1
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Marin-Recinos MF, Pucker B. Genetic factors explaining anthocyanin pigmentation differences. BMC PLANT BIOLOGY 2024; 24:627. [PMID: 38961369 PMCID: PMC11221117 DOI: 10.1186/s12870-024-05316-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/20/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Anthocyanins are important contributors to coloration across a wide phylogenetic range of plants. Biological functions of anthocyanins span from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins. RESULTS A systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties was performed within numerous plant species covering the taxonomic diversity of flowering plants. The literature was screened for cases in which genetic factors causing anthocyanin loss were reported. Additionally, transcriptomic data sets from four previous studies were reanalyzed to determine the genes possibly responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the intraspecific pigmentation differences was quantified. Differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are significantly more prone to account for pigmentation differences compared to bHLH or WD40 genes. Among the structural genes, DFR genes are most often associated with anthocyanin loss. CONCLUSIONS These findings support previous assumptions about the susceptibility of transcriptional regulation to evolutionary changes and its importance for the evolution of novel coloration phenotypes. Our findings underline the particular significance of MYBs and their apparent prevalent role in the specificity of the MBW complex.
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Affiliation(s)
- Maria F Marin-Recinos
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology and BRICS, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology and BRICS, TU Braunschweig, Braunschweig, Germany.
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2
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Song J, Kong H, Yang J, Jing J, Li S, Ma N, Yang R, Cao Y, Wang Y, Hu T, Yang P. Genome assembly and multi-omic analyses reveal the mechanisms underlying flower color formation in Torenia fournieri. THE PLANT GENOME 2024; 17:e20439. [PMID: 38485674 DOI: 10.1002/tpg2.20439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/15/2024] [Accepted: 01/27/2024] [Indexed: 07/02/2024]
Abstract
Torenia fournieri Lind. is an ornamental plant that is popular for its numerous flowers and variety of colors. However, its genomic evolutionary history and the genetic and metabolic bases of flower color formation remain poorly understood. Here, we report the first T. fournieri reference genome, which was resolved to the chromosome scale and was 164.4 Mb in size. Phylogenetic analyses clarified relationships with other plant species, and a comparative genomic analysis indicated that the shared ancestor of T. fournieri and Antirrhinum majus underwent a whole genome duplication event. Joint transcriptomic and metabolomic analyses identified many metabolites related to pelargonidin, peonidin, and naringenin production in rose (TfR)-colored flowers. Samples with blue (TfB) and deep blue (TfD) colors contained numerous derivatives of petunidin, cyanidin, quercetin, and malvidin; differences in the abundances of these metabolites and expression levels of the associated genes were hypothesized to be responsible for variety-specific differences in flower color. Furthermore, the genes encoding flavonoid 3-hydroxylase, anthocyanin synthase, and anthocyanin reductase were differentially expressed between flowers of different colors. Overall, we successfully identified key genes and metabolites involved in T. fournieri flower color formation. The data provided by the chromosome-scale genome assembly establish a basis for understanding the differentiation of this species and will facilitate future genetic studies and genomic-assisted breeding.
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Affiliation(s)
- Jiaxing Song
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Haiming Kong
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Jiaxian Jing
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Siyu Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Yuman Cao
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Yafang Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
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3
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Liu J, Wang Y, Deng X, Zhang M, Sun H, Gao L, Song H, Xin J, Ming R, Yang D, Yang M. Transcription factor NnMYB5 controls petal color by regulating GLUTATHIONE S-TRANSFERASE2 in Nelumbo nucifera. PLANT PHYSIOLOGY 2023; 193:1213-1226. [PMID: 37348874 PMCID: PMC10517185 DOI: 10.1093/plphys/kiad363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/24/2023]
Abstract
Lotus (Nelumbo spp.) is an important aquatic ornamental genus in the family Nelumbonaceae comprising only 2 species: Nelumbo lutea with yellow flowers and Nelumbo nucifera with red or white flowers. The petal color variations between these 2 species have previously been associated with the potential activities of FLAVONOL SYNTHASE (FLS) and MYB5. However, the underlying genetic mechanisms of flower color divergence within the N. nucifera species remain unclear. Here, quantitative trait locus mapping led to the identification of MYB5, a candidate gene controlling petal color in N. nucifera. Genotyping of 213 natural lotus accessions revealed an 80 kb presence/absence variant (PAV) of the NnMYB5 gene that is associated with petal color variation. Transcriptome analysis, dual-luciferase, and yeast 1-hybrid assays showed that NnMYB5 could directly activate the anthocyanin transporter gene GLUTATHIONE S-TRANSFERASE2 (NnGST2). Heterologous expression of NnGST2 in Arabidopsis (Arabidopsis thaliana) and its overexpression in lotus petals induced anthocyanin accumulation. Deletion of the 80 kb PAV within NnMYB5 inactivated NnGST2 expression and blocked anthocyanin accumulation in white N. nucifera petals. In contrast, the anthocyanin deficiency of N. lutea occurred due to pseudogenized NlMYB5 alleles. Our results establish a regulatory link between NnMYB5 and NnGST2 in petal anthocyanin accumulation and demonstrate the independent mechanisms controlling flower coloration in Nelumbo.
