction, and enhance the activity of key enzymes involved in related processes. This regulation facilitated nitrogen absorption and utilization, and photosynthetic abilities such as light capture, light transport, and electron transport, which faintly synergistically regulate the growth of poplar plantations. These results provide a reference for proposing highly efficient precision intensive management to optimize the expression of target genes.
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Affiliation(s)
- Zhou Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yongxiu Xia
- 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, 100023, P.R. China
| | - Zhengsai Yuan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jiangtao Guo
- Heibei Agricultural University, Baoding, 071001, P.R. China
| | - Jinjin Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Bingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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Xue L, Wang Y, Fan Y, Jiang Z, Wei Z, Zhai H, He S, Zhang H, Yang Y, Zhao N, Gao S, Liu Q. IbNF-YA1 is a key factor in the storage root development of sweet potato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1991-2002. [PMID: 38549549 DOI: 10.1111/tpj.16723] [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: 10/30/2023] [Revised: 01/19/2024] [Accepted: 03/05/2024] [Indexed: 06/14/2024]
Abstract
As a major worldwide root crop, the mechanism underlying storage root yield formation has always been a hot topic in sweet potato [Ipomoea batatas (L.) Lam.]. Previously, we conducted the transcriptome database of differentially expressed genes between the cultivated sweet potato cultivar "Xushu18," its diploid wild relative Ipomoea triloba without storage root, and their interspecific somatic hybrid XT1 with medium-sized storage root. We selected one of these candidate genes, IbNF-YA1, for subsequent analysis. IbNF-YA1 encodes a nuclear transcription factor Y subunit alpha (NF-YA) gene, which is significantly induced by the natural auxin indole-3-acetic acid (IAA). The storage root yield of the IbNF-YA1 overexpression (OE) plant decreased by 29.15-40.22% compared with the wild type, while that of the RNAi plant increased by 10.16-21.58%. Additionally, IAA content increased significantly in OE plants. Conversely, the content of IAA decreased significantly in RNAi plants. Furthermore, real-time quantitative reverse transcription-PCR (qRT-PCR) analysis demonstrated that the expressions of the key genes IbYUCCA2, IbYUCCA4, and IbYUCCA8 in the IAA biosynthetic pathway were significantly changed in transgenic plants. The results indicated that IbNF-YA1 could directly target IbYUCCA4 and activate IbYUCCA4 transcription. The IAA content of IbYUCCA4 OE plants increased by 71.77-98.31%. Correspondingly, the storage root yield of the IbYUCCA4 OE plant decreased by 77.91-80.52%. These findings indicate that downregulating the IbNF-YA1 gene could improve the storage root yield in sweet potato.
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Affiliation(s)
- Luyao Xue
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yuxin Wang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yue Fan
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhicheng Jiang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zihao Wei
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yufeng Yang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
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Liu Y, Song P, Yan M, Luo J, Wang Y, Fan F. Integrated Transcriptome and Proteome Analysis Reveals the Regulatory Mechanism of Root Growth by Protein Disulfide Isomerase in Arabidopsis. Int J Mol Sci 2024; 25:3596. [PMID: 38612408 PMCID: PMC11011405 DOI: 10.3390/ijms25073596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Protein disulfide isomerase (PDI, EC 5.3.4.1) is a thiol-disulfide oxidoreductase that plays a crucial role in catalyzing the oxidation and rearrangement of disulfides in substrate proteins. In plants, PDI is primarily involved in regulating seed germination and development, facilitating the oxidative folding of storage proteins in the endosperm, and also contributing to the formation of pollen. However, the role of PDI in root growth has not been previously studied. This research investigated the impact of PDI gene deficiency in plants by using 16F16 [2-(2-Chloroacetyl)-2,3,4,9-tetrahydro-1-methyl-1H-pyrido[3,4-b]indole-1-carboxylic acid methyl ester], a small-molecule inhibitor of PDI, to remove functional redundancy. The results showed that the growth of Arabidopsis roots was significantly inhibited when treated with 16F16. To further investigate the effects of 16F16 treatment, we conducted expression profiling of treated roots using RNA sequencing and a Tandem Mass Tag (TMT)-based quantitative proteomics approach at both the transcriptomic and proteomic levels. Our analysis revealed 994 differentially expressed genes (DEGs) at the transcript level, which were predominantly enriched in pathways associated with "phenylpropane biosynthesis", "plant hormone signal transduction", "plant-pathogen interaction" and "starch and sucrose metabolism" pathways. Additionally, we identified 120 differentially expressed proteins (DEPs) at the protein level. These proteins were mainly enriched in pathways such as "phenylpropanoid biosynthesis", "photosynthesis", "biosynthesis of various plant secondary metabolites", and "biosynthesis of secondary metabolites" pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network for root shortening in Arabidopsis seedlings under 16F16 treatment, mainly involving phenylpropane biosynthesis and plant hormone signal transduction pathways. This study enhances our understanding of the significant role of PDIs in Arabidopsis root growth and provides insights into the regulatory mechanisms of root shortening following 16F16 treatment.
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Affiliation(s)
| | | | | | | | - Yingjuan Wang
- State Key Laboratory of Biotechnology of Shannxi Province, College of Life Science, Northwest University, Xi’an 710069, China; (Y.L.); (P.S.); (M.Y.); (J.L.)
| | - Fenggui Fan
- State Key Laboratory of Biotechnology of Shannxi Province, College of Life Science, Northwest University, Xi’an 710069, China; (Y.L.); (P.S.); (M.Y.); (J.L.)
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4
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Jiang D, Yang G, Huang LJ, Chen K, Tang Y, Pi X, Yang R, Peng X, Cui C, Li N. Unveiling the toxic effects, physiological responses and molecular mechanisms of tobacco (Nicotiana tabacum) in exposure to organic ultraviolet filters. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133060. [PMID: 38016314 DOI: 10.1016/j.jhazmat.2023.133060] [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: 08/22/2023] [Revised: 10/17/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023]
Abstract
Exposure to organic ultraviolet (UV) filters has raised concerns due to their potential adverse effects on environments. However, their toxic mechanisms on plants remain elusive. In this study, using integrative physiological and transcriptomic approaches we investigated the physiological and molecular responses to three representative UV filters, namely oxybenzone (OBZ), avobenzone (AVB), and octinoxate (OMC), in an agricultural model plant tobacco. The exposure to UV filters disrupts the functionality of photosystem reaction centers and the light-harvesting apparatus. Concurrently, UV filters exert a suppressive effect on the expression of genes encoding Rubisco and Calvin-Benson cycle enzymes, resulting in a decreased efficiency of the Calvin-Benson cycle and consequently hampering the process of photosynthesis. Exposure to UV filters leads to significant generation of reactive oxygen species within tobacco leaves and downregulation of oxidoreductase activities. Moreover, UV filters promote abscisic acid (ABA) accumulation by inducing the expression of ABA biosynthesis genes whereas repress indole-3-acetic acid (IAA) biosynthesis gene expression, which induce leaf yellowing and slow plant growth. In summary, the organic UV filters exert toxic effects on tobacco growth by inhibiting chlorophyll synthesis, photosynthesis, and the Calvin-Benson cycle, while generating excessive reactive oxygen species. This study sheds light on the toxic and tolerance mechanisms of UV filters in agricultural crops.
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Affiliation(s)
- Dong Jiang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
| | - Guoqun Yang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
| | - Li-Jun Huang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Kebin Chen
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
| | - Yangcan Tang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
| | - Xin Pi
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Runke Yang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Xia Peng
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Chuantong Cui
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Ning Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
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5
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Uddin S, Munir MZ, Larriba E, Pérez-Pérez JM, Gull S, Pervaiz T, Mahmood U, Mahmood Z, Sun Y, Li Y. Temporal profiling of physiological, histological, and transcriptomic dissection during auxin-induced adventitious root formation in tetraploid Robinia pseudoacacia micro-cuttings. PLANTA 2024; 259:66. [PMID: 38332379 DOI: 10.1007/s00425-024-04341-1] [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: 10/10/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
MAIN CONCLUSION Optimal levels of indole-3-butyric acid (IBA) applied at the stem base promote adventitious root (AR) initiation and primordia formation, thus promoting the rooting of leafy micro-cuttings of tetraploid Robinia pseudoacacia. Tetraploid Robinia pseudoacacia L. is a widely cultivated tree in most regions of China that has a hard-rooting capability, propagated by stem cuttings. This study utilizes histological, physiological, and transcriptomic approaches to explore how root primordia are induced after indole butyric acid (IBA) treatment of micro-cuttings. IBA application promoted cell divisions in some cells within the vasculature, showing subcellular features associated with adventitious root (AR) founder cells. The anatomical structure explicitly showed that AR initiated from the cambium layer and instigate the inducible development of AR primordia. Meanwhile, the hormone data showed that similar to that of indole-3-acetic acid, the contents of trans-zeatin and abscisic acid peaked at early stages of AR formation and increased gradually in primordia formation across the subsequent stages, suggesting their indispensable roles in AR induction. On the contrary, 24-epibrassinolide roughly maintained at extremely high levels during primordium initiation thoroughly, indicating its presence was involved in cell-specific reorganization during AR development. Furthermore, antioxidant activities transiently increased in the basal region of micro-cuttings and may serve as biochemical indicators for distinct rooting phases, potentially aiding in AR formation. Transcriptomic analysis during the early stages of root formation shows significant downregulation of the abscisic acid and jasmonate signaling pathways, while ethylene and cytokinin signaling seems upregulated. Network analysis of genes involved in carbon metabolism and photosynthesis indicates that the basal region of the micro-cuttings undergoes rapid reprogramming, which results in the breakdown of sugars into pyruvate. This pyruvate is then utilized to fuel the tricarboxylic acid cycle, thereby sustaining growth through aerobic respiration. Collectively, our findings provide a time-course morphophysiological dissection and also suggest the regulatory role of a conserved auxin module in AR development in these species.
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Affiliation(s)
- Saleem Uddin
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Muhammad Zeeshan Munir
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández de Elche, Alicante, Spain
| | | | - Sadia Gull
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Tariq Pervaiz
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 22963, USA
| | - Umer Mahmood
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Zahid Mahmood
- Crop Sciences Institute, National Agricultural Research Centre, Islamabad, 44000, Pakistan
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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6
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Feng YY, Du H, Huang KY, Ran JH, Wang XQ. Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce. Commun Biol 2024; 7:114. [PMID: 38242964 PMCID: PMC10799047 DOI: 10.1038/s42003-024-05786-6] [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: 07/27/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.
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Affiliation(s)
- Yuan-Yuan Feng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Kai-Yuan Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Zhang S, Wang B, Li Q, Hui W, Yang L, Wang Z, Zhang W, Yue F, Liu N, Li H, Lu F, Zhang K, Zeng Q, Wu AM. CRISPR/Cas9 mutated p-coumaroyl shikimate 3'-hydroxylase 3 gene in Populus tomentosa reveals lignin functioning on supporting tree upright. Int J Biol Macromol 2023; 253:126762. [PMID: 37683750 DOI: 10.1016/j.ijbiomac.2023.126762] [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: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
The lignin plays one of the most important roles in plant secondary metabolism. However, it is still unclear how lignin can contribute to the impressive height of wood growth. In this study, C3'H, a rate-limiting enzyme of the lignin pathway, was used as the target gene. C3'H3 was knocked out by CRISPR/Cas9 in Populus tomentosa. Compared with wild-type popular trees, c3'h3 mutants exhibited dwarf phenotypes, collapsed xylem vessels, weakened phloem thickening, decreased hydraulic conductivity and photosynthetic efficiency, and reduced auxin content, except for reduced total lignin content and significantly increased H-subunit lignin. In the c3'h3 mutant, the flavonoid biosynthesis genes CHS, CHI, F3H, DFR, ANR, and LAR were upregulated, and flavonoid metabolite accumulations were detected, indicating that decreasing the lignin biosynthesis pathway enhanced flavonoid metabolic flux. Furthermore, flavonoid metabolites, such as naringenin and hesperetin, were largely increased, while higher hesperetin content suppressed plant cell division. Thus, studying the c3'h3 mutant allows us to deduce that lignin deficiency suppresses tree growth and leads to the dwarf phenotype due to collapsed xylem and thickened phloem, limiting material exchanges and transport.
