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Moya-León MA, Stappung Y, Mattus-Araya E, Herrera R. Insights into the Genes Involved in ABA Biosynthesis and Perception during Development and Ripening of the Chilean Strawberry Fruit. Int J Mol Sci 2023; 24:ijms24108531. [PMID: 37239876 DOI: 10.3390/ijms24108531] [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: 04/13/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Hormones act as master ripening regulators. In non-climacteric fruit, ABA plays a key role in ripening. Recently, we confirmed in Fragaria chiloensis fruit that in response to ABA treatment the fruit induces ripening-associated changes such as softening and color development. In consequence of these phenotypic changes, transcriptional variations associated with cell wall disassembly and anthocyanins biosynthesis were reported. As ABA stimulates the ripening of F. chiloensis fruit, the molecular network involved in ABA metabolism was analyzed. Therefore, the expression level of genes involved in ABA biosynthesis and ABA perception was quantified during the development of the fruit. Four NCED/CCDs and six PYR/PYLs family members were identified in F. chiloensis. Bioinformatics analyses confirmed the existence of key domains related to functional properties. Through RT-qPCR analyses, the level of transcripts was quantified. FcNCED1 codifies a protein that displays crucial functional domains, and the level of transcripts increases as the fruit develops and ripens, in parallel with the increment in ABA. In addition, FcPYL4 codifies for a functional ABA receptor, and its expression follows an incremental pattern during ripening. The study concludes that FcNCED1 is involved in ABA biosynthesis; meanwhile, FcPYL4 participates in ABA perception during the ripening of F. chiloensis fruit.
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Affiliation(s)
- María A Moya-León
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3465548, Chile
| | - Yazmina Stappung
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3465548, Chile
| | - Elena Mattus-Araya
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3465548, Chile
| | - Raúl Herrera
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3465548, Chile
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2
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Zeng L, Zeng L, Wang Y, Xie Z, Zhao M, Chen J, Ye X, Tie W, Li M, Shang S, Tian L, Zeng J, Hu W. Identification and expression of the CCO family during development, ripening and stress response in banana. Genetica 2023; 151:87-96. [PMID: 36652142 DOI: 10.1007/s10709-023-00178-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/17/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Plant hormone abscisic acid (ABA) plays an important role in plant growth, development and response to biotic / abiotic stressors. Thus, it is necessary to investigate the crucial genes associated with ABA synthesis. Currently, the carotenoid cleavage oxygenases (CCOs) family that function as the key step for ABA synthesis are not well understood in banana. In this study, 13 MaCCO genes and 12 MbCCO genes, divided into NCED subgroup and CCD subgroup, were identified from the banana genome, and their evolutionary relationship, protein motifs, and gene structures were also determined. Transcriptomic analysis suggested the involvement of CCO genes in banana development, ripening, and response to abiotic and biotic stressors, and homologous gene pairs showed homoeologue expression bias in the A or B subgenome. Our results identified MaNCED3A, MaCCD1, and MbNCED3B as the genes with the highest expression during fruit development and ripening. MaNCED5 / MbNCED5 and MaNCED9A might respond to abiotic stress, and MaNCED3A, 3B, 6 A, 9 A, and MbNCED9A showed transcriptional changes that could be a response to Foc4 infection. These findings may contribute to the characterization of key enzymes involved in ABA biosynthesis, as well as to identify potential targets for the genetic improvement of banana.
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Affiliation(s)
- Liming Zeng
- Sanya Nanfan Research Institute of Hainan University, Sanya, Hainan, China.,Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Liwang Zeng
- Institute of Scientific and Technical Information, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Yu Wang
- Institute of Scientific and Technical Information, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Zhengnan Xie
- Institute of Scientific and Technical Information, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Minhua Zhao
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern China, Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Jie Chen
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern China, Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Xiaoxue Ye
- Institute of Scientific and Technical Information, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Weiwei Tie
- Institute of Scientific and Technical Information, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Meiying Li
- Institute of Scientific and Technical Information, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Sang Shang
- Sanya Nanfan Research Institute of Hainan University, Sanya, Hainan, China.,School of Life Sciences, Hainan University, Haikou, China
| | - Libo Tian
- Sanya Nanfan Research Institute of Hainan University, Sanya, Hainan, China. .,Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China.
| | - Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern China, Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China.
| | - Wei Hu
- Institute of Scientific and Technical Information, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China. .,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Hainan, China.
