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Yu H, Li D, Wu Y, Miao P, Zhou C, Cheng H, Dong Q, Zhao Y, Liu Z, Zhou L, Pan C. Integrative omics analyses of tea (Camellia sinensis) under glufosinate stress reveal defense mechanisms: A trade-off with flavor loss. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134542. [PMID: 38776809 DOI: 10.1016/j.jhazmat.2024.134542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/18/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
Extensively applied glufosinate (GLU) will trigger molecular alterations in nontarget tea plants (Camellia sinensis), which inadvertently disturbs metabolites and finally affects tea quality. The mechanistic response of tea plants to GLU remains unexplored. This study investigated GLU residue behavior, the impact on photosynthetic capacity, specialized metabolites, secondary pathways, and transcript levels in tea seedlings. Here, GLU mainly metabolized to MPP and accumulated more in mature leaves than in tender ones. GLU catastrophically affected photosynthesis, leading to leaf chlorosis, and decreased Fv/Fm and chlorophyll content. Physiological and biochemical, metabolomics, and transcriptomics analyses were integrated. Showing that GLU disrupted the photosynthetic electron transport chain, triggered ROS and antioxidant system, and inhibited photosynthetic carbon fixation. GLU targeted glutamine synthetase (GS) leading to the accumulation of ammonium and the inhibition of key umami L-theanine, causing a disorder in nitrogen metabolism, especially for amino acids synthesis. Interestingly, biosynthesis of primary flavonoids was sacrificed for defensive phenolic acids and lignin formulation, leading to possible losses in nutrition and tenderness in leaves. This study revealed the defense intricacies and potential quality deterioration of tea plants responding to GLU stress. Valuable insights into detoxification mechanisms for non-target crops post-GLU exposure were offered.
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Affiliation(s)
- Huan Yu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Dong Li
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Yangliu Wu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Peijuan Miao
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Chunran Zhou
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Haiyan Cheng
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Qinyong Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Yingjie Zhao
- Guangxi Research Institute of Tea Science, Guilin 541004, China; Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Zhusheng Liu
- Guangxi Research Institute of Tea Science, Guilin 541004, China
| | - Li Zhou
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Canping Pan
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China.
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Anum H, Li K, Tabusam J, Saleh SAA, Cheng RF, Tong YX. Regulation of anthocyanin synthesis in red lettuce in plant factory conditions: A review. Food Chem 2024; 458:140111. [PMID: 38968716 DOI: 10.1016/j.foodchem.2024.140111] [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: 04/24/2024] [Revised: 06/02/2024] [Accepted: 06/12/2024] [Indexed: 07/07/2024]
Abstract
Anthocyanins, natural pigments known for their vibrant hues and beneficial properties, undergo intricate genetic control. However, red vegetables grown in plant factories frequently exhibit reduced anthocyanin synthesis compared to those in open fields due to factors like inadequate light, temperature, humidity, and nutrient availability. Comprehending these factors is essential for optimizing plant factory environments to enhance anthocyanin synthesis. This review insights the impact of physiological and genetic factors on the production of anthocyanins in red lettuce grown under controlled conditions. Further, we aim to gain a better understanding of the mechanisms involved in both synthesis and degradation of anthocyanins. Moreover, this review summarizes the identified regulators of anthocyanin synthesis in lettuce, addressing the gap in knowledge on controlling anthocyanin production in plant factories, with potential implications for various crops beyond red lettuce.
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Affiliation(s)
- Hadiqa Anum
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture, Beijing, China
| | - Kun Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture, Beijing, China
| | - Javaria Tabusam
- National Key Laboratory of Cotton Bio-Breeding and Integration Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Said Abdelhalim Abdelaty Saleh
- Horticultural Crops Technology Department, Agricultural & Biological Research Institute, National Research Centre, Giza, Egypt
| | - Rui-Feng Cheng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture, Beijing, China.
| | - Yu-Xin Tong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture, Beijing, China.