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Affiliation(s)
- Sufang Zhang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Bo Wang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Qian Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Wenkai Hui
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Linjie Yang
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Zhihua Wang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Wenjuan Zhang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Fengxia Yue
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Nian Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Huiling Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Fachuang Lu
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China; Department of Biochemistry and Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA
| | - Kewei Zhang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Qingyin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China.
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Wakeman A, Bennett T. Auxins and grass shoot architecture: how the most important hormone makes the most important plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6975-6988. [PMID: 37474124 PMCID: PMC10690731 DOI: 10.1093/jxb/erad288] [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: 03/05/2023] [Accepted: 07/19/2023] [Indexed: 07/22/2023]
Abstract
Cereals are a group of grasses cultivated by humans for their grain. It is from these cereal grains that the majority of all calories consumed by humans are derived. The production of these grains is the result of the development of a series of hierarchical reproductive structures that form the distinct shoot architecture of the grasses. Being spatiotemporally complex, the coordination of grass shoot development is tightly controlled by a network of genes and signals, including the key phytohormone auxin. Hormonal manipulation has therefore been identified as a promising potential approach to increasing cereal crop yields and therefore ultimately global food security. Recent work translating the substantial body of auxin research from model plants into cereal crop species is revealing the contribution of auxin biosynthesis, transport, and signalling to the development of grass shoot architecture. This review discusses this still-maturing knowledge base and examines the possibility that changes in auxin biology could have been a causative agent in the evolution of differences in shoot architecture between key grass species, or could underpin the future selective breeding of cereal crops.
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Affiliation(s)
- Alex Wakeman
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Tom Bennett
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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9
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Jiang Y, Du Y, Chen C, Wang D, Zhong Y, Deng Y. Integrative Metabolomic and Transcriptomic Landscape during Akebia trifoliata Fruit Ripening and Cracking. Int J Mol Sci 2023; 24:16732. [PMID: 38069056 PMCID: PMC10706055 DOI: 10.3390/ijms242316732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Akebia trifoliata fruit is prone to crack after ripening, but little is known about the mechanism underlying the cracking process. This study integrated transcriptomic and metabolomic data, revealing significant changes in 398 metabolites and 8414 genes during ripening and cracking, mainly impacting cell-wall metabolism. Multi-omics joint analysis indicated that genes related to polygalacturonase, pectate lyase, α-amylase, and glycogen phosphorylase were up-regulated after cracking, degrading cell wall and starch. Concurrently, diminished photosynthetic metabolism and heightened phenylpropanoid metabolism suggested alterations in cuticle structure, potentially impacting cell-wall robustness. Numerous auxin and abscisic acid signaling-related genes were expressed, and we assume that they contributed to the promoting peel growth. These alterations collectively might compromise peel strength and elevate expanding pressure, potentially leading to A. trifoliata cracking. Transcription factors, predominantly ethylene response factors and helix-loop-helix family members, appeared to regulate these metabolic shifts. These findings provide valuable insights into A. trifoliata cracking mechanisms; however, direct experimental validation of these assumptions is necessary to strengthen these conclusions and expedite their commercial utilization.
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Affiliation(s)
- Yongli Jiang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (Y.J.); (Y.D.); (C.C.)
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China (Y.Z.)
| | - Yanlin Du
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (Y.J.); (Y.D.); (C.C.)
| | - Chongyang Chen
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (Y.J.); (Y.D.); (C.C.)
| | - Danfeng Wang
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China (Y.Z.)
| | - Yu Zhong
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China (Y.Z.)
| | - Yun Deng
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China (Y.Z.)
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10
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Zhang H, Chen B, Zhao X, Hu J, Dong Z, Xiao H, Yuan Y, Guo F, Wang Y, Ni D, Wang P. Novel insights into the role of leaf in the cutting process of Camellia sinensis using physiological, biochemical and transcriptome analyses. TREE PHYSIOLOGY 2023; 43:2031-2045. [PMID: 37742093 DOI: 10.1093/treephys/tpad101] [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: 05/22/2023] [Accepted: 08/12/2023] [Indexed: 09/25/2023]
Abstract
Cuttage is the preferred approach for rapid propagation of many species including tea plant (Camellia sinensis). Leaf serves as a key part of nodal cutting, but there is a lack of systematic research on its role in the cutting process. In this study, 24 tea cultivars were employed to prove the necessity of leaf and light during cuttage. Further leaf physiological parameters found that lower net photosynthesis rate probably promoted rooting. Phytohormone content detection showed that auxin content and composition pattern were related to rooting ability. Leaf transcriptome analyses of cuttings from a representative easy-to-root cultivar (cv. Echa 10) revealed that genes involved in carbohydrate metabolism, signal transduction, metabolite biosynthesis and transportation were differentially expressed during the rooting process. CsTSA1, CsYUC10, CsAUX1s, CsPIN3 and CsPIN5 were selected as the candidate genes, which possibly regulate the rooting of nodal cuttings. These results illustrate the necessity of the leaf in cuttage and provide molecular evidence that leaf is an important place for signal transduction, metabolite synthesis and transport during the rooting process.
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Affiliation(s)
- Hong Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Binrui Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyi Zhao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Hu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhijie Dong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Xiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanwen Yuan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Guo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dejiang Ni
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Pu Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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11
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Yu L, Yao M, Mao L, Ma T, Nie Y, Ma H, Shao K, An H, Zhao J. Rice DSP controls stigma, panicle and tiller primordium initiation. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2358-2373. [PMID: 37523341 PMCID: PMC10579714 DOI: 10.1111/pbi.14137] [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: 10/12/2021] [Revised: 06/19/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Tiller and seed number are key determinants of rice (Oryza sativa) yield. These traits are mainly affected by tiller, panicle, spikelet and stigma formation, but to date, no single gene involved in the development of all these organs has been identified. Here, we found a rice mutant defective stigma and panicle (dsp) with greatly reduced numbers of tillers and panicle branches, and ovaries lacking stigmas, due to defects in primordium initiation. We cloned DSP using sequencing-based mapping and verified its function with the CRISPR/Cas9 system. DSP encodes a transcription factor containing an APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain that recognizes the GCC motif and a transcription-activating domain at the site of 244-314 that contains an angiosperm-related (AR) motif. Mutating the AR motif resulted in the dsp mutant phenotypes, whereas mutating the AP2/ERF domain led to seedling death. DSP directly regulated PINOID (PID) expression to determine the emergence of rice stigmas, and PID overexpression partially rescued the stigma defect in the dsp cr2-8 and dsp mutants. Moreover, DSP indirectly affected LAX PANICLE1 (LAX1) expression to determine tiller primordium formation and synergistically regulated panicle primordium development. Our results indicated that DSP was a key regulator that modulated different genetic pathways to control the initiation of stigma primordia, the axillary meristem formation of tillers and panicle branches, which revealed their molecular mechanisms and cross-networks, laying the vital foundation for rice yield and trait improvement.
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Affiliation(s)
- Li Yu
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Min Yao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Lianlian Mao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Tengfei Ma
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Yanshen Nie
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Haoli Ma
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Kun Shao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Hongqiang An
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
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12
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Li X, Xi D, Gao L, Zhu H, Yang X, Song X, Zhang C, Miao L, Zhang D, Zhang Z, Hou X, Zhu Y, Wei M. Integrated Transcriptome and Proteome Analysis Revealed the Regulatory Mechanism of Hypocotyl Elongation in Pakchoi. Int J Mol Sci 2023; 24:13808. [PMID: 37762111 PMCID: PMC10531338 DOI: 10.3390/ijms241813808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Hypocotyl length is a critical determinant for the efficiency of mechanical harvesting in pakchoi production, but the knowledge on the molecular regulation of hypocotyl growth is very limited. Here, we report a spontaneous mutant of pakchoi, lhy7.1, and identified its characteristics. We found that it has an elongated hypocotyl phenotype compared to the wild type caused by the longitudinal growth of hypocotyl cells. Different light quality treatments, transcriptome, and proteomic analyses were performed to reveal the molecular mechanisms of hypocotyl elongation. The data showed that the hypocotyl length of lhy7.1 was significantly longer than that of WT under red, blue, and white lights but there was no significant difference under dark conditions. Furthermore, we used transcriptome and label-free proteome analyses to investigate differences in gene and protein expression levels between lhy7.1 and WT. At the transcript level, 4568 differentially expressed genes (DEGs) were identified, which were mainly enriched in "plant hormone signal transduction", "photosynthesis", "photosynthesis-antenna proteins", and "carbon fixation in photosynthetic organisms" pathways. At the protein level, 1007 differentially expressed proteins (DEPs) were identified and were mainly enriched in photosynthesis-related pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network of hypocotyl elongation involving plant hormone signal transduction and photosynthesis-related pathways. The findings of this study help elucidate the regulatory mechanisms of hypocotyl elongation in lhy7.1.
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Affiliation(s)
- Xiaofeng Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China;
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.X.); (L.G.); (H.Z.); (X.Y.); (L.M.); (D.Z.); (Z.Z.)
| | - Dandan Xi
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.X.); (L.G.); (H.Z.); (X.Y.); (L.M.); (D.Z.); (Z.Z.)
| | - Lu Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.X.); (L.G.); (H.Z.); (X.Y.); (L.M.); (D.Z.); (Z.Z.)
| | - Hongfang Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.X.); (L.G.); (H.Z.); (X.Y.); (L.M.); (D.Z.); (Z.Z.)
| | - Xiuke Yang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.X.); (L.G.); (H.Z.); (X.Y.); (L.M.); (D.Z.); (Z.Z.)
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (X.H.)
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China;
| | - Changwei Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (X.H.)
| | - Liming Miao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.X.); (L.G.); (H.Z.); (X.Y.); (L.M.); (D.Z.); (Z.Z.)
| | - Dingyu Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.X.); (L.G.); (H.Z.); (X.Y.); (L.M.); (D.Z.); (Z.Z.)
| | - Zhaohui Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.X.); (L.G.); (H.Z.); (X.Y.); (L.M.); (D.Z.); (Z.Z.)
| | - Xilin Hou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (X.H.)
| | - Yuying Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.X.); (L.G.); (H.Z.); (X.Y.); (L.M.); (D.Z.); (Z.Z.)
| | - Min Wei
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China;
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13
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Qi Y, Wang L, Li W, Dang Z, Xie Y, Zhao W, Zhao L, Li W, Yang C, Xu C, Zhang J. Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum. Int J Mol Sci 2023; 24:11006. [PMID: 37446183 DOI: 10.3390/ijms241311006] [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: 05/24/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Auxin response factors (ARFs) are critical components of the auxin signaling pathway, and are involved in diverse plant biological processes. However, ARF genes have not been investigated in flax (Linum usitatissimum L.), an important oilseed and fiber crop. In this study, we comprehensively analyzed the ARF gene family and identified 33 LuARF genes unevenly distributed on the 13 chromosomes of Longya-10, an oil-use flax variety. Detailed analysis revealed wide variation among the ARF family members and predicted nuclear localization for all proteins. Nineteen LuARFs contained a complete ARF structure, including DBD, MR, and CTD, whereas the other fourteen lacked the CTD. Phylogenetic analysis grouped the LuARFs into four (I-V) clades. Combined with sequence analysis, the LuARFs from the same clade showed structural conservation, implying functional redundancy. Duplication analysis identified twenty-seven whole-genome-duplicated LuARF genes and four tandem-duplicated LuARF genes. These duplicated gene pairs' Ka/Ks ratios suggested a strong purifying selection pressure on the LuARF genes. Collinearity analysis revealed that about half of the LuARF genes had homologs in other species, indicating a relatively conserved nature of the ARFs. The promoter analysis identified numerous hormone- and stress-related elements, and the qRT-PCR experiment revealed that all LuARF genes were responsive to phytohormone (IAA, GA3, and NAA) and stress (PEG, NaCl, cold, and heat) treatments. Finally, expression profiling of LuARF genes in different tissues by qRT-PCR indicated their specific functions in stem or capsule growth. Thus, our findings suggest the potential functions of LuARFs in flax growth and response to an exogenous stimulus, providing a basis for further functional studies on these genes.