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3
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Yue XQ, Zhang Y, Yang CK, Li JG, Rui X, Ding F, Hu FC, Wang XH, Ma WQ, Zhou KB. Genome-wide identification and expression analysis of carotenoid cleavage oxygenase genes in Litchi (Litchi chinensis Sonn.). BMC PLANT BIOLOGY 2022; 22:394. [PMID: 35945492 PMCID: PMC9361530 DOI: 10.1186/s12870-022-03772-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 07/20/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Carotenoid cleavage oxygenases (CCOs) include the carotenoid cleavage dioxygenase (CCD) and 9-cis-epoxycarotenoid (NCED), which can catalize carotenoid to form various apocarotenoids and their derivatives, has been found that play important role in the plant world. But little information of CCO gene family has been reported in litchi (Litchi chinensis Sonn.) till date. RESULTS In this study, a total of 15 LcCCO genes in litchi were identified based on genome wide lever. Phylogeny analysis showed that LcCCO genes could be classified into six subfamilies (CCD1, CCD4, CCD7, CCD8, CCD-like, and NCED), which gene structure, domain and motifs exhibited similar distribution patterns in the same subfamilies. MiRNA target site prediction found that there were 32 miRNA target sites in 13 (86.7%) LcCCO genes. Cis-elements analysis showed that the largest groups of elements were light response related, following was plant hormones, stress and plant development related. Expression pattern analysis revealed that LcCCD4, LcNCED1, and LcNCED2 might be involving with peel coloration, LcCCDlike-b might be an important factor deciding fruit flavor, LcNCED2 and LcNCED3 might be related to flower control, LcNCED1 and LcNCED2 might function in fruitlet abscission, LcCCD4a1, LcCCD4a2, LcCCD1, LcCCD4, LcNCED1, and LcNCED2 might participate in postharvest storage of litchi. CONCLUSION Herein, Genome-wide analysis of the LcCCO genes was conducted in litchi to investigate their structure features and potential functions. These valuable and expectable information of LcCCO genes supplying in this study will offer further more possibility to promote quality improvement and breeding of litchi and further function investigation of this gene family in plant.
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Affiliation(s)
- Xiao-Qi Yue
- Engineering Research Center of Selecting and Breeding New Tropical Crops Varieties, Ministry of Education, Horticulture College, Hainan University, Hainan, 570311, Haikou, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, Hainan University, Hainan, 570311, Haikou, China
| | - Yue Zhang
- Engineering Research Center of Selecting and Breeding New Tropical Crops Varieties, Ministry of Education, Horticulture College, Hainan University, Hainan, 570311, Haikou, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, Hainan University, Hainan, 570311, Haikou, China
| | - Cheng-Kun Yang
- Engineering Research Center of Selecting and Breeding New Tropical Crops Varieties, Ministry of Education, Horticulture College, Hainan University, Hainan, 570311, Haikou, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, Hainan University, Hainan, 570311, Haikou, China
| | - Jian-Guo Li
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Xia Rui
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Feng Ding
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Fu-Chu Hu
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Hainan Academy of Agricultural Science, Haikou, 571100, China
| | - Xiang-He Wang
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Hainan Academy of Agricultural Science, Haikou, 571100, China
| | - Wu-Qiang Ma
- Engineering Research Center of Selecting and Breeding New Tropical Crops Varieties, Ministry of Education, Horticulture College, Hainan University, Hainan, 570311, Haikou, China.
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, Hainan University, Hainan, 570311, Haikou, China.
| | - Kai-Bing Zhou
- Engineering Research Center of Selecting and Breeding New Tropical Crops Varieties, Ministry of Education, Horticulture College, Hainan University, Hainan, 570311, Haikou, China.
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, Hainan University, Hainan, 570311, Haikou, China.
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4
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Comprehensive Analysis of Carotenoid Cleavage Dioxygenases Gene Family and Its Expression in Response to Abiotic Stress in Poplar. Int J Mol Sci 2022; 23:ijms23031418. [PMID: 35163346 PMCID: PMC8836127 DOI: 10.3390/ijms23031418] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 02/06/2023] Open
Abstract
Carotenoid cleavage dioxygenases (CCDs) catalyzes the cleavage of various carotenoids into smaller apocarotenoids which are essential for plant growth and development and response to abiotic stresses. CCD family is divided into two subfamilies: 9-cis epoxycarotenoid dioxygenases (NCED) family and CCD family. A better knowledge of carotenoid biosynthesis and degradation could be useful for regulating carotenoid contents. Here, 23 CCD genes were identified from the Populus trichocarpa genome, and their characterizations and expression profiling were validated. The PtCCD members were divided into PtCCD and PtNCED subfamilies. The PtCCD family contained the PtCCD1, 4, 7, and 8 classes. The PtCCDs clustered in the same clade shared similar intron/exon structures and motif compositions and distributions. In addition, the tandem and segmental duplications resulted in the PtCCD gene expansion based on the collinearity analysis. An additional integrated collinearity analysis among poplar, Arabidopsis, rice, and willow revealed the gene pairs between poplar and willow more than that between poplar and rice. Identifying tissue-special expression patterns indicated that PtCCD genes display different expression patterns in leaves, stems, and roots. Abscisic acid (ABA) treatment and abiotic stress suggested that many PtCCD genes are responsive to osmotic stress regarding the comprehensive regulation networks. The genome-wide identification of PtCCD genes may provide the foundation for further exploring the putative regulation mechanism on osmotic stress and benefit poplar molecular breeding.
