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Zhang J, Yang J, Yin Y. Germination Promotes Flavonoid Accumulation of Finger Millet ( Eleusine coracana L.): Response Surface Optimization and Investigation of Accumulation Mechanism. PLANTS (BASEL, SWITZERLAND) 2024; 13:2191. [PMID: 39204627 PMCID: PMC11360649 DOI: 10.3390/plants13162191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/06/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Germination is an effective measure to regulate the accumulation of secondary metabolites in plants. In this study, we optimized the germination conditions of finger millet by response surface methodology. Meanwhile, physiological characteristics and gene expression were measured to investigate the mechanism of flavonoid accumulation in finger millet at the germination stage. The results showed that when germination time was 5.7 d, germination temperature was 31.2 °C, and light duration was 17.5 h, the flavonoid content of millet sprouts was the highest (7.0 μg/sprout). The activities and relative gene expression of key enzymes for flavonoid synthesis (phenylalanine ammonia-lyase, 4-coumarate-coenzyme a ligase, and cinnamate 4-hydroxylase) were significantly higher in finger millet sprouts germinated at 3 and 5 d compared with that in ungerminated seeds (p < 0.05). In addition, germination enhanced the activities of four antioxidant enzymes (catalase, peroxidase, superoxide dismutase, and ascorbate peroxidase) and up-regulated the gene expression of PAL and APX. Germination increased malondialdehyde content in sprouts, which resulted in cell damage. Subsequently, the antioxidant capacity of the sprouts was enhanced through the activation of antioxidant enzymes and the up-regulation of their gene expression, as well as the synthesis of active substances, including flavonoids, total phenolics, and anthocyanins. This process served to alleviate germination-induced cellular injury. These findings provide a research basis for the regulation of finger millet germination and the enhancement of its nutritional and functional properties.
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Affiliation(s)
- Jing Zhang
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China;
| | - Jia Yang
- Yangzhou Center for Food and Drug Control, Yangzhou 225000, China
| | - Yongqi Yin
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China;
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Pérez-Llorca M, Müller M. Unlocking Nature's Rhythms: Insights into Secondary Metabolite Modulation by the Circadian Clock. Int J Mol Sci 2024; 25:7308. [PMID: 39000414 PMCID: PMC11241833 DOI: 10.3390/ijms25137308] [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: 06/09/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Plants, like many other living organisms, have an internal timekeeper, the circadian clock, which allows them to anticipate photoperiod rhythms and environmental stimuli to optimally adjust plant growth, development, and fitness. These fine-tuned processes depend on the interaction between environmental signals and the internal interactive metabolic network regulated by the circadian clock. Although primary metabolites have received significant attention, the impact of the circadian clock on secondary metabolites remains less explored. Transcriptome analyses revealed that many genes involved in secondary metabolite biosynthesis exhibit diurnal expression patterns, potentially enhancing stress tolerance. Understanding the interaction mechanisms between the circadian clock and secondary metabolites, including plant defense mechanisms against stress, may facilitate the development of stress-resilient crops and enhance targeted management practices that integrate circadian agricultural strategies, particularly in the face of climate change. In this review, we will delve into the molecular mechanisms underlying circadian rhythms of phenolic compounds, terpenoids, and N-containing compounds.
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Affiliation(s)
- Marina Pérez-Llorca
- Department of Biology, Health and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08028 Barcelona, Spain
| | - Maren Müller
- Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08028 Barcelona, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
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Wu G, Cao A, Wen Y, Bao W, She F, Wu W, Zheng S, Yang N. Characteristics and Functions of MYB (v-Myb avivan myoblastsis virus oncogene homolog)-Related Genes in Arabidopsis thaliana. Genes (Basel) 2023; 14:2026. [PMID: 38002969 PMCID: PMC10671209 DOI: 10.3390/genes14112026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The MYB (v-Myb avivan myoblastsis virus oncogene homolog) transcription factor family is one of the largest families of plant transcription factors which plays a vital role in many aspects of plant growth and development. MYB-related is a subclass of the MYB family. Fifty-nine Arabidopsis thaliana MYB-related (AtMYB-related) genes have been identified. In order to understand the functions of these genes, in this review, the promoters of AtMYB-related genes were analyzed by means of bioinformatics, and the progress of research into the functions of these genes has been described. The main functions of these AtMYB-related genes are light response and circadian rhythm regulation, root hair and trichome development, telomere DNA binding, and hormone response. From an analysis of cis-acting elements, it was found that the promoters of these genes contained light-responsive elements and plant hormone response elements. Most genes contained elements related to drought, low temperature, and defense and stress responses. These analyses suggest that AtMYB-related genes may be involved in A. thaliana growth and development, and environmental adaptation through plant hormone pathways. However, the functions of many genes do not occur independently but instead interact with each other through different pathways. In the future, the study of the role of the gene in different pathways will be conducive to a comprehensive understanding of the function of the gene. Therefore, gene cloning and protein functional analyses can be subsequently used to understand the regulatory mechanisms of AtMYB-related genes in the interaction of multiple signal pathways. This review provides theoretical guidance for the follow-up study of plant MYB-related genes.
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Affiliation(s)
- Guofan Wu
- College of Life Sciences, Northwest Normal University, Lanzhou 730070, China; (A.C.); (Y.W.); (W.B.); (F.S.); (W.W.); (S.Z.); (N.Y.)
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Wang Y, Zhou H, He Y, Shen X, Lin S, Huang L. MYB transcription factors and their roles in the male reproductive development of flowering plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111811. [PMID: 37574139 DOI: 10.1016/j.plantsci.2023.111811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/29/2023] [Accepted: 07/25/2023] [Indexed: 08/15/2023]
Abstract
As one of the largest transcription factor families with complex functional differentiation in plants, the MYB transcription factors (MYB TFs) play important roles in the physiological and biochemical processes of plant growth and development. Male reproductive development, an essential part of sexual reproduction in flowering plants, is undoubtedly regulated by MYB TFs. In this review, we summarize the roles of the MYB TFs involved in the three stages of male reproductive development: pollen grains formation and maturation, filament elongation and anther dehiscence, and fertilization. Also, the potential downstream target genes and upstream regulators of these MYB TFs are discussed. Furthermore, we propose the underlying regulatory mechanisms of these MYB TFs: (1) A complex network of MYB TFs regulates various aspects of male reproductive development; (2) MYB homologous genes in different species may be functionally conserved or differentiated; (3) MYB TFs often form regulatory complexes with bHLH TFs.
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Affiliation(s)
- Yijie Wang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Huiyan Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Yuanrong He
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya, China
| | - Xiuping Shen
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Sue Lin
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou 325000, Zhejiang, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya, China.