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Affiliation(s)
- Yanni Qi
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Limin Wang
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Wenjuan Li
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Zhao Dang
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Yaping Xie
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Wei Zhao
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Lirong Zhao
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Wen Li
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Chenxi Yang
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Chenmeng Xu
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Jianping Zhang
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
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14
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He S, Zhi F, Min Y, Ma R, Ge A, Wang S, Wang J, Liu Z, Guo Y, Chen M. The MYB59 transcription factor negatively regulates salicylic acid- and jasmonic acid-mediated leaf senescence. PLANT PHYSIOLOGY 2023; 192:488-503. [PMID: 36542529 PMCID: PMC10152657 DOI: 10.1093/plphys/kiac589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 05/03/2023]
Abstract
Leaf senescence is the final stage of leaf development and is affected by various exogenous and endogenous factors. Transcriptional regulation is essential for leaf senescence, however, the underlying molecular mechanisms remain largely unclear. In this study, we report that the transcription factor MYB59, which was predominantly expressed in early senescent rosette leaves, negatively regulates leaf senescence in Arabidopsis (Arabidopsis thaliana). RNA sequencing revealed a large number of differentially expressed genes involved in several senescence-related biological processes in myb59-1 rosette leaves. Chromatin immunoprecipitation and transient dual-luciferase reporter assays demonstrated that MYB59 directly repressed the expression of SENESCENCE ASSOCIATED GENE 18 and indirectly inhibited the expression of several other senescence-associated genes to delay leaf senescence. Moreover, MYB59 was induced by salicylic acid (SA) and jasmonic acid (JA). MYB59 inhibited SA production by directly repressing the expression of ISOCHORISMATE SYNTHASE 1 and PHENYLALANINE AMMONIA-LYASE 2 and restrained JA biosynthesis by directly suppressing the expression of LIPOXYGENASE 2, thus forming two negative feedback regulatory loops with SA and JA and ultimately delaying leaf senescence. These results help us understand the novel function of MYB59 and provide insights into the regulatory network controlling leaf senescence in Arabidopsis.
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Affiliation(s)
- Shuangcheng He
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fang Zhi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuanchang Min
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Rong Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ankang Ge
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shixiang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jianjun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zijin Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuan Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Mingxun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
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15
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Ma Q, Wang F, Song W, Huang C, Xie K, Wei Z, Li Y, Chen J, Zhang H, Sun Z. Transcriptome analysis of auxin transcription factor OsARF17-mediated rice stripe mosaic virus response in rice. Front Microbiol 2023; 14:1131212. [PMID: 36970706 PMCID: PMC10033593 DOI: 10.3389/fmicb.2023.1131212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
IntroductionPlant auxin response factors (ARFs) play an irreplaceable role in regulating the expression of auxin response genes. Our previous studies have indicated that auxin response factor OsARF17 plays a crucial role in plant defense against diverse rice viruses.MethodsUtilizing a comparative transcriptome analysis of Rice stripe mosaic virus (RSMV)-inoculated OsARF17 mutant rice plants, to further elucidate the molecular mechanism of OsARF17 in antiviral defense pathway.ResultsKEGG enrichment analyses showed that the down-regulated differentially expressed genes (DEGs) belonged to plant-pathogen interaction and plant hormone signal transduction pathways were markedly enriched in OsARF17 mutants under RSMV inoculation. Furthermore, Gene ontology (GO) analyses revealed that these genes were enriched in a variety of hormone biosynthetic process, including jasmonic acid (JA), auxin, and abscisic acid (ABA). RT-qPCR assays showed that the induction of plant defense-related genes, such as WRKY transcription factors, OsAHT2 and OsDR8, and JA-related genes, were significantly suppressed in OsARF17 mutants in response to RSMV.DiscussionOur study reveals that OsARF17-mediated antiviral immunity may be achieved through affecting the interaction between different phytohormones and regulating defense gene expression in rice. This study provides new insights into the molecular mechanisms of auxin signaling in the rice-virus interaction.
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16
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Genome-wide evolutionary analysis of AUX/IAA gene family in wheat identifies a novel gene TaIAA15-1A regulating flowering time by interacting with ARF. Int J Biol Macromol 2023; 227:285-296. [PMID: 36549029 DOI: 10.1016/j.ijbiomac.2022.12.175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Flowering time is a critical agronomic trait that has strong effects on crop yields. Auxin signaling pathway plays an important role in various development processes, such as flowering, grain development. However, no Aux/IAA gene had been reported to have functions involving in wheat flowering time. Here, we systematically performed genome-wide identification, classification, domain distribution, exon-intron structure, chromosome locations and global expression pattern of Aux/IAA gene family in 14 plant genomes (including Triticum aestivum). A phylogenetic model was proposed to infer the Aux/IAA evolutionary history involving in a central exon-intron structure "2121" during evolution. Overexpression of TaIAA15-1A caused an early flowering time in Brachypodium. RNA-seq analysis showed that TaIAA15-1A overexpression alters various pathways including phytohormone signaling pathway, flowering-related pathway, and polyamine biosynthesis pathway. Screening of auxin response factor (ARF) genes identified BdARF16 that interacted with TaIAA15-1A. Exogenous polyamine (spermidine and spermine) treatments promoted early flowering and (putrescine and DCHA) delayed flowering time of WT plants. Our finding will provide insights on mechanisms of Aux/IAAs gene family and TaIAA15-1A, illustrating the potential during crop improvement programs.
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Jiang Z, Zhang H, Jiao P, Wei X, Liu S, Guan S, Ma Y. The Integration of Metabolomics and Transcriptomics Provides New Insights for the Identification of Genes Key to Auxin Synthesis at Different Growth Stages of Maize. Int J Mol Sci 2022; 23:13195. [PMID: 36361983 PMCID: PMC9659120 DOI: 10.3390/ijms232113195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 10/29/2023] Open
Abstract
As a staple food crop, maize is widely cultivated worldwide. Sex differentiation and kernel development are regulated by auxin, but the mechanism regulating its synthesis remains unclear. This study explored the influence of the growth stage of maize on the secondary metabolite accumulation and gene expression associated with auxin synthesis. Transcriptomics and metabonomics were used to investigate the changes in secondary metabolite accumulation and gene expression in maize leaves at the jointing, tasseling, and pollen-release stages of plant growth. In total, 1221 differentially accumulated metabolites (DAMs) and 4843 differentially expressed genes (DEGs) were screened. KEGG pathway enrichment analyses of the DEGs and DAMs revealed that plant hormone signal transduction, tryptophan metabolism, and phenylpropanoid biosynthesis were highly enriched. We summarized the key genes and regulatory effects of the tryptophan-dependent auxin biosynthesis pathways, giving new insights into this type of biosynthesis. Potential MSTRG.11063 and MSTRG.35270 and MSTRG.21978 genes in auxin synthesis pathways were obtained. A weighted gene co-expression network analysis identified five candidate genes, namely TSB (Zm00001d046676 and Zm00001d049610), IGS (Zm00001d020008), AUX2 (Zm00001d006283), TAR (Zm00001d039691), and YUC (Zm00001d025005 and Zm00001d008255), which were important in the biosynthesis of both tryptophan and auxin. This study provides new insights for understanding the regulatory mechanism of auxin synthesis in maize.
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Affiliation(s)
- Zhenzhong Jiang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
| | - Honglin Zhang
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Peng Jiao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
| | - Xiaotong Wei
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Siyan Liu
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Shuyan Guan
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Yiyong Ma
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
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Zhang Y, Yu J, Xu X, Wang R, Liu Y, Huang S, Wei H, Wei Z. Molecular Mechanisms of Diverse Auxin Responses during Plant Growth and Development. Int J Mol Sci 2022; 23:ijms232012495. [PMID: 36293351 PMCID: PMC9604407 DOI: 10.3390/ijms232012495] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
The plant hormone auxin acts as a signaling molecule to regulate numerous developmental processes throughout all stages of plant growth. Understanding how auxin regulates various physiological and developmental processes has been a hot topic and an intriguing field. Recent studies have unveiled more molecular details into how diverse auxin responses function in every aspect of plant growth and development. In this review, we systematically summarized and classified the molecular mechanisms of diverse auxin responses, and comprehensively elaborated the characteristics and multilevel regulation mechanisms of the canonical transcriptional auxin response. On this basis, we described the characteristics and differences between different auxin responses. We also presented some auxin response genes that have been genetically modified in plant species and how their changes impact various traits of interest. Finally, we summarized some important aspects and unsolved questions of auxin responses that need to be focused on or addressed in future research. This review will help to gain an overall understanding of and some insights into the diverse molecular mechanisms of auxin responses in plant growth and development that are instrumental in harnessing genetic resources in molecular breeding of extant plant species.
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Affiliation(s)
- Yang Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiuyue Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shan Huang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Zhigang Wei
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
- Correspondence: or
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Yu Y, Meng N, Chen S, Zhang H, Liu Z, Wang Y, Jing Y, Wang Y, Chen S. Transcriptomic profiles of poplar (Populus simonii × P. nigra) cuttings during adventitious root formation. Front Genet 2022; 13:968544. [PMID: 36160010 PMCID: PMC9493132 DOI: 10.3389/fgene.2022.968544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/16/2022] [Indexed: 11/21/2022] Open
Abstract
The formation of adventitious roots (ARs) is vital for the vegetative propagation of poplars. However, the relevant mechanisms remain unclear. To reveal the underlying molecular mechanism, we used RNA-seq to investigate the transcriptional alterations of poplar cuttings soaked in water for 0, 2, 4, 6, 8, and 10 d; 3,798 genes were differentially expressed at all the time points, including 2,448 upregulated and 1,350 downregulated genes. Biological processes including “cell cycle,” “photosynthesis,” “regulation of hormone levels,” and “auxin transport” were enriched in the differentially expressed genes (DEGs). KEGG results showed that the common DEGs were most enriched in the pathway of “Carbon fixation in photosynthetic organisms” and “Starch and sucrose metabolism.” We further dissected 38 DEGs related to root and auxin, including two lateral root primordium 1 (LRP1), one root meristem growth factor (RGF9), one auxin-induced in the root (AIR12), three rooting-associated genes (AUR1 and AUR3), eight auxin transcription factors (ARFs and LBDs), 10 auxin respective genes (SAURs and GH3s), nine auxin transporters (PINs, ABCs, LAX2, and AUXs), and four auxin signal genes (IAAs and TIR1). We found that the rooting abilities of poplar cuttings with and without leaves are different. By applying different concentrations of IBA and sucrose to the top of cuttings without leaves, we found that 0.2 mg/ml IBA and 2 mg/ml sucrose had the best effect on promoting AR formation. The transcriptome results indicated photosynthesis may influence AR formation in poplar cuttings with leaves and revealed a potential regulatory mechanism of leafy cuttage from poplar cuttings. In addition, we provided a new perspective to resolve rooting difficulties in recalcitrant species.