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5
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Varghese R, S UK, C GPD, Ramamoorthy S. Unraveling the versatility of CCD4: Metabolic engineering, transcriptomic and computational approaches. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110991. [PMID: 34315605 DOI: 10.1016/j.plantsci.2021.110991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/16/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Carotenoids are economically valuable isoprenoids synthesized by plants and microorganisms, which play a paramount role in their overall growth and development. Carotenoid cleavage dioxygenases are a vast group of enzymes that specifically cleave thecarotenoids to produce apocarotenoids. Recently, CCDs are a subject of talk because of their contributions to different aspects of plant growth and due to their significance in the production of economically valuable apocarotenoids. Among them, CCD4 stands unique because of its versatility in performing metabolic roles. This review focuses on the multiple functionalities of CCD4 like pigmentation, volatile apocarotenoid production, stress responses, etc. Interestingly, through our literature survey we arrived at a conclusion that CCD4 could perform functions of other carotenoid cleaving enzymes.The metabolic engineering, transcriptomic, and computational approaches adopted to reveal the contributions of CCD4 were also considered here for the study.Phylogenetic analysis was performed to delve into the evolutionary relationships of CCD4 in different plant groups. A tree of 81CCD genes from 64 plant species was constructed, signifying the presence of well-conserved families. Gene structures were illustrated and the difference in the number and position of exons could be considered as a factor behind functional versatility and substrate tolerance of CCD4 in different plants.
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Affiliation(s)
- Ressin Varghese
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Udhaya Kumar S
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - George Priya Doss C
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Siva Ramamoorthy
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
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6
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Cai X, Jiang Z, Tang L, Zhang S, Li X, Wang H, Liu C, Chi J, Zhang X, Zhang J. Genome-wide characterization of carotenoid oxygenase gene family in three cotton species and functional identification of GaNCED3 in drought and salt stress. J Appl Genet 2021; 62:527-543. [PMID: 34109531 DOI: 10.1007/s13353-021-00634-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Cotton that serves natural fiber for the textile industry is an important industrial crop. However, abiotic stress imposed a significant negative impact on yield and quality of cotton fiber. Carotenoid cleavage oxygenases (CCOs) that specifically catalyze the cleavage of carotenoid are essential for plant growth and development and abiotic stress response. While information of cotton CCOs and their potential functions in abiotic stress is still far from satisfactory, which imposes restrictions on application in genetic breeding for stress resistance. In this study, 15, 15, and 30 CCOs were identified from Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum, respectively. Phylogenetic relationship indicated that CCO genes could be classified into two groups (NCEDs and CCDs). Cis-elements prediction showed that there were 18 types of stress-related cis-elements in promoter regions. Analysis with transcriptome data revealed tissue-specific expression pattern of cotton CCOs. qRT-PCR analysis revealed only that GhNCED3a_A/D and GhNCED3c_A/D had strong response to drought, salt, and cold stress, while GhCCD1_A/D and GhCCD4_A showed relatively slight expression changes. Virus-induced gene silencing of GaNCED3a, the ortholog gene of GhNCED3a_A/D, suggested that silenced plants exhibited decreased resistance not only to drought but also to salt, with significantly reduced proline content, and high malondialdehyde content and water loss rate. In addition, stress response genes RD29A, DREB1A, and SOS1 significantly downregulated under drought and salt stress in silenced plants compared to control plants, indicating that GaNCED3a played an important role in drought and salt response. The results provided valuable insights into function analysis of cotton CCOs in abiotic stress response, and suggested potential benefit genes for stress-resistant breeding.
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Affiliation(s)
- Xiao Cai
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | | | - Liyuan Tang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Sujun Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Xinghe Li
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Haitao Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Cunjing Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Jina Chi
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Xiangyun Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China. .,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China.
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China. .,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China.
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7
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Zhang S, Guo Y, Zhang Y, Guo J, Li K, Fu W, Jia Z, Li W, Tran LSP, Jia KP, Miao Y. Genome-wide identification, characterization and expression profiles of the CCD gene family in Gossypium species. 3 Biotech 2021; 11:249. [PMID: 33968592 DOI: 10.1007/s13205-021-02805-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/21/2021] [Indexed: 01/17/2023] Open
Abstract
Carotenoid cleavage dioxygenases (CCDs) are a group of enzymes that catalyze the selective oxidative cleavage steps from carotenoids to apocarotenoids, which are essential for the synthesis of biologically important molecules such as retinoids, and the phytohormones abscisic acid (ABA) and strigolactones. In addition, CCDs play important roles in plant biotic and abiotic stress responses. Till now, a comprehensive characterization of the CCD gene family in the economically important crop cotton (Gossypium spp.) is still missing. Here, we performed a genome-wide analysis and identified 33, 31, 16 and 15 CCD genes from two allotetraploid Gossypium species, G. hirsutum and G. barbadense, and two diploid Gossypium species, G. arboreum and G. raimondii, respectively. According to the phylogenetic tree analysis, cotton CCDs are classified as six subgroups including CCD1, CCD4, CCD7, CCD8, nine-cis-epoxycarotenoid dioxygenase (NCED) and zaxinone synthase (ZAS) sub-families. Evolutionary analysis shows that purifying selection dominated the evolution of these genes in G. hirsutum and G. barbadense. Predicted cis-acting elements in 2 kb promoters of CCDs in G. hirsutum are mainly involved in light, stress and hormone responses. The transcriptomic analysis of GhCCDs showed that different GhCCDs displayed diverse expression patterns and were ubiquitously expressed in most tissues; moreover, GhCCDs displayed specific inductions by different abiotic stresses. Quantitative reverse-transcriptional PCR (qRT-PCR) confirmed the induction of GhCCDs by heat stress, salinity, polyethylene glycol (PEG) and ABA application. In summary, the bioinformatics and expression analysis of CCD gene family provide evidence for the involvement in regulating abiotic stresses and useful information for in-depth studies of their biological functions in G. hirsutum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02805-9.