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Affiliation(s)
- Juan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Yuxin Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- College of Life Science, University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Xianbao Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Minghua Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- College of Life Science, University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Heng Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Lei Gao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Heyun Song
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- College of Life Science, University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Jia Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- College of Life Science, University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
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4
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Qi H, Yu F, Deng J, Zhang L, Yang P. The high-quality genome of lotus reveals tandem duplicate genes involved in stress response and secondary metabolites biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad040. [PMID: 37159801 PMCID: PMC10163359 DOI: 10.1093/hr/uhad040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/23/2023] [Indexed: 05/11/2023]
Affiliation(s)
- Huanhuan Qi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430026, China
| | - Feng Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430026, China
| | - Jiao Deng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430026, China
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang 550001, China
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5
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Lai J, Li C, Zhang Y, Wu Z, Li W, Zhang Z, Ye W, Guo H, Wang C, Long T, Wang S, Yang J. Integrated Transcriptomic and Metabolomic Analyses Reveal the Molecular and Metabolic Basis of Flavonoids in Areca catechu L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4851-4862. [PMID: 36940468 DOI: 10.1021/acs.jafc.2c08864] [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] [Indexed: 06/18/2023]
Abstract
Areca catechu L., of the Arecaceae family, is widely distributed in tropical Asia. In A. catechu, the extracts and compounds, including flavonoids, have various pharmacological activities. Although there are many studies of flavonoids, the molecular mechanism of their biosynthesis and regulation remains unclear in A. catechu. In this study, 331 metabolites were identified from the root, stem, and leaf of A. catechu using untargeted metabolomics, including 107 flavonoids, 71 lipids, 44 amino acids and derivatives, and 33 alkaloids. The transcriptome analysis identified 6119 differentially expressed genes, and some were enriched in the flavonoid pathway. To analyze the biosynthetic mechanism of the metabolic differences in A. catechu tissues, 36 genes were identified through combined transcriptomic and metabolomic analysis, in which glycosyltransferase genes Acat_15g017010 and Acat_16g013670 were annotated as being involved in the glycosylation of kaempferol and chrysin by their expression and in vitro activities. Flavonoid biosynthesis could be regulated by the transcription factors, AcMYB5 and AcMYB194. This study laid a foundation for further research on the flavonoid biosynthetic pathway of A. catechu.
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Affiliation(s)
- Jun Lai
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Chun Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Yueran Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Zeyong Wu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Weiguan Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Zhonghui Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Weizhen Ye
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Hao Guo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Chao Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Tuan Long
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Shouchuang Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Jun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
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6
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Gao Z, Yang X, Chen J, Rausher MD, Shi T. Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation. PLANT PHYSIOLOGY 2023; 191:1662-1683. [PMID: 36417237 PMCID: PMC10022630 DOI: 10.1093/plphys/kiac522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Both cis- and trans-regulatory mutations drive changes in gene expression that underpin plant phenotypic evolution. However, how and why these two major types of regulatory mutations arise in different genes and how gene expression is inherited and associated with these regulatory changes are unclear. Here, by studying allele-specific expression in F1 hybrids of pink-flowered sacred lotus (Nelumbo nucifera) and yellow-flowered American lotus (N. lutea), we reveal the relative contributions of cis- and trans-regulatory changes to interspecific expression rewiring underlying petal color change and how the expression is inherited in hybrids. Although cis-only variants influenced slightly more genes, trans-only variants had a stronger impact on expression differences between species. In F1 hybrids, genes under cis-only and trans-only regulatory effects showed a propensity toward additive and dominant inheritance, respectively, whereas transgressive inheritance was observed in genes carrying both cis- and trans-variants acting in opposite directions. By investigating anthocyanin and carotenoid coexpression networks in petals, we found that the same category of regulatory mutations, particularly trans-variants, tend to rewire hub genes in coexpression modules underpinning flower color differentiation between species; we identified 45 known genes with cis- and trans-regulatory variants significantly correlated with flower coloration, such as ANTHOCYANIN 5-AROMATIC ACYLTRANSFERASE (ACT), GLUTATHIONE S-TRANSFERASE F11 (GSTF11), and LYCOPENE Ε-CYCLASE (LCYE). Notably, the relative abundance of genes in different categories of regulatory divergence was associated with the inferred magnitude of constraints like expression level and breadth. Overall, our study suggests distinct selective constraints and modes of gene expression inheritance among different regulatory mutations underlying lotus petal color divergence.