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Affiliation(s)
- Yue Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Nan Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hongjiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhijie Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yiran Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yanan Jing
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yuting Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- *Correspondence: Su Chen,
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Dai X, Zhang S, Liu S, Qi H, Duan X, Han Z, Wang J. Functional Characterization and Phenotyping of Protoplasts on a Microfluidics-Based Flow Cytometry. BIOSENSORS 2022; 12:bios12090688. [PMID: 36140072 PMCID: PMC9496511 DOI: 10.3390/bios12090688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022]
Abstract
A better understanding of the phenotypic heterogeneity of protoplasts requires a comprehensive analysis of the morphological and metabolic characteristics of many individual cells. In this study, we developed a microfluidic flow cytometry with fluorescence sensor for functional characterization and phenotyping of protoplasts to allow an unbiased assessment of the influence of environmental factors at the single cell level. First, based on the measurement of intracellular homeostasis of reactive oxygen species (ROS) with a DCFH-DA dye, the effects of various external stress factors such as H2O2, temperature, ultraviolet (UV) light, and cadmium ions on intracellular ROS accumulation in Arabidopsis mesophyll protoplasts were quantitatively investigated. Second, a faster and stronger oxidative burst was observed in Petunia protoplasts isolated from white petals than in those isolated from purple petals, demonstrating the photoprotective role of anthocyanins. Third, using mutants with different endogenous auxin, we demonstrated the beneficial effect of auxin during the process of primary cell wall regeneration. Moreover, UV-B irradiation has a similar accelerating effect by increasing the intracellular auxin level, as shown by double fluorescence channels. In summary, our work has revealed previously underappreciated phenotypic variability within a protoplast population and demonstrated the advantages of a microfluidic flow cytometry for assessing the in vivo dynamics of plant metabolic and physiological indices at the single-cell level.
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Affiliation(s)
- Xingda Dai
- School of Environmental Science and Engineering, Tianjin University, Weijin Rd. 92, Tianjin 300072, China
| | - Shuaihua Zhang
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Weijin Rd. 92, Tianjin 300072, China
| | - Siyuan Liu
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Weijin Rd. 92, Tianjin 300072, China
| | - Hang Qi
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Weijin Rd. 92, Tianjin 300072, China
| | - Xuexin Duan
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Weijin Rd. 92, Tianjin 300072, China
| | - Ziyu Han
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Weijin Rd. 92, Tianjin 300072, China
- Correspondence: (Z.H.); (J.W.)
| | - Jiehua Wang
- School of Environmental Science and Engineering, Tianjin University, Weijin Rd. 92, Tianjin 300072, China
- Correspondence: (Z.H.); (J.W.)
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Yang Y, Chen T, Dai X, Yang D, Wu Y, Chen H, Zheng Y, Zhi Q, Wan X, Tan X. Comparative transcriptome analysis revealed molecular mechanisms of peanut leaves responding to Ralstonia solanacearum and its type III secretion system mutant. Front Microbiol 2022; 13:998817. [PMID: 36090119 PMCID: PMC9453164 DOI: 10.3389/fmicb.2022.998817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease that limits peanut production and quality, but the molecular mechanisms of the peanut response to R. solanacearum remain unclear. In this study, we reported the first work analyzing the transcriptomic changes of the resistant and susceptible peanut leaves infected with R. solanacearum HA4-1 and its type III secretion system mutant strains by the cutting leaf method at different timepoints (0, 24, 36, and 72 h post inoculation). A total of 125,978 differentially expressed genes (DEGs) were identified and subsequently classified into six groups to analyze, including resistance-response genes, susceptibility-response genes, PAMPs induced resistance-response genes, PAMPs induced susceptibility-response genes, T3Es induced resistance-response genes, and T3Es induced susceptibility-response genes. KEGG enrichment analyses of these DEGs showed that plant-pathogen interaction, plant hormone signal transduction, and MAPK signaling pathway were the outstanding pathways. Further analysis revealed that CMLs/CDPKs-WRKY module, MEKK1-MKK2-MPK3 cascade, and auxin signaling played important roles in the peanut response to R. solanacearum. Upon R. solanacearum infection (RSI), three early molecular events were possibly induced in peanuts, including Ca2+ activating CMLs/CDPKs-WRKY module to regulate the expression of resistance/susceptibility-related genes, auxin signaling was induced by AUX/IAA-ARF module to activate auxin-responsive genes that contribute to susceptibility, and MEKK1-MKK2-MPK3-WRKYs was activated by phosphorylation to induce the expression of resistance/susceptibility-related genes. Our research provides new ideas and abundant data resources to elucidate the molecular mechanism of the peanut response to R. solanacearum and to further improve the bacterial wilt resistance of peanuts.
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Affiliation(s)
- Yong Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ting Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiaoqiu Dai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Dong Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yushuang Wu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Huilan Chen
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Yixiong Zheng
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Qingqing Zhi
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiaorong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- *Correspondence: Xiaorong Wan,
| | - Xiaodan Tan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Xiaodan Tan,
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Combined QTL Mapping across Multiple Environments and Co-Expression Network Analysis Identified Key Genes for Embryogenic Callus Induction from Immature Maize Embryos. Int J Mol Sci 2022; 23:ijms23158786. [PMID: 35955919 PMCID: PMC9368897 DOI: 10.3390/ijms23158786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 11/26/2022] Open
Abstract
The ability of immature embryos to induce embryogenic callus (EC) is crucial for genetic transformation in maize, which is highly genotype-dependent. To dissect the genetic basis of maize EC induction, we conducted QTL mapping for four EC induction-related traits, the rate of embryogenic callus induction (REC), rate of shoot formation (RSF), length of shoot (LS), and diameter of callus (DC) under three environments by using an IBM Syn10 DH population derived from a cross of B73 and Mo17. These EC induction traits showed high broad-sense heritability (>80%), and significantly negative correlations were observed between REC and each of the other traits across multiple environments. A total of 41 QTLs for EC induction were identified, among which 13, 12, 10, and 6 QTLs were responsible for DC, RSF, LS, and REC, respectively. Among them, three major QTLs accounted for >10% of the phenotypic variation, including qLS1-1 (11.54%), qLS1-3 (10.68%), and qREC4-1 (11.45%). Based on the expression data of the 215 candidate genes located in these QTL intervals, we performed a weighted gene co-expression network analysis (WGCNA). A combined use of KEGG pathway enrichment and eigengene-based connectivity (KME) values identified the EC induction-associated module and four hub genes (Zm00001d028477, Zm00001d047896, Zm00001d034388, and Zm00001d022542). Gene-based association analyses validated that the variations in Zm00001d028477 and Zm00001d034388, which were involved in tryptophan biosynthesis and metabolism, respectively, significantly affected EC induction ability among different inbred lines. Our study brings novel insights into the genetic and molecular mechanisms of EC induction and helps to promote marker-assisted selection of high-REC varieties in maize.
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Cancé C, Martin-Arevalillo R, Boubekeur K, Dumas R. Auxin response factors are keys to the many auxin doors. THE NEW PHYTOLOGIST 2022; 235:402-419. [PMID: 35434800 DOI: 10.1111/nph.18159] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
In plants, most developmental programs depend on the action of auxin. The best described model of the auxin signaling pathway, which explains most, but not all, of the auxin transcriptional responses, relies on a de-repression mechanism. The auxin/indole-3-acetic acid repressors (Aux/IAAs) interact with the auxin response factors (ARFs), the transcription factors of the auxin signaling pathway, leading to repression of the ARF-controlled genes. Auxin induces Aux/IAA degradation, releases ARFs and activates transcription. However, this elegant model is not suitable for all ARFs. Indeed, in Arabidopsis, which has 22 ARFs, only five of them fit into the model since they are the ones able to interact with Aux/IAAs. The remaining 17 have a limited capacity to interact with the repressors, and their mechanisms of action are still unclear. The differential interactions between ARF and Aux/IAA proteins constitute one of many examples of the biochemical and structural diversification of ARFs that affect their action and therefore affect auxin transcriptional responses. A deeper understanding of the structural properties of ARFs is fundamental to obtaining a better explanation of the action of auxin in plants.
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Affiliation(s)
- Coralie Cancé
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
| | - Raquel Martin-Arevalillo
- Laboratoire de Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Univ. Lyon, Lyon, France
| | - Kenza Boubekeur
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
| | - Renaud Dumas
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
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Tian Z, Han J, Che G, Hasi A. Genome-wide characterization and expression analysis of SAUR gene family in Melon (Cucumis melo L.). PLANTA 2022; 255:123. [PMID: 35552537 DOI: 10.1007/s00425-022-03908-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
We identified 66 melon SAUR genes by bioinformatic analyses. CmSAUR19, 38, 58, 62 genes are specifically expressed in different stages of fruit growth, suggesting their participation in regulating fruit development. Auxin plays a crucial role in plant growth by regulating the multiple auxin response genes. However, in melon (Cucumis melo L.), the functions of the auxin early response gene family SAUR (Small auxin up RNA) genes in fruit development are still poorly understood. Through genome-wide characterization of CmSAUR family in melon, we identified a total of 66 CmSAUR genes. The open reading frames of the CmSAUR genes ranged from 234 to 525 bp, containing only one exon and lacking introns. Chromosomal position and phylogenetic tree analyses found that the two gene clusters in the melon chromosome are highly homologous in the Cucurbitaceae plants. Among the four conserved motifs in CmSAUR proteins, motif 1, motif 2, and motif 3 located in most of the family protein sequences, and motif 4 showed a close correlation with the two gene clusters. The CmSAUR28 and CmSAUR58 genes have auxin response elements located in the promoters, suggesting they may be involved in the auxin signaling pathway to regulate fruit development. Through transcriptomic profiling in the four developmental stages of fruit and different lateral organs, we selected 16 differentially-expressed SAUR genes for performing further expression analyses. qRT-PCR results showed that five SAUR genes are specifically expressed in flower organs and ovaries. CmSAUR19 and CmSAUR58 were significantly accumulated in the early developmental stage of the fruit. CmSAUR38 and CmAUR62 showed high expression in the climacteric and post-climacteric stages, suggesting their specific role in controlling fruit ripening. This work provides a foundation for further exploring the function of the SAUR gene in fruit development.