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Zhang YS, Xu Y, Xing WT, Wu B, Huang DM, Ma FN, Zhan RL, Sun PG, Xu YY, Song S. Identification of the passion fruit ( Passiflora edulis Sims) MYB family in fruit development and abiotic stress, and functional analysis of PeMYB87 in abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1124351. [PMID: 37215287 PMCID: PMC10196401 DOI: 10.3389/fpls.2023.1124351] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/21/2023] [Indexed: 05/24/2023]
Abstract
Environmental stresses are ubiquitous in agricultural cultivation, and they affect the healthy growth and development of edible tissues in passion fruit. The study of resistance mechanisms is important in understanding the adaptation and resistance of plants to environmental stresses. In this work, two differently resistant passion fruit varieties were selected, using the expression characteristics of the transcription factor MYB, to explore the resistance mechanism of the MYB gene under various environmental stresses. A total of 174 MYB family members were identified using high-quality passion fruit genomes: 98 2R-MYB, 5 3R-MYB, and 71 1R-MYB (MYB-relate). Their family information was systematically analyzed, including subcellular localization, physicochemical properties, phylogeny at the genomic level, promoter function, encoded proteins, and reciprocal regulation. In this study, bioinformatics and transcriptome sequencing were used to identify members of the PeMYB genes in passion fruit whole-genome data, and biological techniques, such as qPCR, gene clone, and transient transformation of yeast, were used to determine the function of the passion fruit MYB genes in abiotic stress tolerance. Transcriptomic data were obtained for differential expression characteristics of two resistant and susceptible varieties, three expression patterns during pulp development, and four induced expression patterns under abiotic stress conditions. We further focused on the resistance mechanism of PeMYB87 in environmental stress, and we selected 10 representative PeMYB genes for quantitative expression verification. Most of the genes were differentially induced by four abiotic stresses, among which PeMYB87 responded significantly to high-temperature-induced expression and overexpression of the PeMYB87 gene in the yeast system. The transgenic PeMYB87 in yeast showed different degrees of stress resistance under exposure to cold, high temperatures, drought, and salt stresses. These findings lay the foundation for further analysis of the biological functions of PeMYBs involved in stress resistance in passion fruit.
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Affiliation(s)
- Yan-shu Zhang
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, Yunnan, China
| | - Yi Xu
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Wen-ting Xing
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Bin Wu
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Dong-mei Huang
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Fu-ning Ma
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Ru-lin Zhan
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Pei-guang Sun
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Yong-yan Xu
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, Yunnan, China
| | - Shun Song
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
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Li Y, Li H, Wang S, Li J, Bacha SAS, Xu G, Li J. Metabolomic and transcriptomic analyses of the flavonoid biosynthetic pathway in blueberry ( Vaccinium spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1082245. [PMID: 37152168 PMCID: PMC10157174 DOI: 10.3389/fpls.2023.1082245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
As a highly economic small fruit crop, blueberry is enjoyed by most people in terms of color, taste, and rich nutrition. To better understand its coloring mechanism on the process of ripening, an integrative analysis of the metabolome and transcriptome profiles was performed in three blueberry varieties at three developmental stages. In this study, 41 flavonoid metabolites closely related to the coloring in blueberry samples were analyzed. It turned out that the most differential metabolites in the ripening processes were delphinidin-3-O-arabinoside (dpara), peonidin-3-O-glucoside (pnglu), and delphinidin-3-O-galactoside (dpgal), while the most differential metabolites among different varieties were flavonols. Furthermore, to obtain more accurate and comprehensive transcripts of blueberry during the developmental stages, PacBio and Illumina sequencing technology were combined to obtain the transcriptome of the blueberry variety Misty, for the very first time. Finally, by applying the gene coexpression network analysis, the darkviolet and bisque4 modules related to flavonoid synthesis were determined, and the key genes related to two flavonoid 3', 5'-hydroxylase (F3'5'H) genes in the darkviolet module and one bHLH transcription factor in the bisque4 module were predicted. It is believed that our findings could provide valuable information for the future study on the molecular mechanism of flavonoid metabolites and flavonoid synthesis pathways in blueberries.
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Affiliation(s)
- Yinping Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Haifei Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Shiyao Wang
- Department of Applied Biosciences, Toyo University, Ora-gun, Japan
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Syed Asim Shah Bacha
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Guofeng Xu
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
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Qin C, Du T, Zhang R, Wang Q, Liu Y, Wang T, Cao H, Bai Q, Zhang Y, Su S. Integrated transcriptome, metabolome and phytohormone analysis reveals developmental differences between the first and secondary flowering in Castanea mollissima. FRONTIERS IN PLANT SCIENCE 2023; 14:1145418. [PMID: 37008486 PMCID: PMC10060901 DOI: 10.3389/fpls.2023.1145418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/16/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Chestnut (Castanea mollissima BL.) is an important woody grain, and its flower formation has a significant impact on fruit yield and quality. Some chestnut species in northern China re-flower in the late summer. On the one hand, the second flowering consumes a lot of nutrients in the tree, weakening the tree and thus affecting flowering in the following year. On the other hand, the number of female flowers on a single bearing branch during the second flowering is significantly higher than that of the first flowering, which can bear fruit in bunches. Therefore, these can be used to study the sex differentiation of chestnut. METHODS In this study, the transcriptomes, metabolomes, and phytohormones of male and female chestnut flowers were determined during spring and late summer. We aimed to understand the developmental differences between the first and secondary flowering stages in chestnuts. We analysed the reasons why the number of female flowers is higher in the secondary flowering than in the first flowering and found ways to increase the number of female flowers or decrease the number of male flowers in chestnuts. RESULTS Transcriptome analysis of male and female flowers in different developmental seasons revealed that EREBP-like mainly affected the development of secondary female flowers and HSP20 mainly affected the development of secondary male flowers. KEGG enrichment analysis showed that 147 common differentially-regulated genes were mainly enriched from circadian rhythm-plant, carotenoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. Metabolome analysis showed that the main differentially accumulated metabolites in female flowers were flavonoids and phenolic acids, whereas the main differentially accumulated metabolites in male flowers were lipids, flavonoids, and phenolic acids. These genes and their metabolites are positively correlated with secondary flower formation. Phytohormone analysis showed that abscisic and salicylic acids were negatively correlated with secondary flower formation. MYB305, a candidate gene for sex differentiation in chestnuts, promoted the synthesis of flavonoid substances and thus increased the number of female flowers. DISCUSSION We constructed a regulatory network for secondary flower development in chestnuts, which provides a theoretical basis for the reproductive development mechanism of chestnuts. This study has important practical implications for improving chestnut yield and quality.
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Chen N, Pan L, Yang Z, Su M, Xu J, Jiang X, Yin X, Wang T, Wan F, Chi X. A MYB-related transcription factor from peanut, AhMYB30, improves freezing and salt stress tolerance in transgenic Arabidopsis through both DREB/CBF and ABA-signaling pathways. FRONTIERS IN PLANT SCIENCE 2023; 14:1136626. [PMID: 36925750 PMCID: PMC10013196 DOI: 10.3389/fpls.2023.1136626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/14/2023] [Indexed: 06/12/2023]
Abstract
Abiotic stresses such as salinity and low temperature have serious impact on peanut growth and yield. The present work investigated the function of a MYB-related transcription factor gene AhMYB30 obtained from peanut under salt and low temperature stresses by transgenic methods. The results indicated that the overexpression of AhMYB30 in Arabidopsis could enhance the resistance of transgenic plants to freezing and salt stresses. The expression of stress-response genes RD29A (Response-to-Dehydration 29A), COR15A (Cold-Regulated 15A), KIN1 (Kinesin 1) and ABI2 (Abscisic acid Insensitive 2) increased in transgenic plants compared with in wild-type. Subcellular localization and transcriptional autoactivation validation demonstrated that AhMYB30 has essential features of transcription factors. Therefore, AhMYB30 may increase salt and freezing stress tolerance as the transcription factor (TF) in Arabidopsis through both DREB/CBF and ABA-signaling pathways. Our results lay the theoretical foundation for exploring stress resistance mechanisms of peanut and offering novel genetic resources for molecular breeding.