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Affiliation(s)
- Zhiyan Gao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan 430081, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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7
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Yang W, Feng L, Luo J, Zhang H, Jiang F, He Y, Li X, Du J, Owusu Adjei M, Luan A, Ma J. Genome-Wide Identification and Characterization of R2R3-MYB Provide Insight into Anthocyanin Biosynthesis Regulation Mechanism of Ananas comosus var. bracteatus. Int J Mol Sci 2023; 24:3133. [PMID: 36834551 PMCID: PMC9964748 DOI: 10.3390/ijms24043133] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
The R2R3-MYB proteins comprise the largest class of MYB transcription factors, which play an essential role in regulating anthocyanin synthesis in various plant species. Ananas comosus var. bracteatus is an important colorful anthocyanins-rich garden plant. The spatio-temporal accumulation of anthocyanins in chimeric leaves, bracts, flowers, and peels makes it an important plant with a long ornamental period and highly improves its commercial value. We conducted a comprehensive bioinformatic analysis of the R2R3-MYB gene family based on genome data from A. comosus var. bracteatus. Phylogenetic analysis, gene structure and motif analysis, gene duplication, collinearity, and promoter analysis were used to analyze the characteristics of this gene family. In this work, a total of 99 R2R3-MYB genes were identified and classified into 33 subfamilies according to phylogenetic analysis, and most of them were localized in the nucleus. We found these genes were mapped to 25 chromosomes. Gene structure and protein motifs were conserved among AbR2R3-MYB genes, especially within the same subfamily. Collinearity analysis revealed four pairs of tandem duplicated genes and 32 segmental duplicates in AbR2R3-MYB genes, indicating that segmental duplication contributed to the amplification of the AbR2R3-MYB gene family. A total of 273 ABRE responsiveness, 66 TCA elements, 97 CGTCA motifs, and TGACG motifs were the main cis elements in the promoter region under response to ABA, SA, and MEJA. These results revealed the potential function of AbR2R3-MYB genes in response to hormone stress. Ten R2R3-MYBs were found to have high homology to MYB proteins reported to be involved in anthocyanin biosynthesis from other plants. RT-qPCR results revealed the 10 AbR2R3-MYB genes showed tissue-specific expression patterns, six of them expressed the highest in the flower, two genes in the bract, and two genes in the leaf. These results suggested that these genes may be the candidates that regulate anthocyanin biosynthesis of A. comosus var. bracteatus in the flower, leaf, and bract, respectively. In addition, the expressions of these 10 AbR2R3-MYB genes were differentially induced by ABA, MEJA, and SA, implying that these genes may play crucial roles in hormone-induced anthocyanin biosynthesis. Our study provided a comprehensive and systematic analysis of AbR2R3-MYB genes and identified the AbR2R3-MYB genes regulating the spatial-temporal anthocyanin biosynthesis in A. comosus var. bracteatus, which would be valuable for further study on the anthocyanin regulation mechanism of A. comosus var. bracteatus.
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Affiliation(s)
- Wei Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 625014, China
| | - Lijun Feng
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 625014, China
| | - Jiaheng Luo
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 625014, China
| | - Huiling Zhang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 625014, China
| | - Fuxing Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 625014, China
| | - Yehua He
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 625014, China
| | - Juan Du
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 625014, China
| | - Mark Owusu Adjei
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 625014, China
| | - Aiping Luan
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jun Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 625014, China
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Liu X, Du F, Sun L, Li J, Chen S, Li N, Chang Y, Cui J, Chen W, Yao D. Anthocyanin metabolism in Nelumbo: translational and post-translational regulation control transcription. BMC PLANT BIOLOGY 2023; 23:61. [PMID: 36710356 PMCID: PMC9885672 DOI: 10.1186/s12870-023-04068-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Lotus (Nelumbo Adans.) is used as an herbal medicine and the flowers are a source of natural flavonoids. 'Da Sajin', which was firstly found in the plateau area, is a natural mutant in flower color with red streamers dyeing around white petals. RESULTS The LC-MS-MS results showed that eight anthocyanin compounds, including cyanidin 3-O-glucoside, cyanidin 3-O-galactoside, malvidin 3-O-galactoside, and malvidin 3-O-glucoside, were differentially enriched in red-pigmented tissues of the petals, whereas most of these metabolites were undetected in white tissues of the petals. Transcriptome profiling indicated that the relative high expression levels of structural genes, such as NnPAL, NnF3H, and NnANS, was inconsistent with the low anthocyanin concentration in white tissues. Members of the NnMYB and NnbHLH transcription factor families were presumed to play a role in the metabolic flux in the anthocyanin and proanthocyanidin biosynthetic pathway. The expression model of translational initiation factor, ribosomal proteins and SKP1-CUL1-F-box protein complex related genes suggested an important role for translational and post-translational network in anthocyanin biosynthesis. In addition, pathway analysis indicated that light reaction or photo destruction might be an important external cause for floral color determination in lotus. CONCLUSIONS In this study, it is supposed that the natural lotus mutant 'Da Sajin' may have originated from a red-flowered ancestor. Partial loss of anthocyanin pigments in petals may result from metabolic disorder caused by light destruction. This disorder is mainly regulated at post translation and translation level, resulting in a non-inherited phenotype. These results contribute to an improved understanding of anthocyanin metabolism in lotus, and indicate that the translational and post-translational regulatory network determines the metabolic flux of anthocyanins and proanthocyanidins under specific environmental conditions.
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Affiliation(s)
- Xiaojing Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Fengfeng Du
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Linhe Sun
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jinfeng Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Shaozhou Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Naiwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yajun Chang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jian Cui
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Wen Chen
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Zhejiang, 311300, Hangzhou, China
| | - Dongrui Yao
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
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9
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Gao Z, Liang Y, Wang Y, Xiao Y, Chen J, Yang X, Shi T. Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations. FRONTIERS IN PLANT SCIENCE 2022; 13:973347. [PMID: 36212363 PMCID: PMC9539442 DOI: 10.3389/fpls.2022.973347] [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: 06/20/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Understanding the genetic variants responsible for floral trait diversity is important for the molecular breeding of ornamental flowers. Widely used in water gardening for thousands of years, the sacred lotus exhibits a wide range of diversity in floral organs. Nevertheless, the genetic variations underlying various morphological characteristics in lotus remain largely unclear. Here, we performed a genome-wide association study of sacred lotus for 12 well-recorded ornamental traits. Given a moderate linkage disequilibrium level of 32.9 kb, we successfully identified 149 candidate genes responsible for seven flower traits and plant size variations, including many pleiotropic genes affecting multiple floral-organ-related traits, such as NnKUP2. Notably, we found a 2.75-kb presence-and-absence genomic fragment significantly associated with stamen petaloid and petal number variations, which was further confirmed by re-examining another independent population dataset with petal number records. Intriguingly, this fragment carries MITE transposons bound by siRNAs and is related to the expression differentiation of a nearby candidate gene between few-petalled and double-petalled lotuses. Overall, these genetic variations and candidate genes responsible for diverse lotus traits revealed by our GWAS highlight the role of transposon variations, particularly MITEs, in shaping floral trait diversity.