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Affiliation(s)
- Ze Tian
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Jiadi Han
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Gen Che
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Agula Hasi
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Jiang D, Lin R, Tan M, Yan J, Yan S. The mycorrhizal-induced growth promotion and insect resistance reduction in Populus alba × P. berolinensis seedlings: a multi-omics study. TREE PHYSIOLOGY 2022; 42:1059-1069. [PMID: 35022794 DOI: 10.1093/treephys/tpab155] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/13/2021] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are an alternative to chemical insecticides or fertilizers, and there is an urgent need to extend the application of AM fungi to woody plants. This study aims to investigate the growth and resistance against the gypsy moth larvae (Lymantria dispar) in Glomus intraradices-colonized Populus alba × P. berolinensis seedlings, and to unravel the transcriptome and metabolome phenotypes recruited by AM fungus colonization that affect plant growth and insect resistance. Our results showed a positive mycorrhizal growth response, i.e., growth and biomass of mycorrhizal seedlings were enhanced. However, AM fungus inoculation reduced the resistance of poplar to gypsy moth larvae, as evidenced by the decreased carbon/nitrogen ratio in leaves, as well as the increased larval growth and shortened larval developmental duration. Transcriptome analysis revealed that in both auxin and gibberellin signaling transductions, all nodes were responsive to AM symbiosis and most differentially expressed genes belonging to effectors were up-regulated in mycorrhizal seedlings. Furthermore, the two key enzymes (4-coumarate-CoA ligase and trans-cinnamate 4-monooxygenase) involved in the synthesis of p-Coumaroyl-CoA, an initial metabolite in flavonoid biosynthesis and the first rate-limiting enzyme (chalcone synthase) in flavonoid biosynthesis, were down-regulated at the transcriptional level. Consistent with the transcriptome results, metabolome analysis found that the amounts of all differentially accumulated flavonoid compounds (e.g., catechin and quercetin) identified in mycorrhizal seedlings were decreased. Taken together, these findings highlight the diverse outcomes of AM fungi-host plant-insect interaction and reveal the regulatory network of the positive mycorrhizal growth response and mycorrhizal-induced reduction of insect resistance in poplar.
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Affiliation(s)
- Dun Jiang
- Department of Forestry School of Forestry, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
- College of Forestry Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
| | - Ruoxuan Lin
- Department of Economics College of Economics and Management, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R.China
| | - Mingtao Tan
- Department of Forestry School of Forestry, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
- College of Forestry Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
| | - Junxin Yan
- Department of Landscape Architecture College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
| | - Shanchun Yan
- Department of Forestry School of Forestry, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
- College of Forestry Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
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Shi G, Wang S, Wang P, Zhan J, Tang Y, Zhao G, Li F, Ge X, Wu J. Cotton miR393-TIR1 Module Regulates Plant Defense Against Verticillium dahliae via Auxin Perception and Signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:888703. [PMID: 35592575 PMCID: PMC9111529 DOI: 10.3389/fpls.2022.888703] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
Plant auxin is essential in plant growth and development. However, the molecular mechanisms of auxin involvement in plant immunity are unclear. Here, we addressed the function of the cotton (Gossypium hirsutum) miR393-TIR1 module in plant defense against Verticillium dahliae infection via auxin perception and signaling. GhTIR1 was directedly cleaved by ghr-miR393 according to mRNA degradome data, 5'-RACE analysis, and a GUS reporter assay. Ghr-miR393 knockdown significantly increased plant susceptibility to V. dahliae compared to the control, while ghr-miR393 overexpression and GhTIR1 knockdown significantly increased plant resistance. External indole-3-acetic acid (IAA) application significantly enhanced susceptibility to V. dahliae in ghr-miR393 knockdown and control plants compared to mock treatment, and only slightly increased susceptibility in overexpressing ghr-miR393 and GhTIR1-silenced plants. Application of external PEO-IAA (an auxin antagonist) had a contrary trend with IAA application. Based on yeast two-hybrid and bimolecular fluorescence complementation assays, GhTIR1 interacted with GhIAA14 in the nucleus, and GhIAA14 knockdown reduced plant resistance to V. dahliae infection. The results suggested that the ghr-miR393-GhTIR1 module regulates plant defense via auxin perception and signaling. Additionally, simultaneous knockdown of GhTIR1 and GhICS1 significantly increased plant susceptibility to V. dahliae compared to the control, indicating that salicylic acid (SA) accumulation is vital for the ghr-miR393-GhTIR1 module to regulates plant resistance. Transcriptome data also demonstrated that GhTIR1 knockdown significantly downregulated expression of auxin-related genes and upregulated expression of SA-related genes. Overall, the ghr-miR393-GhTIR1 module participates in plant response to V. dahliae infection via IAA perception and signaling partially depending on the SA defense pathway.
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Affiliation(s)
- Gege Shi
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Saisai Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Peng Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingjing Zhan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ye Tang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ge Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jiahe Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Su X, Gao T, Zhang P, Li F, Wang D, Tian Y, Lu H, Zhang H, Wei S. Comparative physiological and transcriptomic analysis of sesame cultivars with different tolerance responses to heat stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1131-1146. [PMID: 35722520 PMCID: PMC9203651 DOI: 10.1007/s12298-022-01195-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 05/03/2023]
Abstract
High temperature is the main factor affecting plant growth and can cause plant growth inhibition and yield reduction. Here, seedlings of two contrasting sesame varieties, i.e., Zheng Taizhi 3 (heat-tolerant) and SP19 (heat-sensitive), were treated at 43 °C for 10 days. The results showed that the relative electrical conductivity, hydrogen peroxide levels, and superoxide anion radical levels of both varieties increased significantly under high temperature stress. Additionally, dry matter accumulation and chlorophyll content decreased significantly, and the activities of peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) increased. However, under HT stress, the content of reactive oxygen species in Zheng Taizhi 3 was lower than that in SP19, and the activities of SOD, CAT, and POD as well as the chlorophyll content in Zheng Taizhi 3 were higher than those in SP19. Comparative transcriptome analysis identified 6736 differentially expressed genes (DEGs); 5526 DEGs (2878 up and 2648 down) were identified in Zheng Taizhi 3, and 5186 DEGs (2695 up and 2491 down) were identified in SP19, with 3976 overlapping DEGs. These DEGs included stress tolerance-related heat-shock proteins, as well as genes related to carbohydrate and energy metabolism, signal transduction, endoplasmic reticulum protein processing, amino acid metabolism, and secondary metabolism. Overall, our results showed that the heat tolerance of Zheng Taizhi 3 was attributed to a stronger antioxidant defense system, enabling the variety to avoid oxidative damage compared with the heat-sensitive SP19. Moreover, some specifically expressed and high-abundance genes in Zheng Taizhi 3 were involved in regulatory mechanisms related to heat tolerance, including plant hormone signal transduction and heat shock protein regulation, thereby enhancing heat tolerance. The study contributes to a deeper understanding of the underlying complex molecular mechanisms involved in the responses of sesame seedlings to heat stress and provides a potential strategy for heat-resistant new varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01195-3.
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Affiliation(s)
- Xiaoyu Su
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, #116 Huayuan Road, Zhengzhou, 450000 Henan People’s Republic of China
- The Shennong Laboratory, Zhengzhou, 450002 Henan People’s Republic of China
| | - Tongmei Gao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, #116 Huayuan Road, Zhengzhou, 450000 Henan People’s Republic of China
- The Shennong Laboratory, Zhengzhou, 450002 Henan People’s Republic of China
| | - Pengyu Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, #116 Huayuan Road, Zhengzhou, 450000 Henan People’s Republic of China
- The Shennong Laboratory, Zhengzhou, 450002 Henan People’s Republic of China
| | - Feng Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, #116 Huayuan Road, Zhengzhou, 450000 Henan People’s Republic of China
| | - Dongyong Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, #116 Huayuan Road, Zhengzhou, 450000 Henan People’s Republic of China
| | - Yuan Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, #116 Huayuan Road, Zhengzhou, 450000 Henan People’s Republic of China
| | - Hailing Lu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, #116 Huayuan Road, Zhengzhou, 450000 Henan People’s Republic of China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, #116 Huayuan Road, Zhengzhou, 450000 Henan People’s Republic of China
- The Shennong Laboratory, Zhengzhou, 450002 Henan People’s Republic of China
| | - Shuangling Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, #116 Huayuan Road, Zhengzhou, 450000 Henan People’s Republic of China
- The Shennong Laboratory, Zhengzhou, 450002 Henan People’s Republic of China
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Wang Y, Xu J, Yu J, Zhu D, Zhao Q. Maize GSK3-like kinase ZmSK2 is involved in embryonic development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 318:111221. [PMID: 35351312 DOI: 10.1016/j.plantsci.2022.111221] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 05/28/2023]
Abstract
Grain size and weight are closely related to the yield of cereal crops. Abnormal development of the embryo, an important part of the grain, not only affects crop yield but also impacts next-generation survival. Here, we found that maize GSK3-like kinase ZmSK2, a homolog of BIN2 in Arabidopsis, is involved in embryonic development. ZmSK2 overexpression resulted in severe BR defective phenotypes and arrested embryonic development at the transition stage, while the zmsk2 knockout lines showed enlarged embryos. ZmSK2 interacts with Aux/IAA-transcription factor 28 (ZmIAA28), a negative regulator of auxin signaling, and the interaction region is the auxin degron "GWPPV" motif of ZmIAA28 domain II. Coexpression of ZmSK2 with ZmIAA28 increased the accumulation of ZmIAA28 in maize protoplasts, which may have been due to phosphorylation by ZmSK2. In conclusion, this study reveals the function of ZmSK2 in maize embryonic development and proposes that ZmSK2-ZmIAA28 may be another link in the signaling pathway that integrates BR and auxin.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jianghai Xu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jingjuan Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Dengyun Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Qian Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China.
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Liu B, Zhu J, Lin L, Yang Q, Hu B, Wang Q, Zou XX, Zou SQ. Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis. Front Genet 2022; 12:737293. [PMID: 35069676 PMCID: PMC8766721 DOI: 10.3389/fgene.2021.737293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.
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Affiliation(s)
- Bobin Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, China.,College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Juanli Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Lina Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Qixin Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Bangping Hu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Qingying Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Xiao-Xing Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Shuang-Quan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
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Hou Q, Qiu Z, Wen Z, Zhang H, Li Z, Hong Y, Qiao G, Wen X. Genome-Wide Identification of ARF Gene Family Suggests a Functional Expression Pattern during Fruitlet Abscission in Prunus avium L. Int J Mol Sci 2021; 22:11968. [PMID: 34769398 PMCID: PMC8584427 DOI: 10.3390/ijms222111968] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Auxin response factors (ARFs) play a vital role in plant growth and development. In the current study, 16 ARF members have been identified in the sweet cherry (Prunus avium L.) genome. These genes are all located in the nucleus. Sequence analysis showed that genes in the same subgroup have similar exon-intron structures. A phylogenetic tree has been divided into five groups. The promoter sequence includes six kinds of plant hormone-related elements, as well as abiotic stress response elements such as low temperature or drought. The expression patterns of PavARF in different tissues, fruitlet abscission, cold and drought treatment were comprehensively analyzed. PavARF10/13 was up-regulated and PavARF4/7/11/12/15 was down-regulated in fruitlet abscising. These genes may be involved in the regulation of fruit drop in sweet cherry fruits. This study comprehensively analyzed the bioinformatics and expression pattern of PavARF, which can lay the foundation for further understanding the PavARF family in plant growth development and fruit abscission.
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Affiliation(s)
- Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Zhilang Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Huimin Zhang
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, China; (H.Z.); (Z.L.)
| | - Zhengchun Li
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, China; (H.Z.); (Z.L.)
| | - Yi Hong
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
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SmSPL6 Induces Phenolic Acid Biosynthesis and Affects Root Development in Salvia miltiorrhiza. Int J Mol Sci 2021; 22:ijms22157895. [PMID: 34360660 PMCID: PMC8348295 DOI: 10.3390/ijms22157895] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
Salvia miltiorrhiza is a renowned model medicinal plant species for which 15 SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family genes have been identified; however, the specific functions of SmSPLs have not been well characterized as of yet. For this study, the expression patterns of SmSPL6 were determined through its responses to treatments of exogenous hormones, including indole acetic acid (IAA), gibberellic acid (GA3), methyl jasmonic acid (MeJA), and abscisic acid (ABA). To characterize its functionality, we obtained SmSPL6-ovexpressed transgenic S. miltiorrhiza plants and found that overexpressed SmSPL6 promoted the accumulation of phenolic acids and repressed the biosynthesis of anthocyanin. Meanwhile, the root lengths of the SmSPL6-overexpressed lines were significantly longer than the control; however, both the fresh weights and lateral root numbers decreased. Further investigations indicated that SmSPL6 regulated the biosynthesis of phenolic acid by directly binding to the promoter regions of the enzyme genes Sm4CL9 and SmCYP98A14 and activated their expression. We concluded that SmSPL6 regulates not only the biosynthesis of phenolic acids, but also the development of roots in S. miltiorrhiza.