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Affiliation(s)
- Shulin Zhang
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Yutao Guo
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Yanqi Zhang
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Jinggong Guo
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Kun Li
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Weiwei Fu
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Zhenzhen Jia
- Agricultural Research Center, Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
| | - Weiqiang Li
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock,, TX USA
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
| | - Kun-Peng Jia
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
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8
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Gao J, Yang S, Tang K, Li G, Gao X, Liu B, Wang S, Feng X. GmCCD4 controls carotenoid content in soybeans. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:801-813. [PMID: 33131209 PMCID: PMC8051601 DOI: 10.1111/pbi.13506] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 10/06/2020] [Accepted: 10/26/2020] [Indexed: 05/23/2023]
Abstract
To better understand the mechanisms regulating plant carotenoid metabolism in staple crop, we report the map-based cloning and functional characterization of the Glycine max carotenoid cleavage dioxygenase 4 (GmCCD4) gene, which encodes a carotenoid cleavage dioxygenase enzyme involved in metabolizing carotenoids into volatile β-ionone. Loss of GmCCD4 protein function in four Glycine max increased carotenoid content (gmicc) mutants resulted in yellow flowers due to excessive accumulation of carotenoids in flower petals. The carotenoid contents also increase three times in gmicc1 seeds. A genome-wide association study indicated that the GmCCD4 locus was one major locus associated with carotenoid content in natural population. Further analysis indicated that the haplotype-1 of GmCCD4 gene was positively associated with higher carotenoid levels in soybean cultivars and accumulated more β-carotene in engineered E. coli with ectopic expression of different GmCCD4 haplotypes. These observations uncovered that GmCCD4 was a negative regulator of carotenoid content in soybean, and its various haplotypes provide useful resources for future soybean breeding practice.
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Affiliation(s)
- Jinshan Gao
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Kuanqiang Tang
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Guang Li
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE)Northeast Normal UniversityChangchunChina
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE)Northeast Normal UniversityChangchunChina
| | - Shaodong Wang
- Key Laboratory of Soybean Biology of Education MinistryNortheast Agricultural UniversityHarbinChina
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
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9
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Dhar MK, Mishra S, Bhat A, Chib S, Kaul S. Plant carotenoid cleavage oxygenases: structure-function relationships and role in development and metabolism. Brief Funct Genomics 2020; 19:1-9. [PMID: 31875900 DOI: 10.1093/bfgp/elz037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022] Open
Abstract
A plant communicates within itself and with the outside world by deploying an array of agents that include several attractants by virtue of their color and smell. In this category, the contribution of 'carotenoids and apocarotenoids' is very significant. Apocarotenoids, the carotenoid-derived compounds, show wide representation among organisms. Their biosynthesis occurs by oxidative cleavage of carotenoids, a high-value reaction, mediated by carotenoid cleavage oxygenases or carotenoid cleavage dioxygenases (CCDs)-a family of non-heme iron enzymes. Structurally, this protein family displays wide diversity but is limited in its distribution among plants. Functionally, this protein family has been recognized to offer a role in phytohormones, volatiles and signal production. Further, their wide presence and clade-specific functional disparity demands a comprehensive account. This review focuses on the critical assessment of CCDs of higher plants, describing recent progress in their functional aspects and regulatory mechanisms, domain architecture, classification and localization. The work also highlights the relevant discussion for further exploration of this multi-prospective protein family for the betterment of its functional understanding and improvement of crops.