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Affiliation(s)
- Na Chen
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Lijuan Pan
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Zhen Yang
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Maowen Su
- Department of Animal and Plant Quarantine, Qingdao Customs, Qingdao, China
| | - Jing Xu
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Xiao Jiang
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Xiangzhen Yin
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Tong Wang
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Feifei Wan
- Division for Guidance of Cooperative Economy, Binzhou Agricultural Technology Extension Center, Binzhou, China
| | - Xiaoyuan Chi
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
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Godbole RC, Pable AA, Singh S, Barvkar VT. Interplay of transcription factors orchestrating the biosynthesis of plant alkaloids. 3 Biotech 2022; 12:250. [PMID: 36051988 PMCID: PMC9424429 DOI: 10.1007/s13205-022-03316-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Plants produce a range of secondary metabolites primarily as defence molecules. A plant has to invest considerable energy to synthesise alkaloids, and sometimes they are even toxic to themselves. Hence, the biosynthesis of alkaloids is a spatiotemporally regulated process under quantitative feedback regulation which is accomplished by the signal reception, transcriptional/translational regulation, transport, storage and accumulation. The transcription factors (TFs) initiate the biosynthesis of alkaloids after appropriate cues. The present study recapitulates last decade understanding of the role of TFs in alkaloid biosynthesis. The present review discusses TF families, viz. AP2/ERF, bHLH, WRKY, MYB involved in the biosynthesis of various types of alkaloids. It also highlights the role of the jasmonic acid cascade and post-translational modifications of TF proteins. A thorough understanding of TFs will help us to decide a strategy to facilitate successful pathway manipulation and in vitro production.
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Affiliation(s)
- Rucha C. Godbole
- Department of Botany, Savitribai Phule Pune University, Pune, 411007 India
| | - Anupama A. Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007 India
| | - Sudhir Singh
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre (BARC), Mumbai, 400085 India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094 India
| | - Vitthal T. Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007 India
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Yan X, Ding W, Wu X, Wang L, Yang X, Yue Y. Insights Into the MYB-Related Transcription Factors Involved in Regulating Floral Aroma Synthesis in Sweet Osmanthus. FRONTIERS IN PLANT SCIENCE 2022; 13:765213. [PMID: 35356120 PMCID: PMC8959829 DOI: 10.3389/fpls.2022.765213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
As an important member of the MYB transcription factor (TF) family, the MYB-related TFs play multiple roles in regulating the synthesis of secondary metabolites and developmental processes, as well as in response to numerous biotic and abiotic stressors in plants. However, little is known regarding their roles in regulating the formation of floral volatile organic compounds (VOCs). In this study, we conducted a genome-wide analysis of MYB-related proteins in sweet osmanthus; 212 OfMYB-related TFs were divided into three distinct subgroups based on the phylogenetic analysis. Additionally, we found that the expansion of the OfMYB-related genes occurred primarily through segmental duplication events, and purifying selection occurred in all duplicated gene pairs. RNA-seq data revealed that the OfMYB-related genes were widely expressed in different organs of sweet osmanthus, and some showed flower organ/development stage-preferential expression patterns. Here, three OfMYB-related genes (OfMYB1R70/114/201), which were expressed nuclearly in floral organs, were found to be significantly involved in regulating the synthesis of floral VOCs. Only, OfMYB1R201 had transcriptional activity, thus implying that this gene participates in regulating the expression of VOC synthesis related genes. Remarkably, the transient expression results suggested that OfMYB1R70, OfMYB1R114, and OfMYB1R201 are involved in the regulation of VOC synthesis; OfMYB1R114 and OfMYB1R70 are involved in accelerating β-ionone formation. In contrast, OfMYB1R201 decreases the synthesis of β-ionone. Our results deepen our knowledge of the functions of MYB-related TFs and provide critical candidate genes for the floral aroma breeding of sweet osmanthus in the future.
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Affiliation(s)
- Xin Yan
- Key Laboratory of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenjie Ding
- Key Laboratory of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xiuyi Wu
- Key Laboratory of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lianggui Wang
- Key Laboratory of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xiulian Yang
- Key Laboratory of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yuanzheng Yue
- Key Laboratory of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Li H, Du Y, Zhang J, Feng H, Liu J, Yang G, Zhu Y. Unraveling the Mechanism of Purple Leaf Formation in Brassica napus by Integrated Metabolome and Transcriptome Analyses. FRONTIERS IN PLANT SCIENCE 2022; 13:945553. [PMID: 35903234 PMCID: PMC9315442 DOI: 10.3389/fpls.2022.945553] [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: 05/16/2022] [Accepted: 06/13/2022] [Indexed: 05/12/2023]
Abstract
Brassica napus as both oilseed and vegetable, is widely cultivated in China. The purple leaf of B. napus is rich in anthocyanins and can provide valuable nutrients. Although several high-anthocyanin cultivars have been reported, the molecular mechanism underlying anthocyanin biosynthesis in B. napus remains lesser-known. Therefore, in this study, we conducted integrative metabolome and transcriptome analyses in three B. napus cultivars with different leaf colors. Overall, 39 flavonoids were identified (including 35 anthocyanins), and 22 anthocyanins were differentially accumulated in the leaves, contributing to the different leaf colors. Cyanidin-3,5,3'-O-triglucoside was confirmed as the main contributor of the purple leaf phenotype. Meanwhile, other anthocyanins may play important roles in deepening the color of B. napus leaves. A total of 5,069 differentially expressed genes (DEGs) and 32 overlapping DEGs were identified by RNA-sequencing; hence, the correlation between anthocyanin content and DEG expression levels was explored. Two structural genes (DFR and ANS), three GSTs (homologous to TT19), and 68 differentially expressed transcription factors (TFs), especially MYB-related TFs and WRKY44, were identified in three B. napus varieties characterized by different leaf color, thereby indicating that these genes may contribute to anthocyanin biosynthesis, transport, or accumulation in B. napus leaves. The findings of study provide important insights that may contribute to gaining a better understanding of the transcriptional regulation of anthocyanin metabolism in B. napus.
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12
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Shan B, Wang W, Cao J, Xia S, Li R, Bian S, Li X. Soybean GmMYB133 Inhibits Hypocotyl Elongation and Confers Salt Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:764074. [PMID: 35003158 PMCID: PMC8732865 DOI: 10.3389/fpls.2021.764074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
REVEILLE (RVE) genes generally act as core circadian oscillators to regulate multiple developmental events and stress responses in plants. It is of importance to document their roles in crops for utilizing them to improve agronomic traits. Soybean is one of the most important crops worldwide. However, the knowledge regarding the functional roles of RVEs is extremely limited in soybean. In this study, the soybean gene GmMYB133 was shown to be homologous to the RVE8 clade genes of Arabidopsis. GmMYB133 displayed a non-rhythmical but salt-inducible expression pattern. Like AtRVE8, overexpression of GmMYB133 in Arabidopsis led to developmental defects such as short hypocotyl and late flowering. Seven light-responsive or auxin-associated genes including AtPIF4 were transcriptionally depressed by GmMYB133, suggesting that GmMYB133 might negatively regulate plant growth. Noticeably, the overexpression of GmMYB133 in Arabidopsis promoted seed germination and plant growth under salt stress, and the contents of chlorophylls and malondialdehyde (MDA) were also enhanced and decreased, respectively. Consistently, the expressions of four positive regulators responsive to salt tolerance were remarkably elevated by GmMYB133 overexpression, indicating that GmMYB133 might confer salt stress tolerance. Further observation showed that GmMYB133 overexpression perturbed the clock rhythm of AtPRR5, and yeast one-hybrid assay indicated that GmMYB133 could bind to the AtPRR5 promoter. Moreover, the retrieved ChIP-Seq data showed that AtPRR5 could directly target five clients including AtPIF4. Thus, a regulatory module GmMYB133-PRR5-PIF4 was proposed to regulate plant growth and salt stress tolerance. These findings laid a foundation to further address the functional roles of GmMYB133 and its regulatory mechanisms in soybean.