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Huang C, Yang M, Shao D, Wang Y, Wan S, He J, Meng Z, Guan R. Fine mapping of the BnUC2 locus related to leaf up-curling and plant semi-dwarfing in Brassica napus. BMC Genomics 2020; 21:530. [PMID: 32736518 PMCID: PMC7430850 DOI: 10.1186/s12864-020-06947-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 07/24/2020] [Indexed: 02/06/2023] Open
Abstract
Background Studies of leaf shape development and plant stature have made important contributions to the fields of plant breeding and developmental biology. The optimization of leaf morphology and plant height to improve lodging resistance and photosynthetic efficiency, increase planting density and yield, and facilitate mechanized harvesting is a desirable goal in Brassica napus. Results Here, we investigated a B. napus germplasm resource exhibiting up-curled leaves and a semi-dwarf stature. In progeny populations derived from NJAU5737 and Zhongshuang 11 (ZS11), we found that the up-curled leaf trait was controlled by a dominant locus, BnUC2. We then fine mapped the BnUC2 locus onto an 83.19-kb interval on chromosome A05 using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. We further determined that BnUC2 was a major plant height QTL that explained approximately 70% of the phenotypic variation in two BC5F3 family populations derived from NJAU5737 and ZS11. This result implies that BnUC2 was also responsible for the observed semi-dwarf stature. The fine mapping interval of BnUC2 contained five genes, two of which, BnaA05g16700D (BnaA05.IAA2) and BnaA05g16720D, were revealed by comparative sequencing to be mutated in NJAU5737. This result suggests that the candidate gene mutation (BnaA05g16700D, encoding Aux/IAA2 proteins) in the conserved Degron motif GWPPV (P63S) was responsible for the BnUC2 locus. In addition, investigation of agronomic traits in a segregated population indicated that plant height, main inflorescence length, and branching height were significantly reduced by BnUC2, whereas yield was not significantly altered. The determination of the photosynthetic efficiency showed that the BnUC2 locus was beneficial to improve the photosynthetic efficiency. Our findings may provide an effective foundation for plant type breeding in B. napus. Conclusions Using SNP and SSR markers, a dominant locus (BnUC2) related to up-curled leaves and semi-dwarf stature in B. napus has been fine mapped onto an 83.19-kb interval of chromosome A05 containing five genes. The BnaA05.IAA2 is inferred to be the candidate gene responsible for the BnUC2 locus.
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Affiliation(s)
- Chengwei Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mao Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danlei Shao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yangming Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shubei Wan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zuqing Meng
- Tibet Agriculture and Animal Husbandry College, Linzhi, 860000, Tibet Autonomous Region, China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
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Synergistic Interaction of Phytohormones in Determining Leaf Angle in Crops. Int J Mol Sci 2020; 21:ijms21145052. [PMID: 32709150 PMCID: PMC7404121 DOI: 10.3390/ijms21145052] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Leaf angle (LA), defined as the angle between the plant stem and leaf adaxial side of the blade, generally shapes the plant architecture into a loosen or dense structure, and thus influences the light interception and competition between neighboring plants in natural settings, ultimately contributing to the crop yield and productivity. It has been elucidated that brassinosteroid (BR) plays a dominant role in determining LA, and other phytohormones also positively or negatively participate in regulating LA. Accumulating evidences have revealed that these phytohormones interact with each other in modulating various biological processes. However, the comprehensive discussion of how the phytohormones and their interaction involved in shaping LA is relatively lack. Here, we intend to summarize the advances in the LA regulation mediated by the phytohormones and their crosstalk in different plant species, mainly in rice and maize, hopefully providing further insights into the genetic manipulation of LA trait in crop breeding and improvement in regarding to overcoming the challenge from the continuous demands for food under limited arable land area.
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34
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Huang Z, Bao K, Jing Z, Wang Q, Duan H, Zhu Y, Zhang S, Wu Q. Small Auxin Up RNAs influence the distribution of indole-3-acetic acid and play a potential role in increasing seed size in Euryale ferox Salisb. BMC PLANT BIOLOGY 2020; 20:311. [PMID: 32620077 PMCID: PMC7333270 DOI: 10.1186/s12870-020-02504-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/18/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Aquatic Euryale ferox Salisb. is an economically important crop in China and India. Unfortunately, low yield limitations seriously hinder market growth. Unveiling the control of seed size is of remarkable importance in improvement of crops. Here, we generated a new hybrid line (HL) with larger seeds by crossing South Gordon Euryale and North Gordon Euryale (WT) which hasn't been reported before. However, the functional genes and molecular mechanisms controlling the seed size in Euryale ferox Salisb. remain unclear. In this study, we focused on the differentially expressed genes in the auxin signal transduction pathway during fruit development between HL and WT to explore candidate regulatory genes participated in regulating seed size. RESULTS Both concentration and localization of indole-3-acetic acid (IAA) at two growth stages of fruits of WT and HL were detected by LC-MS and immunofluorescence. Although IAA content between the two lines did not differ, IAA distribution was significantly different. To elucidate the mechanism and to seek the key genes underlying this difference, RNA-seq was performed on young fruits at the two selected growth stages, and differentially expressed genes related to the auxin transduction pathway were selected for further analysis. CONCLUSION Hybrid Euryale ferox Salisb. expressed significant heterosis, resulting in non-prickly, thin-coated, large seeds, which accounted for the significantly larger yield of HL than that of WT. Our study indicated that Small Auxin Up RNAs (SAURs) -mediated localization of IAA regulates seed size in Euryale ferox Salisb. We found that some SAURs may act as a positive mediator of the auxin transduction pathway, thereby contributing to the observed heterosis.
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Affiliation(s)
- Zhiheng Huang
- School of Pharmacy, Nanjing University of Chinese Medicine, 138 xianlin Road, Nanjing, 210023, Jiangsu, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Ke Bao
- School of Pharmacy, Nanjing University of Chinese Medicine, 138 xianlin Road, Nanjing, 210023, Jiangsu, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Zonghui Jing
- School of Pharmacy, Nanjing University of Chinese Medicine, 138 xianlin Road, Nanjing, 210023, Jiangsu, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Qian Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, 138 xianlin Road, Nanjing, 210023, Jiangsu, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Huifang Duan
- School of Pharmacy, Nanjing University of Chinese Medicine, 138 xianlin Road, Nanjing, 210023, Jiangsu, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Yaying Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, 138 xianlin Road, Nanjing, 210023, Jiangsu, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Sen Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, 138 xianlin Road, Nanjing, 210023, Jiangsu, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Qinan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, 138 xianlin Road, Nanjing, 210023, Jiangsu, China.
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China.
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Wang Y, Li W, Chang H, Zhou J, Luo Y, Zhang K, Zuo J, Wang B. SRNAome and transcriptome analysis provide insight into strawberry fruit ripening. Genomics 2020; 112:2369-2378. [PMID: 31945464 DOI: 10.1016/j.ygeno.2020.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 12/20/2022]
Abstract
Strawberry fruit ripening is a complex process affected by multiple factors at different regulation levels. To elucidate the regulation mechanisms, the combined analysis of sRNAome and transcriptome were used. A total of 124 known and 190 novel miRNAs were found, 62 of them were significantly differentially expressed (DE). The targets of the DE miRNAs were parsed and several TFs, such as SPL, ARF, WRKY, and TCP, were found to be involved in ripening. Elevated CO2 can significantly postpone ripening and miR156, miR166f, miR171a, and miR171d were the DE miRNAs. Transcriptome analysis found 313 DE genes related to fruit ripening, including cell wall metabolism-related genes, color-related genes, ethylene-related genes, and genes encoding TFs such as MYB, SPL, NAC, TCP, and ARF. Based on above, a combined regulatory model involved in fruit ripening was created. These results provide valuable information for understanding the complicated coordinated regulatory network of strawberry fruit ripening.
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Affiliation(s)
- Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China; National R&D Center For Fruit Processing, Beijing 100093, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China; Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China
| | - Wensheng Li
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China; National R&D Center For Fruit Processing, Beijing 100093, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China; Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China
| | - Hong Chang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China; National R&D Center For Fruit Processing, Beijing 100093, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China; Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China
| | - Jiahua Zhou
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China; National R&D Center For Fruit Processing, Beijing 100093, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China; Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China
| | - Yunbo Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kaichun Zhang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China; National R&D Center For Fruit Processing, Beijing 100093, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China; Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Baogang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China; National R&D Center For Fruit Processing, Beijing 100093, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China; Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China.
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Ju F, Liu S, Zhang S, Ma H, Chen J, Ge C, Shen Q, Zhang X, Zhao X, Zhang Y, Pang C. Transcriptome analysis and identification of genes associated with fruiting branch internode elongation in upland cotton. BMC PLANT BIOLOGY 2019; 19:415. [PMID: 31590649 PMCID: PMC6781417 DOI: 10.1186/s12870-019-2011-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Appropriate plant architecture can improve the amount of cotton boll opening and allow increased planting density, thus increasing the level of cotton mechanical harvesting and cotton yields. The internodes of cotton fruiting branches are an important part of cotton plant architecture. Thus, studying the molecular mechanism of internode elongation in cotton fruiting branches is highly important. RESULTS In this study, we selected internodes of cotton fruiting branches at three different stages from two cultivars whose internode lengths differed significantly. A total of 76,331 genes were detected by transcriptome sequencing. By KEGG pathway analysis, we found that DEGs were significantly enriched in the plant hormone signal transduction pathway. The transcriptional data and qRT-PCR results showed that members of the GH3 gene family, which are involved in auxin signal transduction, and CKX enzymes, which can reduce the level of CKs, were highly expressed in the cultivar XLZ77, which has relatively short internodes. Genes related to ethylene synthase (ACS), EIN2/3 and ERF in the ethylene signal transduction pathway and genes related to JAR1, COI1 and MYC2 in the JA signal transduction pathway were also highly expressed in XLZ77. Plant hormone determination results showed that the IAA and CK contents significantly decreased in cultivar XLZ77 compared with those in cultivar L28, while the ACC (the precursor of ethylene) and JA contents significantly increased. GO enrichment analysis revealed that the GO categories associated with promoting cell elongation, such as cell division, the cell cycle process and cell wall organization, were significantly enriched, and related genes were highly expressed in L28. However, genes related to the sphingolipid metabolic process and lignin biosynthetic process, whose expression can affect cell elongation, were highly expressed in XLZ77. In addition, 2067 TFs were differentially expressed. The WRKY, ERF and bHLH TF families were the top three largest families whose members were active in the two varieties, and the expression levels of most of the genes encoding these TFs were upregulated in XLZ77. CONCLUSIONS Auxin and CK are positive regulators of internode elongation in cotton branches. In contrast, ethylene and JA may act as negative regulators of internode elongation in cotton branches. Furthermore, the WRKY, ERF and bHLH TFs were identified as important inhibitors of internode elongation in cotton. In XLZ77(a short-internode variety), the mass synthesis of ethylene and amino acid conjugation of auxin led to the inhibition of plant cell elongation, while an increase in JA content and degradation of CKs led to a slow rate of cell division, which eventually resulted in a phenotype that presented relatively short internodes on the fruiting branches. The results of this study not only provide gene resources for the genetic improvement of cotton plant architecture but also lay a foundation for improved understanding of the molecular mechanism of the internode elongation of cotton branches.