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Affiliation(s)
- Zhiyan Gao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuting Liang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Yuhan Wang
- Wuhan Institute of Design and Sciences, Wuhan, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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10
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Studies on Lotus Genomics and the Contribution to Its Breeding. Int J Mol Sci 2022; 23:ijms23137270. [PMID: 35806274 PMCID: PMC9266308 DOI: 10.3390/ijms23137270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
Lotus (Nelumbo nucifera), under the Nelumbonaceae family, is one of the relict plants possessing important scientific research and economic values. Because of this, much attention has been paid to this species on both its biology and breeding among the scientific community. In the last decade, the genome of lotus has been sequenced, and several high-quality genome assemblies are available, which have significantly facilitated functional genomics studies in lotus. Meanwhile, re-sequencing of the natural and genetic populations along with different levels of omics studies have not only helped to classify the germplasm resources but also to identify the domestication of selected regions and genes controlling different horticultural traits. This review summarizes the latest progress of all these studies on lotus and discusses their potential application in lotus breeding.
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Zheng P, Sun H, Liu J, Lin J, Zhang X, Qin Y, Zhang W, Xu X, Deng X, Yang D, Wang M, Zhang Y, Song H, Huang Y, Orozco‐Obando W, Ming R, Yang M. Comparative analyses of American and Asian lotus genomes reveal insights into petal color, carpel thermogenesis and domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1498-1515. [PMID: 35362164 PMCID: PMC9325450 DOI: 10.1111/tpj.15753] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Nelumbo lutea (American lotus), which differs from Nelumbo nucifera (Asian lotus) morphologically, is one of the two remaining species in the basal eudicot family Nelumbonaceae. Here, we assembled the 843-Mb genome of American lotus into eight pseudochromosomes containing 31 382 protein-coding genes. Comparative analyses revealed conserved synteny without large chromosomal rearrangements between the genomes of American and Asian lotus and identified 29 533 structural variants (SVs). Carotenoid and anthocyanin pigments determine the yellow and red petal colors of American and Asian lotus, respectively. The structural genes encoding enzymes of the carotenoid and anthocyanin biosynthesis pathways were conserved between two species but differed in expression. We detected SVs caused by repetitive sequence expansion or contraction among the anthocyanin biosynthesis regulatory MYB genes. Further transient overexpression of candidate NnMYB5 induced anthocyanin accumulation in lotus petals. Alternative oxidase (AOX), uncoupling proteins (UCPs), and sugar metabolism and transportation contributed to carpel thermogenesis. Carpels produce heat with sugars transported from leaves as the main substrates, because there was weak tonoplast sugar transporter (TST) activity, and with SWEETs were highly expressed during thermogenesis. Cell proliferation-related activities were particularly enhanced in the warmer carpels compared with stamens during the cold night before blooming, which suggested that thermogenesis plays an important role in flower protogyny. Population genomic analyses revealed deep divergence between American and Asian lotus, and independent domestication affecting seed, rhizome, and flower traits. Our findings provide a high-quality reference genome of American lotus for exploring the genetic divergence and variation between two species and revealed possible genomic bases for petal color, carpel thermogenesis and domestication in lotus.
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Affiliation(s)
- Ping Zheng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of CorpsMinistry of Education, Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina
| | - Heng Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhan430074China
- Center of Economic BotanyCore Botanical Gardens, Chinese Academy of SciencesWuhan430074China
| | - Juan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhan430074China
- Center of Economic BotanyCore Botanical Gardens, Chinese Academy of SciencesWuhan430074China
| | - Jishan Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of CorpsMinistry of Education, Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of CorpsMinistry of Education, Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina
| | - Yuan Qin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of CorpsMinistry of Education, Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina
| | - Wenping Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of CorpsMinistry of Education, Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina
| | - Xiuming Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of CorpsMinistry of Education, Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina
| | - Xianbao Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhan430074China
- Center of Economic BotanyCore Botanical Gardens, Chinese Academy of SciencesWuhan430074China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhan430074China
- Center of Economic BotanyCore Botanical Gardens, Chinese Academy of SciencesWuhan430074China
| | - Meng Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of CorpsMinistry of Education, Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina
| | - Yanting Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of CorpsMinistry of Education, Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina
| | - Heyun Song
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhan430074China
- Center of Economic BotanyCore Botanical Gardens, Chinese Academy of SciencesWuhan430074China
| | - Yongji Huang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of CorpsMinistry of Education, Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina
| | - Warner Orozco‐Obando
- Virginia Cooperative of ExtensionVirginia Polytechnic Institute and State UniversityBlacksburgVA24061USA
| | - Ray Ming
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhan430074China
- Center of Economic BotanyCore Botanical Gardens, Chinese Academy of SciencesWuhan430074China
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12
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Liu J, Wang Y, Zhang M, Wang Y, Deng X, Sun H, Yang D, Xu L, Song H, Yang M. Color fading in lotus (Nelumbo nucifera) petals is manipulated both by anthocyanin biosynthesis reduction and active degradation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 179:100-107. [PMID: 35325657 DOI: 10.1016/j.plaphy.2022.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/22/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Flower color is a key trait that determines the ornamental quality of aquatic lotus (Nelumbo nucifera). Color fading significantly decreases the ornamental value of lotus flowers. However, the molecular mechanism underlying lotus petal discoloration remains largely unknown. Here, the anthocyanin content and global transcriptional profiling of lotus petals of cultivar 'Qiusanse' in four developmental stages were analyzed. Five anthocyanin components were detected, and the total anthocyanin content decreased as the petal color changed from red to nearly white. Moreover, the malondialdehyde (MDA) content and peroxidase (POD) activity increased during color fading. RNA-seq analysis revealed a total of 4,092 differentially expressed genes (DEGs) between petal developmental stages. Notably, oxidoreductase and hydrolase activity related genes were overrepresented in DEGs. The expression pattern of key anthocyanin biosynthesis genes including, CHS, F3H, ANS, UFGT, and transcription factor regulators, including MYBs, WRKYs and bHLHs were correlated with anthocyanin accumulation. Interestingly, DEGs associated with anthocyanin degradation and vacuolar pH regulation, including peroxidase, proton pumps regulators such as WRKY3 and MYB5-like, were significantly upregulated during the late stages of flowering. This study reveals for the first time the transcriptional dynamics during lotus petal discoloration. Our results suggest the involvement of anthocyanin biosynthesis repressors and degrading genes as well as pH regulators in controlling color fading of lotus petals. The study also provides valuable information and candidate genes for improving the lotus flower color.