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Affiliation(s)
- Binghui Shan
- College of Plant Science, Jilin University, Changchun, China
| | - Wei Wang
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou, China
- Academy of Agricultural and Forestry Sciences, Cangzhou, China
| | - Jinfeng Cao
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou, China
- Academy of Agricultural and Forestry Sciences, Cangzhou, China
| | - Siqi Xia
- College of Plant Science, Jilin University, Changchun, China
| | - Ruihua Li
- College of Plant Science, Jilin University, Changchun, China
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, China
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13
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Qiu H, Li C, Yang W, Tan K, Yi Q, Yang M, Bai G. Fine Mapping of a New Major QTL- qGLS8 for Gray Leaf Spot Resistance in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:743869. [PMID: 34603363 PMCID: PMC8484643 DOI: 10.3389/fpls.2021.743869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Gray leaf spot (GLS), caused by different species of Cercospora, is a fungal, non-soil-borne disease that causes serious reductions in maize yield worldwide. The identification of major quantitative trait loci (QTLs) for GLS resistance in maize is essential for developing marker-assisted selection strategies in maize breeding. Previous research found a significant difference (P < 0.01) in GLS resistance between T32 (highly resistant) and J51 (highly susceptible) genotypes of maize. Initial QTL analysis was conducted in an F2 : 3 population of 189 individuals utilizing genetic maps that were constructed using 181 simple sequence repeat (SSR) markers. One QTL (qGLS8) was detected, defined by the markers umc1130 and umc2354 in three environments. The qGLS8 QTL detected in the initial analysis was located in a 51.96-Mb genomic region of chromosome 8 and explained 7.89-14.71% of the phenotypic variation in GLS resistance in different environments. We also developed a near isogenic line (NIL) BC3F2 population with 1,468 individuals and a BC3F2-Micro population with 180 individuals for fine mapping. High-resolution genetic and physical maps were constructed using six newly developed SSRs. The QTL-qGLS8 was narrowed down to a 124-kb region flanked by the markers ym20 and ym51 and explained up to 17.46% of the phenotypic variation in GLS resistance. The QTL-qGLS8 contained seven candidate genes, such as an MYB-related transcription factor 24 and a C 3 H transcription factor 347), and long intergenic non-coding RNAs (lincRNAs). The present study aimed to provide a foundation for the identification of candidate genes for GLS resistance in maize.
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Affiliation(s)
- Hongbo Qiu
- *Correspondence: Hongbo Qiu ; orcid.org/0000-0001-8162-1738
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14
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Li J, Lin K, Zhang S, Wu J, Fang Y, Wang Y. Genome-Wide Analysis of Myeloblastosis-Related Genes in Brassica napus L. and Positive Modulation of Osmotic Tolerance by BnMRD107. FRONTIERS IN PLANT SCIENCE 2021; 12:678202. [PMID: 34220898 PMCID: PMC8248502 DOI: 10.3389/fpls.2021.678202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/30/2021] [Indexed: 06/01/2023]
Abstract
Myeloblastosis (MYB)-related transcription factors comprise a large subfamily of the MYB family. They play significant roles in plant development and in stress responses. However, MYB-related proteins have not been comprehensively investigated in rapeseed (Brassica napus L.). In the present study, a genome-wide analysis of MYB-related transcription factors was performed in rapeseed. We identified 251 Brassica napus MYB (BnMYB)-related members, which were divided phylogenetically into five clades. Evolutionary analysis suggested that whole genome duplication and segmental duplication events have played a significant role in the expansion of BnMYB-related gene family. Selective pressure of BnMYB-related genes was estimated using the Ka/Ks ratio, which indicated that BnMYB-related genes underwent strong purifying selection during evolution. In silico analysis showed that various development-associated, phytohormone-responsive, and stress-related cis-acting regulatory elements were enriched in the promoter regions of BnMYB-related genes. Furthermore, MYB-related genes with tissue or organ-specific, stress-responsive expression patterns were identified in B. napus based on temporospatial and abiotic stress expression profiles. Among the stress-responsive MYB-related genes, BnMRD107 was strongly induced by drought stress, and was therefore selected for functional study. Rapeseed seedlings overexpressing BnMRD107 showed improved resistance to osmotic stress. Our findings not only lay a foundation for further functional characterization of BnMYB-related genes, but also provide valuable clues to determine candidate genes for future genetic improvement of B. napus.
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Affiliation(s)
- Jian Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Keyun Lin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Shuai Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Jian Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
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15
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Li X, Xiang F, Han W, Qie B, Zhai R, Yang C, Wang Z, Xu L. The MIR-Domain of PbbHLH2 Is Involved in Regulation of the Anthocyanin Biosynthetic Pathway in "Red Zaosu" ( PyrusBretschneideri Rehd.) Pear Fruit. Int J Mol Sci 2021; 22:ijms22063026. [PMID: 33809693 PMCID: PMC8002321 DOI: 10.3390/ijms22063026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/10/2021] [Accepted: 03/14/2021] [Indexed: 02/05/2023] Open
Abstract
The N-terminal of Myc-like basic helix-loop-helix transcription factors (bHLH TFs) contains an interaction domain, namely the MYB-interacting region (MIR), which interacts with the R2R3-MYB proteins to regulate genes involved in the anthocyanin biosynthetic pathway. However, the functions of MIR-domain bHLHs in this pathway are not fully understood. In this study, PbbHLH2 containing the MIR-domain was identified and its function investigated. The overexpression of PbbHLH2 in ”Zaosu” pear peel increased the anthocyanin content and the expression levels of late biosynthetic genes. Bimolecular fluorescence complementation showed that PbbHLH2 interacted with R2R3-MYB TFs PbMYB9, 10, and 10b in onion epidermal cells and confirmed that MIR-domain plays important roles in the interaction between the MIR-domain bHLH and R2R3-MYB TFs. Moreover, PbbHLH2 bound and activated the dihydroflavonol reductase promoter in yeast one-hybrid (Y1H) and dual-luciferase assays. Taken together these results suggested that the MIR domain of PbbHLH2 regulated anthocyanin biosynthesis in pear fruit peel.
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Affiliation(s)
| | | | | | | | | | | | | | - Lingfei Xu
- Correspondence: ; Tel.: +86-029–87081023
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16
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Badhan S, Ball AS, Mantri N. First Report of CRISPR/Cas9 Mediated DNA-Free Editing of 4CL and RVE7 Genes in Chickpea Protoplasts. Int J Mol Sci 2021; 22:E396. [PMID: 33401455 PMCID: PMC7795094 DOI: 10.3390/ijms22010396] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022] Open
Abstract
The current genome editing system Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR/Cas9) has already confirmed its proficiency, adaptability, and simplicity in several plant-based applications. Together with the availability of a vast amount of genome data and transcriptome data, CRISPR/Cas9 presents a massive opportunity for plant breeders and researchers. The successful delivery of ribonucleoproteins (RNPs), which are composed of Cas9 enzyme and a synthetically designed single guide RNA (sgRNA) and are used in combination with various transformation methods or lately available novel nanoparticle-based delivery approaches, allows targeted mutagenesis in plants species. Even though this editing technique is limitless, it has still not been employed in many plant species to date. Chickpea is the second most crucial winter grain crop cultivated worldwide; there are currently no reports on CRISPR/Cas9 gene editing in chickpea. Here, we selected the 4-coumarate ligase (4CL) and Reveille 7 (RVE7) genes, both associated with drought tolerance for CRISPR/Cas9 editing in chickpea protoplast. The 4CL represents a key enzyme involved in phenylpropanoid metabolism in the lignin biosynthesis pathway. It regulates the accumulation of lignin under stress conditions in several plants. The RVE7 is a MYB transcription factor which is part of regulating circadian rhythm in plants. The knockout of these selected genes in the chickpea protoplast using DNA-free CRISPR/Cas9 editing represents a novel approach for achieving targeted mutagenesis in chickpea. Results showed high-efficiency editing was achieved for RVE7 gene in vivo compared to the 4CL gene. This study will help unravel the role of these genes under drought stress and understand the complex drought stress mechanism pathways. This is the first study in chickpea protoplast utilizing CRISPR/Cas9 DNA free gene editing of drought tolerance associated genes.