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Affiliation(s)
- Feiyan Ju
- State Key Laboratory of Cotton Biology (Hebei Base)/College of Agronomy, Hebei Agricultural University, Baoding, 071001 Hebei China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Shaodong Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Siping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Huijuan Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Jing Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Changwei Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Qian Shen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Xiaomeng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Xinhua Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Yongjiang Zhang
- State Key Laboratory of Cotton Biology (Hebei Base)/College of Agronomy, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
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Combination of Transcriptomic, Proteomic, and Metabolomic Analysis Reveals the Ripening Mechanism of Banana Pulp. Biomolecules 2019; 9:biom9100523. [PMID: 31548496 PMCID: PMC6843284 DOI: 10.3390/biom9100523] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023] Open
Abstract
The banana is one of the most important fruits in the world. Bananas undergo a rapid ripening process after harvest, resulting in a short shelf. In this study, the mechanism underlying pulp ripening of harvested bananas was investigated using integrated transcriptomic, proteomic, and metabolomic analysis. Ribonucleic acid sequencing (RNA-Seq) revealed that a great number of genes related to transcriptional regulation, signal transduction, cell wall modification, and secondary metabolism were up-regulated during pulp ripening. At the protein level, 84 proteins were differentially expressed during pulp ripening, most of which were associated with energy metabolism, oxidation-reduction, cell wall metabolism, and starch degradation. According to partial least squares discriminant analysis, 33 proteins were identified as potential markers for separating different ripening stages of the fruit. In addition to ethylene’s central role, auxin signal transduction might be involved in regulating pulp ripening. Moreover, secondary metabolism, energy metabolism, and the protein metabolic process also played an important role in pulp ripening. In all, this study provided a better understanding of pulp ripening of harvested bananas.
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Wang JG, Gao XM, Ma ZL, Chen J, Liu YN, Shi WQ. Metabolomic and transcriptomic profiling of three types of litchi pericarps reveals that changes in the hormone balance constitute the molecular basis of the fruit cracking susceptibility of Litchi chinensis cv. Baitangying. Mol Biol Rep 2019; 46:5295-5308. [PMID: 31440876 DOI: 10.1007/s11033-019-04986-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 07/18/2019] [Indexed: 01/18/2023]
Abstract
Many Litchi chinensis cv. Baitangying orchards are suffering from a serious fruit cracking problem, but few studies have improved our understanding of the mechanism or the molecular basis of cracking susceptibility in 'Baitangying'. We conducted metabolome and transcriptome analyses of three types of litchi pericarps. To prevent passive progression after fruit cracking from affecting the results, we mainly focused on 11 metabolites and 101 genes that showed the same regulatory status and overlap in pairwise comparisons of cracking 'Baitangying' versus noncracking 'Baitangying' and noncracking 'Baitangying' versus noncracking 'Feizixiao'. Compared with the cracking-resistant cultivar 'Feizixiao', the 'Baitangying' pericarp has higher abscisic acid contents, and the presence of relevant metabolites and genes suggests increased biosynthesis of ethylene and jasmonic acid and decreased auxin and brassinosteroid biosynthesis. The fruit cracking-susceptible trait in 'Baitangying' might be associated with differences in the balance of these five types of hormones between the pericarp of this cultivar and that of 'Feizixiao'. Additionally, combined analyses showed a correspondence between the metabolite profiles and transcript patterns. qRT-PCR validation indicated the reliability of our high-throughput results. The acquired information might help in further studying the mechanisms that mediate fruit cracking susceptibility in 'Baitangying' and other litchi cultivars.
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Affiliation(s)
- Ju-Gang Wang
- College of Agro-forestry Engineering & Planning, Tongren University, Tongren, 554300, China. .,South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, 524091, China. .,Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang, 524091, China. .,Key Laboratory of Tropical Crops Nutrition, Zhanjiang, 524091, Hainan Province, China.
| | - Xiao-Min Gao
- College of Agro-forestry Engineering & Planning, Tongren University, Tongren, 554300, China.,South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, 524091, China.,Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang, 524091, China
| | - Zhi-Ling Ma
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, 524091, China.,Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang, 524091, China
| | - Jing Chen
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, 524091, China.,Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang, 524091, China.,Key Laboratory of Tropical Crops Nutrition, Zhanjiang, 524091, Hainan Province, China
| | - Ya-Nan Liu
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, 524091, China.,Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang, 524091, China.,Key Laboratory of Tropical Crops Nutrition, Zhanjiang, 524091, Hainan Province, China
| | - Wei-Qi Shi
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, 524091, China.,Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang, 524091, China.,Key Laboratory of Tropical Crops Nutrition, Zhanjiang, 524091, Hainan Province, China
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Cheng L, Zhang S, Yang L, Wang Y, Yu B, Zhang F. Comparative proteomics illustrates the complexity of Fe, Mn and Zn deficiency-responsive mechanisms of potato (Solanum tuberosum L.) plants in vitro. PLANTA 2019; 250:199-217. [PMID: 30976909 DOI: 10.1007/s00425-019-03163-w] [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: 10/17/2018] [Accepted: 04/05/2019] [Indexed: 05/05/2023]
Abstract
The present study is the first to integrate physiological and proteomic data providing information on Fe, Mn and Zn deficiency-responsive mechanisms of potato plants in vitro. Micronutrient deficiency is an important limiting factor for potato production that causes substantial tuber yield and quality losses. To under the underlying molecular mechanisms of potato in response to Fe, Mn and Zn deficiency, a comparative proteomic approach was applied. Leaf proteome change of in vitro-propagated potato plantlets subjected to a range of Fe-deficiency treatments (20, 10 and 0 μM Na-Fe-EDTA), Mn-deficiency treatments (1 and 0 μM MnCl2·4H2O) and Zn-deficiency treatment (0 μM ZnCl2) using two-dimensional gel electrophoresis was analyzed. Quantitative image analysis showed a total of 146, 55 and 42 protein spots under Fe, Mn and Zn deficiency with their abundance significantly altered (P < 0.05) more than twofold, respectively. By MALDI-TOF/TOF MS analyses, the differentially abundant proteins were found mainly involved in bioenergy and metabolism, photosynthesis, defence, redox homeostasis and protein biosynthesis/degradation under the metal deficiencies. Signaling, transport, cellular structure and transcription-related proteins were also identified. The hierarchical clustering results revealed that these proteins were involved in a dynamic network in response to Fe, Mn and Zn deficiency. All these metal deficiencies caused cellular metabolic remodeling to improve metal acquisition and distribution in potato plants. The reduced photosynthetic efficiency occurred under each metal deficiency, yet Fe-deficient plants showed a more severe damage of photosynthesis. More defence mechanisms were induced by Fe deficiency than Mn and Zn deficiency, and the antioxidant systems showed different responses to each metal deficiency. Reprogramming of protein biosynthesis/degradation and assembly was more strongly required for acclimation to Fe deficiency. The signaling cascades involving auxin and NDPKs might also play roles in micronutrient stress signaling and pinpoint interesting candidates for future studies. Our results first provide an insight into the complex functional and regulatory networks in potato plants under Fe, Mn and Zn deficiency.
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Affiliation(s)
- Lixiang Cheng
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shaomei Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lili Yang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Bin Yu
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Feng Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China.
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40
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Integrated Transcriptomic, Proteomic, and Metabolomics Analysis Reveals Peel Ripening of Harvested Banana under Natural Condition. Biomolecules 2019; 9:biom9050167. [PMID: 31052343 PMCID: PMC6572190 DOI: 10.3390/biom9050167] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 12/28/2022] Open
Abstract
Harvested banana ripening is a complex physiological and biochemical process, and there are existing differences in the regulation of ripening between the pulp and peel. However, the underlying molecular mechanisms governing peel ripening are still not well understood. In this study, we performed a combination of transcriptomic, proteomic, and metabolomics analysis on peel during banana fruit ripening. It was found that 5784 genes, 94 proteins, and 133 metabolites were differentially expressed or accumulated in peel during banana ripening. Those genes and proteins were linked to ripening-related processes, including transcriptional regulation, hormone signaling, cell wall modification, aroma synthesis, protein modification, and energy metabolism. The differentially expressed transcriptional factors were mainly ethylene response factor (ERF) and basic helix-loop-helix (bHLH) family members. Moreover, a great number of auxin signaling-related genes were up-regulated, and exogenous 3-indoleacetic acid (IAA) treatment accelerated banana fruit ripening and up-regulated the expression of many ripening-related genes, suggesting that auxin participates in the regulation of banana peel ripening. In addition, xyloglucan endotransglucosylase/hydrolase (XTH) family members play an important role in peel softening. Both heat shock proteins (Hsps) mediated-protein modification, and ubiqutin-protesome system-mediated protein degradation was involved in peel ripening. Furthermore, anaerobic respiration might predominate in energy metabolism in peel during banana ripening. Taken together, our study highlights a better understanding of the mechanism underlying banana peel ripening and provides a new clue for further dissection of specific gene functions.
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Shirley NJ, Aubert MK, Wilkinson LG, Bird DC, Lora J, Yang X, Tucker MR. Translating auxin responses into ovules, seeds and yield: Insight from Arabidopsis and the cereals. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:310-336. [PMID: 30474296 DOI: 10.1111/jipb.12747] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/16/2018] [Indexed: 05/27/2023]
Abstract
Grain production in cereal crops depends on the stable formation of male and female gametes in the flower. In most angiosperms, the female gamete is produced from a germline located deep within the ovary, protected by several layers of maternal tissue, including the ovary wall, ovule integuments and nucellus. In the field, germline formation and floret fertility are major determinants of yield potential, contributing to traits such as seed number, weight and size. As such, stimuli affecting the timing and duration of reproductive phases, as well as the viability, size and number of cells within reproductive organs can significantly impact yield. One key stimulant is the phytohormone auxin, which influences growth and morphogenesis of female tissues during gynoecium development, gametophyte formation, and endosperm cellularization. In this review we consider the role of the auxin signaling pathway during ovule and seed development, first in the context of Arabidopsis and then in the cereals. We summarize the gene families involved and highlight distinct expression patterns that suggest a range of roles in reproductive cell specification and fate. This is discussed in terms of seed production and how targeted modification of different tissues might facilitate improvements.
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Affiliation(s)
- Neil J Shirley
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Matthew K Aubert
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Laura G Wilkinson
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Dayton C Bird
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Jorge Lora
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
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Michmizos D, Hilioti Z. A roadmap towards a functional paradigm for learning & memory in plants. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:209-215. [PMID: 30537608 DOI: 10.1016/j.jplph.2018.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/15/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
In plants, the acquisition, processing and storage of empirical information can result in the modification of their behavior according to the nature of the stimulus, and yet this area of research remained relatively understudied until recently. As the body of evidence supporting the inclusion of plants among the higher organisms demonstrating the adaptations to accomplish these tasks keeps increasing, the resistance by traditional botanists and agricultural scientists, who were at first cautious in allowing the application of animal models onto plant physiology and development, subsides. However, the debate retains much of its heat, a good part of it originating from the controversial use of nervous system terms to describe plant processes. By focusing on the latest findings on the cellular and molecular mechanisms underlying the well established processes of Learning and Memory, recognizing what has been accomplished and what remains to be explored, and without seeking to bootstrap neuronal characteristics where none are to be found, a roadmap guiding towards a comprehensive paradigm for Learning and Memory in plants begins to emerge. Meanwhile the applications of the new field of Plant Gnosophysiology look as promising as ever.