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Affiliation(s)
- Juan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yuxin Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Minghua Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Yunmeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Xianbao Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Heng Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Liming Xu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Heyun Song
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China; Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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13
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Tu Z, Xia H, Yang L, Zhai X, Shen Y, Li H. The Roles of microRNA-Long Non-coding RNA-mRNA Networks in the Regulation of Leaf and Flower Development in Liriodendron chinense. FRONTIERS IN PLANT SCIENCE 2022; 13:816875. [PMID: 35154228 PMCID: PMC8829146 DOI: 10.3389/fpls.2022.816875] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/04/2022] [Indexed: 05/27/2023]
Abstract
The leaf and the flower are vital plant organs owing to their roles in photosynthesis and reproduction. Long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and transcription factors (TFs) are very important to the development of these organs. Liriodendron chinense is a common ornamental tree species in southern China with an unusual leaf shape and tulip-like flowers. The genetic mechanisms underlying leaf and flower development in L. chinense and the miRNA-lncRNA-TF regulatory networks are poorly studied. Through the integration and analysis of different types of sequencing data, we identified the miRNA-lncRNA-TF regulatory networks that were related to leaf and flower development. These networks contained 105 miRNAs, 258 lncRNAs, 393 TFs, and 22 endogenous target mimics. Notably, lch-lnc7374-miR156h-SPL3 and lch-lnc7374-miR156j-SPL9 were potential regulators of stamen and pistil development in L. chinense, respectively. miRNA-lncRNA-mRNA regulatory networks were shown to impact anther development, male and female fertility, and petal color by regulating the biosynthesis of phenylpropanoid metabolites. Phenylpropanoid metabolite biosynthesis genes and TFs that were targeted by miRNAs and lncRNAs were differentially expressed in the leaf and flower. Moreover, RT-qPCR analysis confirmed 22 differentially expressed miRNAs, among which most of them showed obvious leaf or flower specificity; miR157a-SPL and miR160a-ARF module were verified by using RLM-RACE, and these two modules were related to leaf and flower development. These findings provide insight into the roles of miRNA-lncRNA-mRNA regulatory networks in organ development and function in L. chinense, and will facilitate further investigation into the regulatory mechanisms of leaf and flower development in L. chinense.
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Affiliation(s)
- Zhonghua Tu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Hui Xia
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lichun Yang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinyu Zhai
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yufang Shen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huogen Li
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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14
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Gao Z, Li H, Yang X, Yang P, Chen J, Shi T. Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera). PLANT MOLECULAR BIOLOGY 2021; 106:207-220. [PMID: 33738679 DOI: 10.1007/s11103-021-01138-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
The genome-wide allele-specific expression in F1 hybrids from the cross of tropical and temperate lotus unveils how cis-regulatory divergences affect genes in key pathways related to ecotypic divergence. Genetic variation, particularly cis-regulatory variation, plays a crucial role in phenotypic variation and adaptive evolution in plants. Temperate and tropical lotus, the two ecotypes of Nelumbo nucifera, show distinction in the degree of rhizome enlargement, which is associated with winter dormancy. To understand the roles of genome-wide cis-regulatory divergences on adaptive evolution of temperate and tropical lotus (Nelumbo nucifera), here we performed allele-specific expression (ASE) analyses on the tissues including flowers, leaves and rhizome from F1 hybrids of tropical and temperate lotus. For all investigated tissues in F1s, about 36% of genes showed ASE and about 3% of genes showed strong consistent ASE. Most of ASEs were biased towards the tropical parent in all surveyed samples, indicating that the tropical genome might be dominant over the temperate genome in gene expression of tissues from their F1 hybrids. We found that promoter sequences with similar allelic expression are more conserved than genes with significant or conditional ASE, suggesting the cis-regulatory sequence divergence underlie the allelic expression bias. We further uncovered biased genes being related to phenotypic differentiation between two lotus ecotypes, especially metabolic and phytohormone-related pathways in the rhizome. Overall, our study provides a global landscape of cis-regulatory variations between two lotus ecotypes and highlights their roles in rhizome growth variation for the climatic adaptation.