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Affiliation(s)
| | | | - Nitin Mantri
- The Pangenomics Lab, School of Science, RMIT University, Melbourne 3000, Australia; (S.B.); (A.S.B.)
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17
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Liu Y, Zeng Y, Li Y, Liu Z, Lin-Wang K, Espley RV, Allan AC, Zhang J. Genomic survey and gene expression analysis of the MYB-related transcription factor superfamily in potato (Solanum tuberosum L.). Int J Biol Macromol 2020; 164:2450-2464. [DOI: 10.1016/j.ijbiomac.2020.08.062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
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18
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Matsuda H, Nakayasu M, Aoki Y, Yamazaki S, Nagano AJ, Yazaki K, Sugiyama A. Diurnal metabolic regulation of isoflavones and soyasaponins in soybean roots. PLANT DIRECT 2020; 4:e00286. [PMID: 33241173 PMCID: PMC7673354 DOI: 10.1002/pld3.286] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 05/05/2023]
Abstract
Isoflavones and soyasaponins are major specialized metabolites accumulated in soybean roots and secreted into the rhizosphere. Unlike the biosynthetic pathway, the transporters involved in metabolite secretion remain unknown. The developmental regulation of isoflavone and soyasaponin secretions has been recently reported, but the diurnal regulation of their biosynthesis and secretion still needs to be further studied. To address these challenges, we conducted transcriptome and metabolite analysis using hydroponically grown soybean plants at 6-hr intervals for 48 hr in a 12-hr-light/12-hr-dark condition. Isoflavone and soyasaponin biosynthetic genes showed opposite patterns in the root tissues; that is, the former genes are highly expressed in the daytime, while the latter ones are strongly induced at nighttime. GmMYB176 encoding a transcription factor of isoflavone biosynthesis was upregulated from ZT0 (6:00 a.m.) to ZT6 (12:00 a.m.), followed by the induction of isoflavone biosynthetic genes at ZT6. The isoflavone aglycone content in the roots accordingly increased from ZT6 to ZT18 (0:00 a.m.). The isoflavone aglycone content in root exudates was kept consistent throughout the day, whereas that of glucosides increased at ZT6, which reflected the decreased expression of the gene encoding beta-glucosidase involved in the hydrolysis of apoplast-localized isoflavone conjugates. Co-expression analysis revealed that those isoflavone and soyasaponin biosynthetic genes formed separate clusters, which exhibited a correlation to ABC and MATE transporter genes. In summary, the results in this study indicated the diurnal regulation of isoflavone biosynthesis in soybean roots and the putative transporter genes responsible for isoflavone and soyasaponin transport.
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Affiliation(s)
- Hinako Matsuda
- Research Institute for Sustainable HumanosphereKyoto UniversityGokasho, UjiJapan
| | - Masaru Nakayasu
- Research Institute for Sustainable HumanosphereKyoto UniversityGokasho, UjiJapan
| | - Yuichi Aoki
- Tohoku Medical Megabank OrganizationTohoku UniversitySendaiJapan
| | | | | | - Kazufumi Yazaki
- Research Institute for Sustainable HumanosphereKyoto UniversityGokasho, UjiJapan
| | - Akifumi Sugiyama
- Research Institute for Sustainable HumanosphereKyoto UniversityGokasho, UjiJapan
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19
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Gam DT, Khoi PH, Ngoc PB, Linh LK, Hung NK, Anh PTL, Thu NT, Hien NTT, Khanh TD, Ha CH. LED Lights Promote Growth and Flavonoid Accumulation of Anoectochilus roxburghii and Are Linked to the Enhanced Expression of Several Related Genes. PLANTS 2020; 9:plants9101344. [PMID: 33053736 PMCID: PMC7599663 DOI: 10.3390/plants9101344] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/30/2020] [Accepted: 10/06/2020] [Indexed: 01/01/2023]
Abstract
Anoectochilus roxburghii is a wild edible species and has been traditionally used for a wide range of diseases in many countries. Our research aims to find the optimal light-emitting diode (LED) lighting conditions to improve the growth and development of A. roxburghii seedling at the acclimation stage. Two-month-old explants were cultured under the various lighting conditions including red (R), blue (B), BR (one blue: four red), BRW151 (one blue: five red: one white), BRW142 (one blue: four red: two white), and fluorescent lamp (FL). The results showed that the lighting conditions not only affect the growth and morphology of plants but also the accumulation of total flavonoids. Single wavelengths (B or R LED) inhibited the growth and secondary biosynthesis of A. roxburghii, while the BR LED showed an enhancement in both growth and biomass accumulation. A. roxburghii plants were grown under BR LED light has average plant height (7.18 cm), stem diameter (17.6mm), number of leaves (5.78 leaves/tree), leaf area (4.67 cm2), fresh weight (0.459 g/tree), dry matter percentages (11.69%), and total flavonoid (1.811 mg/g FW) is considered to be superior to FL lamps and other LEDs in the experiment. This indicates that both blue and red wavelengths are required for the normal growth of A. roxburghii. To learn more about how light affects flavonoid biosynthesis, we evaluated the expression of genes involved in this process (pal, chs, chi, and fls) and found that BR LED light enhances the expression level of chi and fls genes compared to fluorescent lamps (1.18 and 1.21 times, respectively), leading to an increase in the flavonoid content of plant. Therefore, applying BR LED during in vitro propagation of A. roxburghii could be a feasible way to improve the medicinal value of this plant.
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Affiliation(s)
- Do Thi Gam
- Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (D.T.G.); (P.B.N.); (L.K.L.); (N.K.H.); (N.T.T.H.)
- Center for High Technology Development, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (P.H.K.); (P.T.L.A.); (N.T.T.)
| | - Phan Hong Khoi
- Center for High Technology Development, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (P.H.K.); (P.T.L.A.); (N.T.T.)
| | - Pham Bich Ngoc
- Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (D.T.G.); (P.B.N.); (L.K.L.); (N.K.H.); (N.T.T.H.)
- Vietnam Academy of Science and Technology (VAST), Graduate University of Science and Technology, 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam
| | - Ly Khanh Linh
- Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (D.T.G.); (P.B.N.); (L.K.L.); (N.K.H.); (N.T.T.H.)
| | - Nguyen Khac Hung
- Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (D.T.G.); (P.B.N.); (L.K.L.); (N.K.H.); (N.T.T.H.)
| | - Phan Thi Lan Anh
- Center for High Technology Development, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (P.H.K.); (P.T.L.A.); (N.T.T.)
| | - Nguyen Thi Thu
- Center for High Technology Development, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (P.H.K.); (P.T.L.A.); (N.T.T.)
| | - Nguyen Thi Thu Hien
- Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (D.T.G.); (P.B.N.); (L.K.L.); (N.K.H.); (N.T.T.H.)
| | - Tran Dang Khanh
- Agricultural Genetics Institute, Pham Van Dong, North Tu Liem, Hanoi 123000, Vietnam;
- Center for Agricultural Innovation, Vietnam National University of Agriculture, Hanoi 131000, Vietnam
| | - Chu Hoang Ha
- Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam; (D.T.G.); (P.B.N.); (L.K.L.); (N.K.H.); (N.T.T.H.)