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Affiliation(s)
- Manoj Kumar Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Sonal Mishra
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Archana Bhat
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Sudha Chib
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
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Effects of Exogenous Abscisic Acid (ABA) on Carotenoids and Petal Color in Osmanthus fragrans 'Yanhonggui'. PLANTS 2020; 9:plants9040454. [PMID: 32260328 PMCID: PMC7238031 DOI: 10.3390/plants9040454] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/16/2023]
Abstract
Osmanthus fragrans is a well-known native plant in China, and carotenoids are the main group of pigments in the petals. Abscisic acid (ABA) is one of the products of the metabolic pathway of carotenoids. Application of ABA could affect pigmentation of flower petals by changing the carotenoid content. However, little is known about the effects of ABA treatment on carotenoid accumulation in O. fragrans. In this study, different concentrations of ABA (0, 150 and 200 mg/L) were spread on the petals of O. fragrans 'Yanhonggui'. The petal color of 'Yanhonggui' receiving every ABA treatment was deeper than that of the control. The content of total carotenoids in the petals significantly increased with 200 mg/L ABA treatment. In the petals, α-carotene and β-carotene were the predominant carotenoids. The expression of several genes involved in the metabolism of carotenoids increased with 200 mg/L ABA treatment, including PSY1, PDS1, Z-ISO1, ZDS1, CRTISO, NCED3 and CCD4. However, the transcription levels of the latter two carotenoid degradation-related genes were much lower than of the five former carotenoid biosynthesis-related genes; the finding would explain the significant increase in total carotenoids in 'Yanhonggui' petals receiving the 200 mg/L ABA treatment.
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11
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Ma XJ, Yu TF, Li XH, Cao XY, Ma J, Chen J, Zhou YB, Chen M, Ma YZ, Zhang JH, Xu ZS. Overexpression of GmNFYA5 confers drought tolerance to transgenic Arabidopsis and soybean plants. BMC PLANT BIOLOGY 2020; 20:123. [PMID: 32192425 PMCID: PMC7082914 DOI: 10.1186/s12870-020-02337-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/10/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Crop productivity is challenged by abiotic stresses, among which drought stress is the most common. NF-Y genes, especially NF-YA genes, regulate tolerance to abiotic stress. RESULTS Soybean NF-Y gene GmNFYA5 was identified to have the highest transcript level among all 21 NF-YA genes in soybean (Glycine max L.) under drought stress. Drought-induced transcript of GmNFYA5 was suppressed by the ABA synthesis inhibitor naproxen (NAP). GmNFYA5 transcript was detected in various tissues at vegetative and reproductive growth stages with higher levels in roots and leaves than in other tissues, which was consist with the GmNFYA5 promoter: GUS fusion assay. Overexpression of GmNFYA5 in transgenic Arabidopsis plants caused enhanced drought tolerance in seedlings by decreasing stomatal aperture and water loss from leaves. Overexpression and suppression of GmNFYA5 in soybean resulted in increased and decreased drought tolerance, respectively, relative to plants with an empty vector (EV). Transcript levels of ABA-dependent genes (ABI2, ABI3, NCED3, LEA3, RD29A, P5CS1, GmWRKY46, GmNCED2 and GmbZIP1) and ABA-independent genes (DREB1A, DREB2A, DREB2B, GmDREB1, GmDREB2 and GmDREB3) in transgenic plants overexpressing GmNFYA5 were higher than those of wild-type plants under drought stress; suppression of GmNFYA5 transcript produced opposite results. GmNFYA5 probably regulated the transcript abundance of GmDREB2 and GmbZIP1 by binding to the promoters in vivo. CONCLUSIONS Our results suggested that overexpression of GmNFYA5 improved drought tolerance in soybean via both ABA-dependent and ABA-independent pathways.
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Affiliation(s)
- Xiao-Jun Ma
- College of Agronomy, Northeast Agricultural University, Harbin, 150030 China
- Institute of Crop Science, 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
| | - Tai-Fei Yu
- Institute of Crop Science, 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
| | - Xiao-Hui Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100 China
| | - Xin-You Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement, Jinan, 250100 China
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun, 130118 China
| | - Jun Chen
- Institute of Crop Science, 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 Science, 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
| | - Ming Chen
- Institute of Crop Science, 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 Science, 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-Hua Zhang
- College of Agronomy, Northeast Agricultural University, Harbin, 150030 China
| | - Zhao-Shi Xu
- Institute of Crop Science, 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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12
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Zhou Q, Li Q, Li P, Zhang S, Liu C, Jin J, Cao P, Yang Y. Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco. Int J Mol Sci 2019; 20:E5796. [PMID: 31752180 PMCID: PMC6888377 DOI: 10.3390/ijms20225796] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022] Open
Abstract
Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.
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Affiliation(s)
- Qianqian Zhou
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China; (Q.Z.); (P.L.); (S.Z.); (C.L.)
| | - Qingchang Li
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450002, China; (Q.L.); (J.J.); (P.C.)
| | - Peng Li
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China; (Q.Z.); (P.L.); (S.Z.); (C.L.)
| | - Songtao Zhang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China; (Q.Z.); (P.L.); (S.Z.); (C.L.)
| | - Che Liu
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China; (Q.Z.); (P.L.); (S.Z.); (C.L.)
| | - Jingjing Jin
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450002, China; (Q.L.); (J.J.); (P.C.)
| | - Peijian Cao
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450002, China; (Q.L.); (J.J.); (P.C.)
| | - Yongxia Yang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China; (Q.Z.); (P.L.); (S.Z.); (C.L.)