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Affiliation(s)
- Zhiyan Gao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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15
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Yan H, Pei X, Zhang H, Li X, Zhang X, Zhao M, Chiang VL, Sederoff RR, Zhao X. MYB-Mediated Regulation of Anthocyanin Biosynthesis. Int J Mol Sci 2021; 22:3103. [PMID: 33803587 PMCID: PMC8002911 DOI: 10.3390/ijms22063103] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022] Open
Abstract
Anthocyanins are natural water-soluble pigments that are important in plants because they endow a variety of colors to vegetative tissues and reproductive plant organs, mainly ranging from red to purple and blue. The colors regulated by anthocyanins give plants different visual effects through different biosynthetic pathways that provide pigmentation for flowers, fruits and seeds to attract pollinators and seed dispersers. The biosynthesis of anthocyanins is genetically determined by structural and regulatory genes. MYB (v-myb avian myeloblastosis viral oncogene homolog) proteins are important transcriptional regulators that play important roles in the regulation of plant secondary metabolism. MYB transcription factors (TFs) occupy a dominant position in the regulatory network of anthocyanin biosynthesis. The TF conserved binding motifs can be combined with other TFs to regulate the enrichment and sedimentation of anthocyanins. In this study, the regulation of anthocyanin biosynthetic mechanisms of MYB-TFs are discussed. The role of the environment in the control of the anthocyanin biosynthesis network is summarized, the complex formation of anthocyanins and the mechanism of environment-induced anthocyanin synthesis are analyzed. Some prospects for MYB-TF to modulate the comprehensive regulation of anthocyanins are put forward, to provide a more relevant basis for further research in this field, and to guide the directed genetic modification of anthocyanins for the improvement of crops for food quality, nutrition and human health.
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Affiliation(s)
- Huiling Yan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Xiaona Pei
- Harbin Research Institute of Forestry Machinery, State Administration of Forestry and Grassland, Harbin 150086, China;
- Research Center of Cold Temperate Forestry, CAF, Harbin 150086, China
| | - Heng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Xiang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Xinxin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Minghui Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA;
| | - Ronald Ross Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA;
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
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16
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Deng J, Li J, Su M, Lin Z, Chen L, Yang P. A bHLH gene NnTT8 of Nelumbo nucifera regulates anthocyanin biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:518-523. [PMID: 33272791 DOI: 10.1016/j.plaphy.2020.11.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Lotus is an important aquatic ornamental plant, whose flower color is one of the key horticultural traits that determines its ornamental value. Previous studies revealed that anthocyanins largely determined the red color of lotus flower, which are also the main component that has beneficial effects on human health. However, the regulation mechanism of flower pigmentation in lotus flower remains unclear. In the present study, in order to further understand the regulatory mechanism underlying the anthocyanin biosynthesis, a bHLH gene NnTT8 was characterized to be phylogenetically close to AtTT8 and the bHLH proteins from other plant species that have been indicated to be involved in the positive regulation of anthocyanin biosynthesis. Complementation analysis in Arabidopsis tt8 mutant showed that NnTT8 could function similarly to AtTT8 in regulating anthocyanin and proanthocyanin biosynthesis. An MYB transcription factor capable of interacting with NnTT8 was also characterized from lotus. The identification of a bHLH transcription factor playing regulatory roles in anthocyanin biosynthesis is crucial, as it might help to obtain more in-depth insight into the coloration of lotus and help in breeding high anthocyanin content lotus variety that can be explored for lotus flower beverages.
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Affiliation(s)
- Jiao Deng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China; Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China.
| | - Juanjuan Li
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, College of Life Science and Technology, Hubei Engineering University, Xiaogan, Hubei, 432000, China.
| | - Mengyue Su
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Zhongyuan Lin
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
| | - Lei Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China.
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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Transcriptome Analysis Reveals Candidate Genes Related to Anthocyanin Biosynthesis in Different Carrot Genotypes and Tissues. PLANTS 2020; 9:plants9030344. [PMID: 32182858 PMCID: PMC7154819 DOI: 10.3390/plants9030344] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 12/13/2022]
Abstract
Black carrots are characterized by a significant amount of anthocyanins, which are not only a good source of natural food colorant, but can also provide many health benefits to humans. In the present work, taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis, with particular a focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had a genotypic dependent expression and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. DcbHLH3 (LOC108204485) was upregulated in all black samples compared with the orange ones. We also found that GST1 (LOC108205254) might be an important anthocyanin transporter, and its upregulated expression resulted in the increasing of vacuolar anthocyanin accumulation in black samples. Moreover, high performance liquid chromatographic (HPLC) analysis and liquid chromatography coupled to mass spectrometry (LC-MS) were used to identify the individual anthocyanin in the purple tissues of two carrot cultivars. The results showed that five main anthocyanin compounds and the most abundant anthocyanin were the same in different tissues, while the second-highest anthocyanin between three tissues was different, even in the same cultivar. In conclusion, this study combined anthocyanin profiles and comparative transcriptomic analysis to identify candidate genes involved in anthocyanin biosynthesis in carrots, thus providing a better foundation for improving anthocyanin accumulation in carrots as a source of colorants.