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3
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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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4
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Bhattarai A, Nimmakayala P, Davenport B, Natarajan P, Tonapi K, Kadiyala SS, Lopez-Ortiz C, Ibarra-Muñoz L, Chakrabarti M, Benedito V, Adjeroh DA, Balagurusamy N, Reddy UK. Genetic tapestry of Capsicum fruit colors: a comparative analysis of four cultivated species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:130. [PMID: 38744692 DOI: 10.1007/s00122-024-04635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/17/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE Genome-wide association study of color spaces across the four cultivated Capsicum spp. revealed a shared set of genes influencing fruit color, suggesting mechanisms and pathways across Capsicum species are conserved during the speciation. Notably, Cytochrome P450 of the carotenoid pathway, MYB transcription factor, and pentatricopeptide repeat-containing protein are the major genes responsible for fruit color variation across the Capsicum species. Peppers (Capsicum spp.) rank among the most widely consumed spices globally. Fruit color, serving as a determinant for use in food colorants and cosmeceuticals and an indicator of nutritional contents, significantly influences market quality and price. Cultivated Capsicum species display extensive phenotypic diversity, especially in fruit coloration. Our study leveraged the genetic variance within four Capsicum species (Capsicum baccatum, Capsicum chinense, Capsicum frutescens, and Capsicum annuum) to elucidate the genetic mechanisms driving color variation in peppers and related Solanaceae species. We analyzed color metrics and chromatic attributes (Red, Green, Blue, L*, a*, b*, Luminosity, Hue, and Chroma) on samples cultivated over six years (2015-2021). We resolved genomic regions associated with fruit color diversity through the sets of SNPs obtained from Genotyping by Sequencing (GBS) and genome-wide association study (GWAS) with a Multi-Locus Mixed Linear Model (MLMM). Significant SNPs with FDR correction were identified, within the Cytochrome P450, MYB-related genes, Pentatricopeptide repeat proteins, and ABC transporter family were the most common among the four species, indicating comparative evolution of fruit colors. We further validated the role of a pentatricopeptide repeat-containing protein (Chr01:31,205,460) and a cytochrome P450 enzyme (Chr08:45,351,919) via competitive allele-specific PCR (KASP) genotyping. Our findings advance the understanding of the genetic underpinnings of Capsicum fruit coloration, with developed KASP assays holding potential for applications in crop breeding and aligning with consumer preferences. This study provides a cornerstone for future research into exploiting Capsicum's diverse fruit color variation.
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Affiliation(s)
- Ambika Bhattarai
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA.
| | - Brittany Davenport
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Purushothaman Natarajan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Krittika Tonapi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Sai Satish Kadiyala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Carlos Lopez-Ortiz
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Lizbeth Ibarra-Muñoz
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, 27275, Torreon, Coahuila, Mexico
| | - Manohar Chakrabarti
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Vagner Benedito
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, 26506, USA
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, 27275, Torreon, Coahuila, Mexico.
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA.
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Wong DCJ, Wang Z, Perkins J, Jin X, Marsh GE, John EG, Peakall R. The road less taken: Dihydroflavonol 4-reductase inactivation and delphinidin anthocyanin loss underpins a natural intraspecific flower colour variation. Mol Ecol 2024:e17334. [PMID: 38651763 DOI: 10.1111/mec.17334] [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: 11/14/2023] [Revised: 02/22/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
Visual cues are of critical importance for the attraction of animal pollinators, however, little is known about the molecular mechanisms underpinning intraspecific floral colour variation. Here, we combined comparative spectral analysis, targeted metabolite profiling, multi-tissue transcriptomics, differential gene expression, sequence analysis and functional analysis to investigate a bee-pollinated orchid species, Glossodia major with common purple- and infrequent white-flowered morphs. We found uncommon and previously unreported delphinidin-based anthocyanins responsible for the conspicuous and pollinator-perceivable colour of the purple morph and three genetic changes underpinning the loss of colour in the white morph - (1) a loss-of-function (LOF; frameshift) mutation affecting dihydroflavonol 4-reductase (DFR1) coding sequence due to a unique 4-bp insertion, (2) specific downregulation of functional DFR1 expression and (3) the unexpected discovery of chimeric Gypsy transposable element (TE)-gene (DFR) transcripts with potential consequences to the genomic stability and post-transcriptional or epigenetic regulation of DFR. This is one of few known cases where regulatory changes and LOF mutation in an anthocyanin structural gene, rather than transcription factors, are important. Furthermore, if TEs prove to be a frequent source of mutation, the interplay between environmental stress-induced TE evolution and pollinator-mediated selection for adaptive colour variation may be an overlooked mechanism maintaining floral colour polymorphism in nature.
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Zemin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - James Perkins
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xin Jin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Grace Emma Marsh
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Emma Grace John
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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6
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Jiang L, Chen J, Qian J, Xu M, Qing H, Cheng H, Fu J, Zhang C. The R2R3-MYB transcription factor ZeMYB32 negatively regulates anthocyanin biosynthesis in Zinnia elegans. PLANT MOLECULAR BIOLOGY 2024; 114:48. [PMID: 38632151 DOI: 10.1007/s11103-024-01441-0] [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: 04/06/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024]
Abstract
KEY MESSAGE This study identified an R2R3-MYB from Zinnia elegans, ZeMYB32, which negatively regulates anthocyanin biosynthesis.
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Affiliation(s)
- Lingli Jiang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Jiahong Chen
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Jieyu Qian
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Menghan Xu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Hongsheng Qing
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Hefeng Cheng
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Jianxin Fu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China.