- Vietnam Academy of Science and Technology (VAST), Graduate University of Science and Technology, 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi 100000, Vietnam
- Correspondence: ; Tel.: 84-9121-75636
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20
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Tu X, Mejía-Guerra MK, Valdes Franco JA, Tzeng D, Chu PY, Shen W, Wei Y, Dai X, Li P, Buckler ES, Zhong S. Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors. Nat Commun 2020; 11:5089. [PMID: 33037196 PMCID: PMC7547689 DOI: 10.1038/s41467-020-18832-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/17/2020] [Indexed: 11/29/2022] Open
Abstract
The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex network. In this study, we use large-scale ChIP-seq to reconstruct it in the maize leaf, and train machine-learning models to predict TF binding and co-localization. The resulting network covers 77% of the expressed genes, and shows a scale-free topology and functional modularity like a real-world network. TF binding sequence preferences are conserved within family, while co-binding could be key for their binding specificity. Cross-species comparison shows that core network nodes at the top of the transmission of information being more conserved than those at the bottom. This study reveals the complex and redundant nature of the plant transcription regulatory network, and sheds light on its architecture, organizing principle and evolutionary trajectory.
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Affiliation(s)
- Xiaoyu Tu
- The State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Shandong, China
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | - David Tzeng
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Po-Yu Chu
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei Shen
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yingying Wei
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiuru Dai
- The State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Shandong, China
| | - Pinghua Li
- The State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Shandong, China.
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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21
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Li P, Wen J, Chen P, Guo P, Ke Y, Wang M, Liu M, Tran LSP, Li J, Du H. MYB Superfamily in Brassica napus: Evidence for Hormone-Mediated Expression Profiles, Large Expansion, and Functions in Root Hair Development. Biomolecules 2020; 10:biom10060875. [PMID: 32517318 PMCID: PMC7356979 DOI: 10.3390/biom10060875] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/16/2020] [Accepted: 06/05/2020] [Indexed: 01/08/2023] Open
Abstract
MYB proteins are involved in diverse important biological processes in plants. Herein, we obtained the MYB superfamily from the allotetraploid Brassica napus, which contains 227 MYB-related (BnMYBR/Bn1R-MYB), 429 R2R3-MYB (Bn2R-MYB), 22 R1R2R3-MYB (Bn3R-MYB), and two R1R2R2R1/2-MYB (Bn4R-MYB) genes. Phylogenetic analysis classified the Bn2R-MYBs into 43 subfamilies, and the BnMYBRs into five subfamilies. Sequence characteristics and exon/intron structures within each subfamily of the Bn2R-MYBs and BnMYBRs were highly conserved. The whole superfamily was unevenly distributed on 19 chromosomes and underwent unbalanced expansion in B. napus. Allopolyploidy between B. oleracea and B. rapa mainly contributed to the expansion in their descendent B. napus, in which B. rapa-derived genes were more retained. Comparative phylogenetic analysis of 2R-MYB proteins from nine Brassicaceae and seven non-Brassicaceae species identified five Brassicaceae-specific subfamilies and five subfamilies that are lacking from the examined Brassicaceae species, which provided an example for the adaptive evolution of the 2R-MYB gene family alongside angiosperm diversification. Ectopic expression of four Bn2R-MYBs under the control of the viral CaMV35S and/or native promoters could rescue the lesser root hair phenotype of the Arabidopsis thaliana wer mutant plants, proving the conserved negative roles of the 2R-MYBs of the S15 subfamily in root hair development. RNA-sequencing data revealed that the Bn2R-MYBs and BnMYBRs had diverse transcript profiles in roots in response to the treatments with various hormones. Our findings provide valuable information for further functional characterizations of B. napusMYB genes.
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Affiliation(s)
- Pengfeng Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China; (P.L.); (J.W.); (P.C.); (P.G.); (Y.K.); (M.W.); (M.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China; (P.L.); (J.W.); (P.C.); (P.G.); (Y.K.); (M.W.); (M.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Ping Chen
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China; (P.L.); (J.W.); (P.C.); (P.G.); (Y.K.); (M.W.); (M.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Pengcheng Guo
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China; (P.L.); (J.W.); (P.C.); (P.G.); (Y.K.); (M.W.); (M.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yunzhuo Ke
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China; (P.L.); (J.W.); (P.C.); (P.G.); (Y.K.); (M.W.); (M.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Mangmang Wang
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China; (P.L.); (J.W.); (P.C.); (P.G.); (Y.K.); (M.W.); (M.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Mingming Liu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China; (P.L.); (J.W.); (P.C.); (P.G.); (Y.K.); (M.W.); (M.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam
- Correspondence: (L.-S.P.T.); or (H.D.); Tel.: +86-18223480008 (H.D.)
| | - Jiana Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China; (P.L.); (J.W.); (P.C.); (P.G.); (Y.K.); (M.W.); (M.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Hai Du
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China; (P.L.); (J.W.); (P.C.); (P.G.); (Y.K.); (M.W.); (M.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
- Correspondence: (L.-S.P.T.); or (H.D.); Tel.: +86-18223480008 (H.D.)
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REVEILLE Transcription Factors Contribute to the Nighttime Accumulation of Anthocyanins in 'Red Zaosu' ( Pyrus bretschneideri Rehd.) Pear Fruit Skin. Int J Mol Sci 2020; 21:ijms21051634. [PMID: 32120999 PMCID: PMC7084243 DOI: 10.3390/ijms21051634] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/14/2020] [Accepted: 02/24/2020] [Indexed: 11/17/2022] Open
Abstract
Anthocyanin biosynthesis exhibits a rhythmic oscillation pattern in some plants. To investigate the correlation between the oscillatory regulatory network and anthocyanin biosynthesis in pear, the anthocyanin accumulation and the expression patterns of anthocyanin late biosynthetic genes (ALBGs) were investigated in fruit skin of ‘Red Zaosu’ (Pyrus bretschneideri Rehd.). The anthocyanin accumulated mainly during the night over three continuous days in the fruit skin, and the ALBGs’ expression patterns in ‘Red Zaosu’ fruit skin were oscillatory. However, the expression levels of typical anthocyanin-related transcription factors did not follow this pattern. Here, we found that the expression patterns of four PbREVEILLEs (PbRVEs), members of a class of atypical anthocyanin-regulated MYBs, were consistent with those of ALBGs in ‘Red Zaosu’ fruit skin over three continuous days. Additionally, transient expression assays indicated that the four PbRVEs promoted anthocyanin biosynthesis by regulating the expression of the anthocyanin biosynthetic genes encoding dihydroflavonol-4-reductase (DFR) and anthocyanidin synthase (ANS) in red pear fruit skin, which was verified using a dual-luciferase reporter assay. Moreover, a yeast one-hybrid assay indicated that PbRVE1a, 1b and 7 directly bound to PbDFR and PbANS promoters. Thus, PbRVEs promote anthocyanin accumulation at night by up-regulating the expression levels of PbDFR and PbANS in ‘Red Zaosu’ fruit skin.
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23
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Zhao H, Zhang W, Zhang T, Lin Y, Hu Y, Fang C, Jiang J. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biol 2020; 21:24. [PMID: 32014062 PMCID: PMC6996174 DOI: 10.1186/s13059-020-1927-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species. RESULTS We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~ 90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to "specific MHSs" (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains. CONCLUSION MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.
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Affiliation(s)
- Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, 210095, Jiangsu, China.