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13
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Luo D, Wu Y, Liu J, Zhou Q, Liu W, Wang Y, Yang Q, Wang Z, Liu Z. Comparative Transcriptomic and Physiological Analyses of Medicago sativa L. Indicates that Multiple Regulatory Networks Are Activated during Continuous ABA Treatment. Int J Mol Sci 2018; 20:E47. [PMID: 30583536 PMCID: PMC6337461 DOI: 10.3390/ijms20010047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022] Open
Abstract
Alfalfa is the most extensively cultivated forage legume worldwide. However, the molecular mechanisms underlying alfalfa responses to exogenous abscisic acid (ABA) are still unknown. In this study, the first global transcriptome profiles of alfalfa roots under ABA treatments for 1, 3 and 12 h (three biological replicates for each time point, including the control group) were constructed using a BGISEQ-500 sequencing platform. A total of 50,742 isoforms with a mean length of 2541 bp were generated, and 4944 differentially expressed isoforms (DEIs) were identified after ABA deposition. Metabolic analyses revealed that these DEIs were involved in plant hormone signal transduction, transcriptional regulation, antioxidative defense and pathogen immunity. Notably, several well characterized hormone signaling pathways, for example, the core ABA signaling pathway, was activated, while salicylic acid, jasmonate and ethylene signaling pathways were mainly suppressed by exogenous ABA. Moreover, the physiological work showed that catalase and peroxidase activity and glutathione and proline content were increased after ABA deposition, which is in accordance with the dynamic transcript profiles of the relevant genes in antioxidative defense system. These results indicate that ABA has the potential to improve abiotic stress tolerance, but that it may negatively regulate pathogen resistance in alfalfa.
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Affiliation(s)
- Dong Luo
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Yuguo Wu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Jie Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Qiang Zhou
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China.
| | - Zengyu Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
- Core Research & Transformation, Noble Research Institute, Ardmore, OK 73401, USA.
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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14
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Chen H, Zuo X, Shao H, Fan S, Ma J, Zhang D, Zhao C, Yan X, Liu X, Han M. Genome-wide analysis of carotenoid cleavage oxygenase genes and their responses to various phytohormones and abiotic stresses in apple (Malus domestica). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 123:81-93. [PMID: 29223850 DOI: 10.1016/j.plaphy.2017.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 05/25/2023]
Abstract
Carotenoid cleavage oxygenases (CCOs) are able to cleave carotenoids to produce apocarotenoids and their derivatives, which are important for plant growth and development. In this study, 21 apple CCO genes were identified and divided into six groups based on their phylogenetic relationships. We further characterized the apple CCO genes in terms of chromosomal distribution, structure and the presence of cis-elements in the promoter. We also predicted the cellular localization of the encoded proteins. An analysis of the synteny within the apple genome revealed that tandem, segmental, and whole-genome duplication events likely contributed to the expansion of the apple carotenoid oxygenase gene family. An additional integrated synteny analysis identified orthologous carotenoid oxygenase genes between apple and Arabidopsis thaliana, which served as references for the functional analysis of the apple CCO genes. The net photosynthetic rate, transpiration rate, and stomatal conductance of leaves decreased, while leaf stomatal density increased under drought and saline conditions. Tissue-specific gene expression analyses revealed diverse spatiotemporal expression patterns. Finally, hormone and abiotic stress treatments indicated that many apple CCO genes are responsive to various phytohormones as well as drought and salinity stresses. The genome-wide identification of apple CCO genes and the analyses of their expression patterns described herein may provide a solid foundation for future studies examining the regulation and functions of this gene family.
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Affiliation(s)
- Hongfei Chen
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xiya Zuo
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Hongxia Shao
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Sheng Fan
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Juanjuan Ma
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Dong Zhang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Caiping Zhao
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xiangyan Yan
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xiaojie Liu
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Mingyu Han
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China.