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Affiliation(s)
- Dimitrios Michmizos
- Dept. of Agriculture, Crop Production & Rural Environment, University of Thessaly, Fytokos st, Volos, Magnesia, 384 46, Greece.
| | - Zoe Hilioti
- Institute of Applied Biosciences, Center for Research & Technology (CERTH), Thessaloniki, Greece
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Tiwari S, Lata C, Chauhan PS, Prasad V, Prasad M. A Functional Genomic Perspective on Drought Signalling and its Crosstalk with Phytohormone-mediated Signalling Pathways in Plants. Curr Genomics 2017; 18:469-482. [PMID: 29204077 PMCID: PMC5684651 DOI: 10.2174/1389202918666170605083319] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/03/2016] [Accepted: 10/15/2016] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Drought stress is one of the most important abiotic stresses that negatively influence crop performance and productivity. Plants acclimatize to drought stress conditions through altered molecular, biochemical and physiological responses. Gene and/or protein expression and regulation are thought to be modulated upon stress perception and signal transduction for providing requisite endurance to plants.Plant growth regulators or phytohormones are important molecules required for various biological processes in plants and are also central to stress signalling pathways. Among various phytohormones, Abscisic Acid (ABA) and Ethylene (ET) are considered to be the most vital growth regulators implicated in drought stress signalling and tolerance. Besides the above two known classical phytohormones, Salicylic Acid (SA) and Jasmonic Acid (JA) have also been found to potentially enhance abiotic stress tolerance particularly that of drought, salinity, and heat stress tolerance in plants. Apart from these several other growth regulators such as Cytokinins (CKs), Auxin (AUX), Gibberellic Acid (GA), Brassinosteroids (BRs) and Strigolactones (SLs) have also been reported to actively participate in abiotic stress responses and tolerance in plants. The abiotic stress signalling in plants regulated by these hormones further depends upon the nature, intensity, and duration of exposure to various environmental stresses. It has been reported that all these phytohormones are also involved in extensive crosstalk and signal transduction among themselves and/or with other factors. CONCLUSION This review thus summarizes the molecular mechanism of drought signalling and its crosstalk with various phytohormone signalling pathways implicated in abiotic stress response and tolerance.
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Affiliation(s)
- Shalini Tiwari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, India
- Department of Botany, University of Lucknow, Lucknow-226007, India
| | - Charu Lata
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, India
| | - Puneet Singh Chauhan
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, India
| | - Vivek Prasad
- Department of Botany, University of Lucknow, Lucknow-226007, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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Staswick P, Rowe M, Spalding EP, Splitt BL. Jasmonoyl-L-Tryptophan Disrupts IAA Activity through the AUX1 Auxin Permease. FRONTIERS IN PLANT SCIENCE 2017; 8:736. [PMID: 28533791 PMCID: PMC5420569 DOI: 10.3389/fpls.2017.00736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 04/20/2017] [Indexed: 05/29/2023]
Abstract
Amide-linked conjugates between tryptophan (Trp) and jasmonic (JA) or indole-3-acetic (IAA) acids interfered with gravitropism and other auxin-dependent activities in Arabidopsis, but the mechanism was unclear. To identify structural features necessary for activity several additional Trp conjugates were synthesized. The phenylacetic acid (PAA) conjugate was active, while several others were not. Common features of active conjugates is that they have ring structures that are linked to Trp through an acetic acid side chain, while longer or shorter linkages are inactive or less active. A dominant mutant, called tryptophan conjugate response1-D that is insensitive to JA-Trp, but still sensitive to other active conjugates, was identified and the defect was found to be a substitution of Asn for Asp456 in the C-terminal domain of the IAA cellular permease AUX1. Mutant seedling primary root growth in the absence of added conjugate was 15% less than WT, but otherwise plant phenotype appeared normal. These results suggest that JA-Trp disrupts AUX1 activity, but that endogenous JA-Trp has only a minor role in regulating plant growth. In contrast with IAA- and JA-Trp, which are present at <2 pmole g-1 FW, PAA-Trp was found at about 30 pmole g-1 FW. The latter, or other undiscovered Trp conjugates, may still have important endogenous roles, possibly helping to coordinate other pathways with auxin response.
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Affiliation(s)
- Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, LincolnNE, USA
| | - Martha Rowe
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, LincolnNE, USA
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin–Madison, MadisonWI, USA
| | - Bessie L. Splitt
- Department of Botany, University of Wisconsin–Madison, MadisonWI, USA
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Li L, Xue M, Yi H. Uncovering microRNA-mediated response to SO2 stress in Arabidopsis thaliana by deep sequencing. JOURNAL OF HAZARDOUS MATERIALS 2016; 316:178-85. [PMID: 27232729 DOI: 10.1016/j.jhazmat.2016.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/24/2016] [Accepted: 05/04/2016] [Indexed: 05/20/2023]
Abstract
Sulfur dioxide (SO2) is a major air pollutant and has significant impacts on plants. MicroRNAs (miRNAs) are a class of gene expression regulators that play important roles in response to environmental stresses. In this study, deep sequencing was used for genome-wide identification of miRNAs and their expression profiles in response to SO2 stress in Arabidopsis thaliana shoots. A total of 27 conserved miRNAs and 5 novel miRNAs were found to be differentially expressed under SO2 stress. qRT-PCR analysis showed mostly negative correlation between miRNA accumulation and target gene mRNA abundance, suggesting regulatory roles of these miRNAs during SO2 exposure. The target genes of SO2-responsive miRNAs encode transcription factors and proteins that regulate auxin signaling and stress response, and the miRNAs-mediated suppression of these genes could improve plant resistance to SO2 stress. Promoter sequence analysis of genes encoding SO2-responsive miRNAs showed that stress-responsive and phytohormone-related cis-regulatory elements occurred frequently, providing additional evidence of the involvement of miRNAs in adaption to SO2 stress. This study represents a comprehensive expression profiling of SO2-responsive miRNAs in Arabidopsis and broads our perspective on the ubiquitous regulatory roles of miRNAs under stress conditions.
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Affiliation(s)
- Lihong Li
- School of Life Science, Shanxi University, Taiyuan, China
| | - Meizhao Xue
- School of Life Science, Shanxi University, Taiyuan, China
| | - Huilan Yi
- School of Life Science, Shanxi University, Taiyuan, China.
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Zhao Z, Xue Y, Yang H, Li H, Sun G, Zhao X, Ding D, Tang J. Genome-Wide Identification of miRNAs and Their Targets Involved in the Developing Internodes under Maize Ears by Responding to Hormone Signaling. PLoS One 2016; 11:e0164026. [PMID: 27695059 PMCID: PMC5047619 DOI: 10.1371/journal.pone.0164026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 09/19/2016] [Indexed: 12/04/2022] Open
Abstract
Internode length is one of the decisive factors affecting plant height (PH) and ear height (EH), which are closely associated with the lodging resistance, biomass and grain yield of maize. miRNAs, currently recognized as important transcriptional/ post-transcriptional regulators, play an essential role in plant growth and development. However, their roles in developing internodes under maize ears remain unclear. To identify the roles of miRNAs and their targets in the development of internodes under maize ears, six miRNA and two degradome libraries were constructed using the 7th, 8th and 9th internodes of two inbred lines, 'Xun928' and 'Xun9058', which had significantly different internode lengths. A total of 45 and 54 miRNAs showed significant changes for each pairwise comparison among the 7th, 8th and 9th internodes of 'Xun9058' and 'Xun928', respectively. The expression of 31 miRNAs showed significant changes were common to the corresponding comparison groups of the 7th, 8th and 9th internodes of 'Xun9058' and 'Xun928'. For the corresponding internodes of 'Xun9058' and 'Xun928', compared with the expression of miRNAs in the 7th, 8th and 9th internodes of 'Xun928', the numbers of up-regulated and down-regulated miRNAs were 11 and 36 in the 7th internode, 9 and 45 in the 8th internode, and 9 and 25 in the 9th internode of 'Xun9058', respectively. Moreover, 10 miRNA families containing 45 members showed significant changes at least in two internodes of 'Xun928' by comparing with the corresponding internodes of 'Xun9058'. Based on the sequencing data, 20 miRNAs related to hormone signaling among the candidates, belonging to five conserved miRNA families, were selected for expression profiling using quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The five miRNA families, zma-miR160, zma-miR167, zma-miR164, zma-miR169 and zma-miR393, targeted the genes encoding auxin response factor, N-acetylcysteine domain containing protein, nuclear transcription factor Y and auxin signaling F-BOX 2 through degradome sequencing. The miRNAs might regulate their targets to respond to hormone signaling, thereby regulating the internode elongation and development under maize ear. These results provide valuable reference for understanding the possible regulation mechanism of the ILs under the ear.
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Affiliation(s)
- Zhan Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Yadong Xue
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Huili Yang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Huimin Li
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Gaoyang Sun
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xiaofeng Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434023, Hubei, China
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Armengot L, Marquès-Bueno MM, Jaillais Y. Regulation of polar auxin transport by protein and lipid kinases. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4015-4037. [PMID: 27242371 PMCID: PMC4968656 DOI: 10.1093/jxb/erw216] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The directional transport of auxin, known as polar auxin transport (PAT), allows asymmetric distribution of this hormone in different cells and tissues. This system creates local auxin maxima, minima, and gradients that are instrumental in both organ initiation and shape determination. As such, PAT is crucial for all aspects of plant development but also for environmental interaction, notably in shaping plant architecture to its environment. Cell to cell auxin transport is mediated by a network of auxin carriers that are regulated at the transcriptional and post-translational levels. Here we review our current knowledge on some aspects of the 'non-genomic' regulation of auxin transport, placing an emphasis on how phosphorylation by protein and lipid kinases controls the polarity, intracellular trafficking, stability, and activity of auxin carriers. We describe the role of several AGC kinases, including PINOID, D6PK, and the blue light photoreceptor phot1, in phosphorylating auxin carriers from the PIN and ABCB families. We also highlight the function of some receptor-like kinases (RLKs) and two-component histidine kinase receptors in PAT, noting that there are probably RLKs involved in co-ordinating auxin distribution yet to be discovered. In addition, we describe the emerging role of phospholipid phosphorylation in polarity establishment and intracellular trafficking of PIN proteins. We outline these various phosphorylation mechanisms in the context of primary and lateral root development, leaf cell shape acquisition, as well as root gravitropism and shoot phototropism.
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Affiliation(s)
- Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Maria Mar Marquès-Bueno
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
- Correspondence to:
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The Arabidopsis Auxin Receptor F-Box Proteins AFB4 and AFB5 Are Required for Response to the Synthetic Auxin Picloram. G3-GENES GENOMES GENETICS 2016; 6:1383-90. [PMID: 26976444 PMCID: PMC4856089 DOI: 10.1534/g3.115.025585] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The plant hormone auxin is perceived by a family of F-box proteins called the TIR1/AFBs. Phylogenetic studies reveal that these proteins fall into four clades in flowering plants called TIR1, AFB2, AFB4, and AFB6. Genetic studies indicate that members of the TIR1 and AFB2 groups act as positive regulators of auxin signaling by promoting the degradation of the Aux/IAA transcriptional repressors. In this report, we demonstrate that both AFB4 and AFB5 also function as auxin receptors based on in vitro assays. We also provide genetic evidence that AFB4 and AFB5 are targets of the picloram family of auxinic herbicides in addition to indole-3-acetic acid. In contrast to previous studies we find that null afb4 alleles do not exhibit obvious defects in seedling morphology or auxin hypersensitivity. We conclude that AFB4 and AFB5 act in a similar fashion to other members of the family but exhibit a distinct auxin specificity.
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