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yaodong Hu
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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Zhao Y, Ma J, Li M, Deng L, Li G, Xia H, Zhao S, Hou L, Li P, Ma C, Yuan M, Ren L, Gu J, Guo B, Zhao C, Wang X. Whole-genome resequencing-based QTL-seq identified AhTc1 gene encoding a R2R3-MYB transcription factor controlling peanut purple testa colour. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:96-105. [PMID: 31131506 PMCID: PMC6920131 DOI: 10.1111/pbi.13175] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/08/2023]
Abstract
Peanut (Arachis hypogaea. L) is an important oil crop worldwide. The common testa colours of peanut varieties are pink or red. But the peanut varieties with dark purple testa have been focused in recent years due to the potential high levels of anthocyanin, an added nutritional value of antioxidant. However, the genetic mechanism regulating testa colour of peanut is unknown. In this study, we found that the purple testa was decided by the female parent and controlled by a single major gene named AhTc1. To identify the candidate gene controlling peanut purple testa, whole-genome resequencing-based approach (QTL-seq) was applied, and a total of 260.9 Gb of data were generated from the parental and bulked lines. SNP index analysis indicated that AhTc1 located in a 4.7 Mb region in chromosome A10, which was confirmed by bulked segregant RNA sequencing (BSR) analysis in three segregation populations derived from the crosses between pink and purple testa varieties. Allele-specific markers were developed and demonstrated that the marker pTesta1089 was closely linked with purple testa. Further, AhTc1 encoding a R2R3-MYB gene was positional cloned. The expression of AhTc1 was significantly up-regulated in the purple testa parent YH29. Overexpression of AhTc1 in transgenic tobacco plants led to purple colour of leaves, flowers, pods and seeds. In conclusion, AhTc1, encoding a R2R3-MYB transcription factor and conferring peanut purple testa, was identified, which will be useful for peanut molecular breeding selection for cultivars with purple testa colour for potential increased nutritional value to consumers.
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Affiliation(s)
- Yuhan Zhao
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Junjie Ma
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong UniversityJinanChina
| | - Ming Li
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
| | - Li Deng
- Kaifeng Academy of Agriculture and ForestryKaifengChina
| | - Guanghui Li
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
| | - Han Xia
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Shuzhen Zhao
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Lei Hou
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
| | - Pengcheng Li
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Changle Ma
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Mei Yuan
- Shandong Peanut Research InstituteShandong, QingdaoChina
| | - Li Ren
- Kaifeng Academy of Agriculture and ForestryKaifengChina
| | - Jianzhong Gu
- Kaifeng Academy of Agriculture and ForestryKaifengChina
| | - Baozhu Guo
- Crop Protection and Management Research UnitUSDA‐Agricultural Research ServiceTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Chuanzhi Zhao
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
- Crop Protection and Management Research UnitUSDA‐Agricultural Research ServiceTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Xingjun Wang
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
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25
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Weizman EN, Tannenbaum M, Tarrant AM, Hakim O, Levy O. Chromatin dynamics enable transcriptional rhythms in the cnidarian Nematostella vectensis. PLoS Genet 2019; 15:e1008397. [PMID: 31693674 PMCID: PMC6834241 DOI: 10.1371/journal.pgen.1008397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 09/02/2019] [Indexed: 12/16/2022] Open
Abstract
In animals, circadian rhythms are driven by oscillations in transcription, translation, and proteasomal degradation of highly conserved genes, resulting in diel cycles in the expression of numerous clock-regulated genes. Transcription is largely regulated through the binding of transcription factors to cis-regulatory elements within accessible regions of the chromatin. Chromatin remodeling is linked to circadian regulation in mammals, but it is unknown whether cycles in chromatin accessibility are a general feature of clock-regulated genes throughout evolution. To assess this, we applied an ATAC-seq approach using Nematostella vectensis, grown under two separate light regimes (light:dark (LD) and constant darkness (DD)). Based on previously identified N. vectensis circadian genes, our results show the coupling of chromatin accessibility and circadian transcription rhythmicity under LD conditions. Out of 180 known circadian genes, we were able to list 139 gene promoters that were highly accessible compared to common promoters. Furthermore, under LD conditions, we identified 259 active enhancers as opposed to 333 active enhancers under DD conditions, with 171 enhancers shared between the two treatments. The development of a highly reproducible ATAC-seq protocol integrated with published RNA-seq and ChIP-seq databases revealed the enrichment of transcription factor binding sites (such as C/EBP, homeobox, and MYB), which have not been previously associated with circadian signaling in cnidarians. These results provide new insight into the regulation of cnidarian circadian machinery. Broadly speaking, this supports the notion that the association between chromatin remodeling and circadian regulation arose early in animal evolution as reflected in this non-bilaterian lineage.
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Affiliation(s)
- Eviatar N. Weizman
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- * E-mail: (ENW); (OL)
| | - Miriam Tannenbaum
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Ann M. Tarrant
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Ofir Hakim
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Oren Levy
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- * E-mail: (ENW); (OL)
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26
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Colle M, Leisner CP, Wai CM, Ou S, Bird KA, Wang J, Wisecaver JH, Yocca AE, Alger EI, Tang H, Xiong Z, Callow P, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Song GQ, Childs KL, Schilmiller A, Vorsa N, Buell CR, VanBuren R, Jiang N, Edger PP. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. Gigascience 2019; 8:giz012. [PMID: 30715294 PMCID: PMC6423372 DOI: 10.1093/gigascience/giz012] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/18/2018] [Accepted: 01/18/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size. FINDINGS Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar "Draper," which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. CONCLUSIONS These findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.
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Affiliation(s)
- Marivi Colle
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
- MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA
| | - Courtney P Leisner
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Shujun Ou
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Jie Wang
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
- Center for Genomics Enabled Plant Science, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, 610 Purdue Mall, West Lafayette, IN, 47907, USA
| | - Alan E Yocca
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Elizabeth I Alger
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Haibao Tang
- Human Longevity Inc., 4570 Executive Drive, San Diego, CA 92121, USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, 221 Aimin Road, Hohhot, 010070, China
| | - Pete Callow
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Gil Ben-Zvi
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Avital Brodt
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Kobi Baruch
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Thomas Swale
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Lily Shiue
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Guo-qing Song
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
- Center for Genomics Enabled Plant Science, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Anthony Schilmiller
- Mass Spectrometry & Metabolomics Core Facility, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824, USA
| | - Nicholi Vorsa
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA
- Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, 125A Lake Oswego Road, Chatsworth, NJ, 08019, USA
| | - C Robin Buell
- MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
- Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
- MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
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27
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Bian S, Li R, Xia S, Liu Y, Jin D, Xie X, Dhaubhadel S, Zhai L, Wang J, Li X. Soybean CCA1-like MYB transcription factor GmMYB133 modulates isoflavonoid biosynthesis. Biochem Biophys Res Commun 2018; 507:324-329. [PMID: 30448057 DOI: 10.1016/j.bbrc.2018.11.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/05/2018] [Indexed: 01/08/2023]
Abstract
MYB transcription factors play important roles in the regulation of phenylpropanoid biosynthesis. However, the knowledge regarding the roles of CCA1-like MYBs in phenylpropanoid pathway is limited in plants. Previously, we identified 54 CCA1-like proteins in soybean. In the study, a CCA1-like MYB (GmMYB133) was functionally characterized as a positive regulator in isoflavonoid synthesis. GmMYB133 encodes a 330 aa protein featured with one CCA1 conserved motif. Further analysis indicated that the expression pattern of GmMYB133 was near-perfectly correlated with isoflavonoid accumulation as soybean embryos develop. GmMYB133 over-expression promoted the expression of two key isoflavonoid biosynthetic genes (GmCHS8 and GmIFS2) and increased total isoflavonoid content in hairy roots. Protein-protein interaction assays indicated that GmMYB133 might form hetero- and homodimers with an isoflavonoid regulator GmMYB176 and itself, respectively, while the subcellular localization of GmMYB133 can be altered by its interaction with 14-3-3 protein. These findings provided new insights into the functional roles of CCA1-like MYB proteins in the regulation of phenylpropanoid pathway, and will contribute to the future genetic engineering in the improvement of soybean seed quality.