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18
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He Y, Chen H, Zhou L, Liu Y, Chen H. Comparative transcription analysis of photosensitive and non-photosensitive eggplants to identify genes involved in dark regulated anthocyanin synthesis. BMC Genomics 2019; 20:678. [PMID: 31455222 PMCID: PMC6712802 DOI: 10.1186/s12864-019-6023-4] [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: 03/14/2019] [Accepted: 08/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Light is a key environmental factor in regulation of anthocyanin biosynthesis. Through a large number of bagging screenings, we obtained non-photosensitive eggplants that still have decent amount of anthocyanin synthesized after bagging. In the present study, transcriptome was made to explore the molecular mechanism of dark-regulated anthocyanin synthesis in non-photosensitive eggplant. RESULTS The transcriptome of the pericarp at 0 h, 0.5 h, 4 h, and 8 h after bag removal were sequenced and analyzed. Comparison of the sequencing data with those of photosensitive eggplant for the same time period showed that anthocyanin synthesis genes had different expression trends. Based on the expression trends of the structural genes, it was discovered that 22 transcription factors and 4 light signal transduction elements may be involved in the anthocyanin synthesis in two types of eggplants. Through transcription factor target gene prediction and yeast one-hybrid assay, SmBIM1, SmAP2, SmHD, SmMYB94, SmMYB19, SmTT8, SmYABBY, SmTTG2, and SmMYC2 were identified to be directly or indirectly bound to the promoter of the structural gene SmCHS. These results indicate that the identified 9 genes participated in the anthocyanin synthesis in eggplant peel and formed a network of interactions among themselves. CONCLUSIONS Based on the comparative transcription, the identified 22 transcription factors and 4 light signal transduction elements may act as the key factors in dark regulated anthocyanin synthesis in non-photosensitive eggplant. The results provided a step stone for further analysis of the molecular mechanism of dark-regulated anthocyanin synthesis in non-photosensitive eggplant.
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Affiliation(s)
- Yongjun He
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Hang Chen
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Lu Zhou
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
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19
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Lin Z, Zhang C, Cao D, Damaris RN, Yang P. The Latest Studies on Lotus ( Nelumbo nucifera)-an Emerging Horticultural Model Plant. Int J Mol Sci 2019; 20:E3680. [PMID: 31357582 PMCID: PMC6696627 DOI: 10.3390/ijms20153680] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/12/2019] [Accepted: 07/20/2019] [Indexed: 12/21/2022] Open
Abstract
Lotus (Nelumbo nucifera) is a perennial aquatic basal eudicot belonging to a small family Nelumbonaceace, which contains only one genus with two species. It is an important horticultural plant, with its uses ranging from ornamental, nutritional to medicinal values, and has been widely used, especially in Southeast Asia. Recently, the lotus obtained a lot of attention from the scientific community. An increasing number of research papers focusing on it have been published, which have shed light on the mysteries of this species. Here, we comprehensively reviewed the latest advancement of studies on the lotus, including phylogeny, genomics and the molecular mechanisms underlying its unique properties, its economic important traits, and so on. Meanwhile, current limitations in the research of the lotus were addressed, and the potential prospective were proposed as well. We believe that the lotus will be an important model plant in horticulture with the generation of germplasm suitable for laboratory operation and the establishment of a regeneration and transformation system.
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Affiliation(s)
- Zhongyuan Lin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Cheng Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Dingding Cao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
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20
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Naing AH, Kim CK. Roles of R2R3-MYB transcription factors in transcriptional regulation of anthocyanin biosynthesis in horticultural plants. PLANT MOLECULAR BIOLOGY 2018; 98:1-18. [PMID: 30167900 DOI: 10.1007/s11103-018-0771-4] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/23/2018] [Indexed: 05/20/2023]
Abstract
This review contains functional roles of MYB transcription factors in the transcriptional regulation of anthocyanin biosynthesis in horticultural plants. This review describes potential uses of MYB TFs as tools for metabolic engineering for anthocyanin production. Anthocyanins (ranging from red to blue) are controlled by specific branches of the anthocyanin biosynthetic pathway and are mostly visible in ornamentals, fruits, and vegetables. In the present review, we describe which R2R3-MYB transcription factors (TFs) control the transcriptional regulation of anthocyanin structural genes involved in the specific branches of the anthocyanin biosynthetic pathway in various horticultural plants (e.g., ornamentals, fruits, and vegetables). In addition, some MYBs responsible for anthocyanin accumulation in specific tissues are described. Moreover, we highlight the phylogenetic relationships of the MYBs that suppress or promote anthocyanin synthesis in horticultural crops. Enhancement of anthocyanin synthesis via metabolic genetic engineering of anthocyanin MYBs, which is described in the review, is indicative of the potential use of the mentioned anthocyanin-related MYBs as tools for anthocyanin production. Therefore, the MYBs would be suitable for metabolic genetic engineering for improvement of flower colors, fruit quality, and vegetable nutrients.
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Affiliation(s)
- Aung Htay Naing
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Chang Kil Kim
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, Republic of Korea.