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15
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Song L, Prince S, Valliyodan B, Joshi T, Maldonado dos Santos JV, Wang J, Lin L, Wan J, Wang Y, Xu D, Nguyen HT. Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. BMC Genomics 2016; 17:57. [PMID: 26769043 PMCID: PMC4714440 DOI: 10.1186/s12864-016-2378-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Soybean is a major crop that provides an important source of protein and oil to humans and animals, but its production can be dramatically decreased by the occurrence of drought stress. Soybeans can survive drought stress if there is a robust and deep root system at the early vegetative growth stage. However, little is known about the genome-wide molecular mechanisms contributing to soybean root system architecture. This study was performed to gain knowledge on transcriptome changes and related molecular mechanisms contributing to soybean root development under water limited conditions. RESULTS The soybean Williams 82 genotype was subjected to very mild stress (VMS), mild stress (MS) and severe stress (SS) conditions, as well as recovery from the severe stress after re-watering (SR). In total, 6,609 genes in the roots showed differential expression patterns in response to different water-deficit stress levels. Genes involved in hormone (Auxin/Ethylene), carbohydrate, and cell wall-related metabolism (XTH/lipid/flavonoids/lignin) pathways were differentially regulated in the soybean root system. Several transcription factors (TFs) regulating root growth and responses under varying water-deficit conditions were identified and the expression patterns of six TFs were found to be common across the stress levels. Further analysis on the whole plant level led to the finding of tissue-specific or water-deficit levels specific regulation of transcription factors. Analysis of the over-represented motif of different gene groups revealed several new cis-elements associated with different levels of water deficit. The expression patterns of 18 genes were confirmed byquantitative reverse transcription polymerase chain reaction method and demonstrated the accuracy and effectiveness of RNA-Seq. CONCLUSIONS The primary root specific transcriptome in soybean can enable a better understanding of the root response to water deficit conditions. The genes detected in root tissues that were associated with key hormones, carbohydrates, and cell wall-related metabolism could play a vital role in achieving drought tolerance and could be promising candidates for future functional characterization. TFs involved in the soybean root and at the whole plant level could be used for future network analysis between TFs and cis-elements. All of these findings will be helpful in elucidating the molecular mechanisms associated with water stress responses in soybean roots.
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Affiliation(s)
- Li Song
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Silvas Prince
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Babu Valliyodan
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Trupti Joshi
- Department of Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
- MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
| | - Joao V Maldonado dos Santos
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Jiaojiao Wang
- Department of Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Li Lin
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Jinrong Wan
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Yongqin Wang
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Dong Xu
- Department of Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
- MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
| | - Henry T Nguyen
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
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Duan H, Lu X, Lian C, An Y, Xia X, Yin W. Genome-Wide Analysis of MicroRNA Responses to the Phytohormone Abscisic Acid in Populus euphratica. FRONTIERS IN PLANT SCIENCE 2016; 7:1184. [PMID: 27582743 PMCID: PMC4988358 DOI: 10.3389/fpls.2016.01184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 07/22/2016] [Indexed: 05/20/2023]
Abstract
MicroRNA (miRNA) is a type of non-coding small RNA with a regulatory function at the posttranscriptional level in plant growth development and in response to abiotic stress. Previous studies have not reported on miRNAs responses to the phytohormone abscisic acid (ABA) at a genome-wide level in Populus euphratica, a model tree for studying abiotic stress responses in woody plants. Here we analyzed the miRNA response to ABA at a genome-wide level in P. euphratica utilizing high-throughput sequencing. To systematically perform a genome-wide analysis of ABA-responsive miRNAs in P. euphratica, nine sRNA libraries derived from three groups (control, treated with ABA for 1 day and treated with ABA for 4 days) were constructed. Each group included three libraries from three individual plantlets as biological replicate. In total, 151 unique mature sequences belonging to 75 conserved miRNA families were identified, and 94 unique sequences were determined to be novel miRNAs, including 56 miRNAs with miRNA(*) sequences. In all, 31 conserved miRNAs and 31 novel miRNAs response to ABA significantly differed among the groups. In addition, 4132 target genes were predicted for the conserved and novel miRNAs. Confirmed by real-time qPCR, expression changes of miRNAs were inversely correlated with the expression profiles of their putative targets. The Populus special or novel miRNA-target interactions were predicted might be involved in some biological process related stress tolerance. Our analysis provides a comprehensive view of how P. euphratica miRNA respond to ABA, and moreover, different temporal dynamics were observed in different ABA-treated libraries.
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Baba SA, Mohiuddin T, Basu S, Swarnkar MK, Malik AH, Wani ZA, Abbas N, Singh AK, Ashraf N. Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis. BMC Genomics 2015; 16:698. [PMID: 26370545 PMCID: PMC4570256 DOI: 10.1186/s12864-015-1894-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/01/2015] [Indexed: 11/30/2022] Open
Abstract
Background Crocus sativus stigmas form rich source of apocarotenoids like crocin, picrocrocin and saffranal which besides imparting color, flavour and aroma to saffron spice also have tremendous pharmacological properties. Inspite of their importance, the biosynthetic pathway of Crocus apocarotenoids is not fully elucidated. Moreover, the mechanism of their stigma specific accumulation remains unknown. Therefore, deep transcriptome sequencing of Crocus stigma and rest of the flower tissue was done to identify the genes and transcriptional regulators involved in the biosynthesis of these compounds. Results Transcriptome of stigma and rest of the flower tissue was sequenced using Illumina Genome Analyzer IIx platform which generated 64,604,402 flower and 51,350,714 stigma reads. Sequences were assembled de novo using trinity resulting in 64,438 transcripts which were classified into 32,204 unigenes comprising of 9853 clusters and 22,351 singletons. A comprehensive functional annotation and gene ontology (GO) analysis was carried out. 58.5 % of the transcripts showed similarity to sequences present in public databases while rest could be specific to Crocus. 5789 transcripts showed similarity to transcription factors representing 76 families out of which Myb family was most abundant. Many genes involved in carotenoid/apocarotenoid pathway were identified for the first time in this study which includes zeta-carotene isomerase and desaturase, carotenoid isomerase and lycopene epsilon-cyclase. GO analysis showed that the predominant classes in biological process category include metabolic process followed by cellular process and primary metabolic process. KEGG mapping analysis indicated that pathways involved in ribosome, carbon and starch and sucrose metabolism were highly represented. Differential expression analysis indicated that key carotenoid/apocarotenoid pathway genes including phytoene synthase, phytoene desaturase and carotenoid cleavage dioxygenase 2 are enriched in stigma thereby providing molecular proof for stigma to be the site of apocarotenoid biosynthesis. Conclusions This data would provide a rich source for understanding the carotenoid/apocarotenoid metabolism in Crocus. The database would also help in investigating many questions related to saffron biology including flower development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1894-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shoib Ahmad Baba
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
| | - Tabasum Mohiuddin
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
| | - Swaraj Basu
- Stazione Zoologica Anton Dohrn di Napoli, Naples, Italy.