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Affiliation(s)
- Shaomin Bian
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Ruihua Li
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Siqi Xia
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Yajing Liu
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Donghao Jin
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Xin Xie
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3, Canada; Department of Biology, Western University, London, ON N6A 3K7, Canada
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Jingying Wang
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China.
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Du YT, Zhao MJ, Wang CT, Gao Y, Wang YX, Liu YW, Chen M, Chen J, Zhou YB, Xu ZS, Ma YZ. Identification and characterization of GmMYB118 responses to drought and salt stress. BMC PLANT BIOLOGY 2018; 18:320. [PMID: 30509166 PMCID: PMC6276260 DOI: 10.1186/s12870-018-1551-7] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/21/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND Abiotic stress severely influences plant growth and development. MYB transcription factors (TFs), which compose one of the largest TF families, play an important role in abiotic stress responses. RESULT We identified 139 soybean MYB-related genes; these genes were divided into six groups based on their conserved domain and were distributed among 20 chromosomes (Chrs). Quantitative real-time PCR (qRT-PCR) indicated that GmMYB118 highly responsive to drought, salt and high temperature stress; thus, this gene was selected for further analysis. Subcellular localization revealed that the GmMYB118 protein located in the nucleus. Ectopic expression (EX) of GmMYB118 increased tolerance to drought and salt stress and regulated the expression of several stress-associated genes in transgenic Arabidopsis plants. Similarly, GmMYB118-overexpressing (OE) soybean plants generated via Agrobacterium rhizogenes (A. rhizogenes)-mediated transformation of the hairy roots showed improved drought and salt tolerance. Furthermore, compared with the control (CK) plants, the clustered, regularly interspaced, short palindromic repeat (CRISPR)-transformed plants exhibited reduced drought and salt tolerance. The contents of proline and chlorophyll in the OE plants were significantly greater than those in the CK plants, whose contents were greater than those in the CRISPR plants under drought and salt stress conditions. In contrast, the reactive oxygen species (ROS) and malondialdehyde (MDA) contents were significantly lower in the OE plants than in the CK plants, whose contents were lower than those in the CRISPR plants under stress conditions. CONCLUSIONS These results indicated that GmMYB118 could improve tolerance to drought and salt stress by promoting expression of stress-associated genes and regulating osmotic and oxidizing substances to maintain cell homeostasis.
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Affiliation(s)
- Yong-Tao Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Meng-Jie Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Chang-Tao Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health/Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, Beijing, 100048 China
| | - Yuan Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Yan-Xia Wang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Research Center of Wheat Engineering Technology of Hebei, Shijiazhuang, 050041 Hebei China
| | - Yong-Wei Liu
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, 050051 Hebei China
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Yong-Bin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Zhao-Shi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - You-Zhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
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Gorshkova T, Chernova T, Mokshina N, Gorshkov V, Kozlova L, Gorshkov O. Transcriptome Analysis of Intrusively Growing Flax Fibers Isolated by Laser Microdissection. Sci Rep 2018; 8:14570. [PMID: 30275452 PMCID: PMC6167358 DOI: 10.1038/s41598-018-32869-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
The intrusive growth, a type of plant cell elongation occurring in the depths of plant tissues, is characterized by the invasion of a growing cell between its neighbours due to a higher rate of elongation. In order to reveal the largely unknown molecular mechanisms of intrusive growth, we isolated primary flax phloem fibers specifically at the stage of intrusive growth by laser microdissection. The comparison of the RNA-Seq data from several flax stem parts enabled the characterization of those processes occurring specifically during the fiber intrusive elongation. The revealed molecular players are summarized as those involved in the supply of assimilates and support of turgor pressure, cell wall enlargement and modification, regulation by transcription factors and hormones, and responses to abiotic stress factors. The data obtained in this study provide a solid basis for developing approaches to manipulate fiber intrusive elongation, which is of importance both for plant biology and the yield of fiber crops.
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Affiliation(s)
- Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation.
| | - Tatyana Chernova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
| | - Liudmila Kozlova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
| | - Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
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Trinh CS, Jeong CY, Lee WJ, Truong HA, Chung N, Han J, Hong SW, Lee H. Paenibacillus pabuli strain P7S promotes plant growth and induces anthocyanin accumulation in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:264-272. [PMID: 29906776 DOI: 10.1016/j.plaphy.2018.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 05/23/2023]
Abstract
In this study, a novel plant growth-promoting rhizobacteria (PGPR), the bacterial strain Paenibacillus pabuli P7S (PP7S), showed promising plant growth-promoting effects. Furthermore, it induced anthocyanin accumulation in Arabidopsis. When co-cultivated with PP7S, there was a significant increase in anthocyanin content and biomass of Arabidopsis seedlings compared with those of the control. The quantitative reverse transcription-polymerase chain reaction analysis revealed higher expression of many key genes regulating anthocyanin and flavonoid biosynthesis pathways in PP7S-treated seedlings when compared with that of the control. Furthermore, higher expression of pathogen-related genes and microbe-associated molecular pattern genes was also observed in response to PP7S, indicating that the PGPR triggered the induced systemic response (ISR) in A. thaliana. These results suggest that PP7S promotes plant growth in A. thaliana and increases anthocyanin biosynthesis by triggering specific ISRs in plant.
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Affiliation(s)
- Cao Son Trinh
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Chan Young Jeong
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea; Odus R&D Center, 262 Daecheong-Ro, Samseong-myeon Eumseong-Gun, Chungcheongbuk-Do 369-830, Republic of Korea
| | - Won Je Lee
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Hai An Truong
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Namhyun Chung
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Juhyeong Han
- Odus R&D Center, 262 Daecheong-Ro, Samseong-myeon Eumseong-Gun, Chungcheongbuk-Do 369-830, Republic of Korea
| | - Suk-Whan Hong
- Department of Molecular Biotechnology, College of Agriculture and Life Sciences, Bioenergy Research Center, Chonnam National University, Gwangju, Republic of Korea
| | - Hojoung Lee
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea.
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Singh D, Kumar D, Satapathy L, Pathak J, Chandra S, Riaz A, Bhaganagre G, Dhariwal R, Kumar M, Prabhu KV, Balyan HS, Gupta PK, Mukhopadhyay K. Insights of Lr28 mediated wheat leaf rust resistance: Transcriptomic approach. Gene 2017; 637:72-89. [DOI: 10.1016/j.gene.2017.09.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/31/2017] [Accepted: 09/14/2017] [Indexed: 01/09/2023]
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Samad AFA, Sajad M, Nazaruddin N, Fauzi IA, Murad AMA, Zainal Z, Ismail I. MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network. FRONTIERS IN PLANT SCIENCE 2017; 8:565. [PMID: 28446918 PMCID: PMC5388764 DOI: 10.3389/fpls.2017.00565] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/29/2017] [Indexed: 05/14/2023]
Abstract
Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions. This present review focuses on the regulatory relationships between miRNAs and different families of TFs like; NF-Y, MYB, AP2, TCP, WRKY, NAC, GRF, and SPL. For instance NF-Y play important role during drought tolerance and flower development, MYB are involved in signal transduction and biosynthesis of secondary metabolites, AP2 regulate the floral development and nodule formation, TCP direct leaf development and growth hormones signaling. WRKY have known roles in multiple stress tolerances, NAC regulate lateral root formation, GRF are involved in root growth, flower, and seed development, and SPL regulate plant transition from juvenile to adult. We also studied the relation between miRNAs and TFs by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.
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Affiliation(s)
- Abdul F. A. Samad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Muhammad Sajad
- Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, PunjabPakistan
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Nazaruddin Nazaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Darussalam, Banda AcehIndonesia
| | - Izzat A. Fauzi
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Abdul M. A. Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Zamri Zainal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
- *Correspondence: Ismanizan Ismail,
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