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21
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Ni X, Xue S, Iqbal S, Wang W, Ni Z, Khalil-Ur-Rehman M, Gao Z. Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot ( Prunus mume). PeerJ 2018; 6:e4625. [PMID: 29740511 PMCID: PMC5937475 DOI: 10.7717/peerj.4625] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/24/2018] [Indexed: 11/29/2022] Open
Abstract
The red-skinned fruit of Japanese apricot (Prunus mume Sieb. et Zucc) appeals to customers due to its eye-catching pigmentation, while the mechanism related to its colour formation is still unclear. In this study, genome re-sequencing of six Japanese apricot cultivars was carried out with approximately 92.2 Gb of clean bases using next-generation sequencing. A total of 32,004 unigenes were assembled with an average of 83.1% coverage rate relative to reference genome. A wide range of genetic variation was detected, including 7,387,057 single nucleotide polymorphisms, 456,222 insertions or deletions and 129,061 structural variations in all genomes. Comparative sequencing data revealed that 13 candidate genes were involved in biosynthesis of anthocyanin. Significantly higher expression patterns were observed in genes encoding three anthocyanin synthesis structural genes (4CL, F3H and UFGT), five transcription factors (MYB–bHLH–WD40 complexes and NAC) and five anthocyanin accumulation related genes (GST1, RT1, UGT85A2, ABC and MATE transporters) in red-skinned than in green-skinned Japanese apricots using reverse transcription-quantitative polymerase chain reaction. Eight main kinds of anthocyanin s were detected by UPLC/MS, and cyanidin 3-glucoside was identified as the major anthocyanin (124.2 mg/kg) in red-skinned cultivars. The activity of UDP-glucose flavonoid-3-O-glycosyltransferase enzyme determined by UPLC was significantly higher in all red-skinned cultivars, suggesting that it is the potential vital regulatory gene for biosynthesis of anthocyanin in Japanese apricot.
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Affiliation(s)
- Xiaopeng Ni
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China.,Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Song Xue
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shahid Iqbal
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wanxu Wang
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhaojun Ni
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Khalil-Ur-Rehman
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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22
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Li J, He YJ, Zhou L, Liu Y, Jiang M, Ren L, Chen H. Transcriptome profiling of genes related to light-induced anthocyanin biosynthesis in eggplant (Solanum melongena L.) before purple color becomes evident. BMC Genomics 2018; 19:201. [PMID: 29554865 PMCID: PMC5859761 DOI: 10.1186/s12864-018-4587-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/08/2018] [Indexed: 12/20/2022] Open
Abstract
Background The anthocyanins are highly enriched in eggplants (Solanum melongena L.) with purple peel. However, our previous study showed that anthocyanins biosynthesis in eggplant cultivar ‘Lanshan Hexian’ was completely regulated by light and color becomes evident at most 2 days after exposure to light. In the present investigation, transcriptome study was made to explore the underlying molecular mechanisms of light-induced anthocyanin biosynthesis in eggplant (Solanum melongena L.) before color becomes evident. Results RNA-Seq was performed for four time points (0, 0.5, 4 and 8 h after bags removal) where concerted changes happened. A total of 32,630 genes or transcripts were obtained by transcriptome sequencing, from which 1956 differentially expressed genes (DEGs) were found. Gene Ontology analysis showed that the 1956 DEGs covered a wide range of cellular components, molecular functions and biological processes. All the DEGs were further divided into 26 clusters based on their distinct expression patterns. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis found out 24 structural anthocyanin biosynthesis genes which distributing in seven clusters. In addition, 102 transcription factors, which exhibited highly dynamic changes in response to light, were found in the seven clusters. Three photoreceptors, UV Resistance Locus 8 (UVR8), Cryptochrome 3 (CRY3) and UVR3, were identified as DEGs. The light signal transduction elements, COP1 and two SPAs, might be responsible for anthocyanin biosynthesis regulation. Conclusion Based on the transcriptome data, the anthocyanin biosynthesis structural genes, transcription factors, photoreceptors and light signal transduction elements were quickly screened which may act as the key regulatory factors in anthocyanin biosynthesis pathway. By comparing the transcriptome data with our previous studies, 869 genes were confirmed to participate in the light-induced anthocyanin biosynthesis. These results expand our knowledge of light-induced anthocyanin biosynthesis in plants, which allowing for fruit coloration to be improved under low-light conditions in future. Electronic supplementary material The online version of this article (10.1186/s12864-018-4587-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yong-Jun He
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Lu Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Mingmin Jiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Li Ren
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.,Institute for Agri-Food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Road, Fengxian District, Shanghai, 201403, China
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
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23
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Jin SW, Rahim MA, Kim HT, Park JI, Kang JG, Nou IS. Molecular analysis of anthocyanin-related genes in ornamental cabbage. Genome 2017; 61:111-120. [PMID: 29232522 DOI: 10.1139/gen-2017-0098] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ornamental cabbage (Brassica oleracea var. acephala) is a winter-grown and important decorative plant of the family Brassicaceae, which displays an exceptional coloration in the central leaves of the rosette. Anthocyanins are the key determinant of the red, purple, and blue colors of vegetative and reproductive parts of many plant species including ornamental cabbage. Total anthocyanin content was measured spectrophotometrically, and the highest anthocyanin content was detected in the red followed by light-red and white ornamental cabbage lines. Anthocyanin biosynthesis is controlled by members of three different transcription factor (TF) families, such as MYB, basic helix-loop-helix (bHLH), and WD40 repeats (WDR), which function as a MBW complex. We identified three MYB, six bHLH, and one WDR TFs that regulate anthocyanin biosynthesis in ornamental cabbage. The expression of the regulatory and biosynthetic genes for anthocyanin synthesis was determined by qPCR. The tested structural genes of the anthocyanin pathway were shown to be up-regulated in the red followed by light-red ornamental cabbage lines; however, the expression levels of the late biosynthetic genes were barely detected in the white ornamental cabbage lines. Among the regulatory genes, BoPAP2 (MYB), BoTT8, BoEGL3.1, and BoMYC1.2 (bHLH), and BoTTG1 (WDR) were identified as candidates for the regulation of anthocyanin biosynthesis. This work could be useful for the breeding of novel colorful ornamental cabbage cultivars.
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Affiliation(s)
- Si-Won Jin
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Md Abdur Rahim
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Hoy-Taek Kim
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Jong-Goo Kang
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea
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