| | - Mohit Kumar Swarnkar
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India.
| | - Aubid Hussain Malik
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
| | - Zahoor Ahmed Wani
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
| | - Nazia Abbas
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India.
| | - Anil Kumar Singh
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India.
| | - Nasheeman Ashraf
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
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Lara-Chavez A, Lowman S, Kim S, Tang Y, Zhang J, Udvardi M, Nowak J, Flinn B, Mei C. Global gene expression profiling of two switchgrass cultivars following inoculation with Burkholderia phytofirmans strain PsJN. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4337-4350. [PMID: 25788737 DOI: 10.1093/jxb/erv096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Improvement and year-to-year stabilization of biomass yields are primary objectives for the development of a low-input switchgrass feedstock production system using microbial endophytes. An earlier investigation of the effect of Burkholderia phytofirmans strain PsJN on switchgrass germplasm demonstrated differential responses between genotypes. PsJN inoculation of cv. Alamo (lowland ecotype) increased the plant root system, shoot length, and biomass yields, whereas it had no beneficial effect on cv. Cave-in-Rock (upland ecotype). To understand the gene networks governing plant growth promotion responses triggered by PsJN, the gene expression profiles were analysed in these two hosts, following seedling inoculation. The Affymetrix platform switchgrass expressed sequence tag (EST) microarray chip representing 122 972 probe sets, developed by the DOE BioEnergy Science Center, was employed to assess transcript abundance at 0.5, 2, 4, and 8 DAI (days after PsJN inoculation). Approximately 20 000 switchgrass probe sets showed significant responses in either cultivar. Switchgrass identifiers were used to map 19 421 genes in MapMan software. There were apparent differences in gene expression profiling between responsive and non-responsive cultivars after PsJN inoculation. Overall, there were 14 984 and 9691 genes affected by PsJN inoculation in Alamo and Cave-in-Rock, respectively. Of these, 394 are annotated as pathogenesis-related genes. In the responsive cv. Alamo, 68 pathogenesis-related genes were affected, compared with only 10 in the non-responsive cv. Cave-in-Rock. At the very early stage at 0.5 DAI, both cultivars exhibited similar recognition and defence responses, such as genes in signalling and proteolysis, after which the defence reaction in the responsive cv. Alamo became weaker while it was sustained in non-responsive cv. Cave-in-Rock.
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Affiliation(s)
- Alejandra Lara-Chavez
- Institute for Sustainable and Renewable Resources, Institute for Advanced Learning and Research, Danville, VA 24540, USA
| | - Scott Lowman
- Institute for Sustainable and Renewable Resources, Institute for Advanced Learning and Research, Danville, VA 24540, USA Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601, USA
| | - Seonhwa Kim
- Institute for Sustainable and Renewable Resources, Institute for Advanced Learning and Research, Danville, VA 24540, USA
| | - Yuhong Tang
- Plant Biology Division, the Samuel Roberts Noble Foundation, Inc., Ardmore, OK 73401, USA BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831, USA
| | - Jiyi Zhang
- Plant Biology Division, the Samuel Roberts Noble Foundation, Inc., Ardmore, OK 73401, USA BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831, USA
| | - Michael Udvardi
- Plant Biology Division, the Samuel Roberts Noble Foundation, Inc., Ardmore, OK 73401, USA BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831, USA
| | - Jerzy Nowak
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601, USA
| | - Barry Flinn
- Institute for Sustainable and Renewable Resources, Institute for Advanced Learning and Research, Danville, VA 24540, USA Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601, USA Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601, USA
| | - Chuansheng Mei
- Institute for Sustainable and Renewable Resources, Institute for Advanced Learning and Research, Danville, VA 24540, USA Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601, USA Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601, USA
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