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China.
| | - Chao Zhang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China.
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China.
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Xiao X, Lang D, Yong J, Zhang X. Bacillus cereus G2 alleviate salt stress in Glycyrrhiza uralensis Fisch. by balancing the downstream branches of phenylpropanoids and activating flavonoid biosynthesis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116129. [PMID: 38430580 DOI: 10.1016/j.ecoenv.2024.116129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/11/2024] [Accepted: 02/18/2024] [Indexed: 03/04/2024]
Abstract
The salinity environment is one of the biggest threats to Glycyrrhiza uralensis Fisch. (G. uralensis) growth, resulting from the oxidative stress caused by excess reactive oxygen species (ROS). Flavonoids are the main pharmacodynamic composition and help maintain ROS homeostasis and mitigate oxidative damage in G. uralensis in the salinity environment. To investigate whether endophytic Bacillus cereus G2 can improve the salt-tolerance of G. uralensis through controlling flavonoid biosynthesis, the transcriptomic and physiological analysis of G. uralensis treated by G2 in the saline environment was conducted, focused on flavonoid biosynthesis-related pathways. Results uncovered that salinity inhibited flavonoids synthesis by decreasing the activities of phenylalanine ammonialyase (PAL) and 4-coumarate-CoA ligase (4CL) (42% and 39%, respectively) due to down-regulated gene Glyur000910s00020578 at substrate level, and then decreasing the activities of chalcone isomerase (CHI) and chalcone synthase (CHS) activities (50% and 42%, respectively) due to down-regulated genes Glyur006062s00044203 and Glyur000051s00003431, further decreasing isoliquiritigenin content by 53%. However, salt stress increased liquiritin content by 43%, which might be a protective mechanism of salt-treated G. uralensis seedlings. Interestingly, G2 enhanced PAL activity by 27% whereas reduced trans-cinnamate 4-monooxygenase (C4H) activity by 43% which could inhibit lignin biosynthesis but promote flavonoid biosynthesis of salt-treated G. uralensis at the substrate level. G2 decreased shikimate O-hydroxycinnamoyltransferase (HCT) activity by 35%, increased CHS activity by 54% through up-regulating the gene Glyur000051s00003431 encoding CHS, and increased CHI activity by 72%, thereby decreasing lignin (34%) and liquiritin (24%) content, but increasing isoliquiritigenin content (35%), which could mitigate oxidative damage and changed salt-tolerance mechanism of G. uralensis.
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Affiliation(s)
- Xiang Xiao
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Duoyong Lang
- College of Basic Medicine, Ningxia Medical University, Yinchuan 750004, China
| | - Jingjiao Yong
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Xinhui Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, China; Ningxia Engineering and Technology Research Center of Regional Characterizistic Traditional Chinese Medicine, Ningxia Collaborative Innovation Center of Regional Characterizistic Traditional Chinese Medicine, Key Laboratory of Ningxia Minority Medicine Modernization, Ministry of Education, Yinchuan 750004, China.
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8
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Lam LPY, Lui ACW, Bartley LE, Mikami B, Umezawa T, Lo C. Multifunctional 5-hydroxyconiferaldehyde O-methyltransferases (CAldOMTs) in plant metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1671-1695. [PMID: 38198655 DOI: 10.1093/jxb/erae011] [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: 08/02/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024]
Abstract
Lignin, flavonoids, melatonin, and stilbenes are plant specialized metabolites with diverse physiological and biological functions, supporting plant growth and conferring stress resistance. Their biosynthesis requires O-methylations catalyzed by 5-hydroxyconiferaldehyde O-methyltransferase (CAldOMT; also called caffeic acid O-methyltransferase, COMT). CAldOMT was first known for its roles in syringyl (S) lignin biosynthesis in angiosperm cell walls and later found to be multifunctional. This enzyme also catalyzes O-methylations in flavonoid, melatonin, and stilbene biosynthetic pathways. Phylogenetic analysis indicated the convergent evolution of enzymes with OMT activities towards the monolignol biosynthetic pathway intermediates in some gymnosperm species that lack S-lignin and Selaginella moellendorffii, a lycophyte which produces S-lignin. Furthermore, neofunctionalization of CAldOMTs occurred repeatedly during evolution, generating unique O-methyltransferases (OMTs) with novel catalytic activities and/or accepting novel substrates, including lignans, 1,2,3-trihydroxybenzene, and phenylpropenes. This review summarizes multiple aspects of CAldOMTs and their related proteins in plant metabolism and discusses their evolution, molecular mechanism, and roles in biorefineries, agriculture, and synthetic biology.
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Affiliation(s)
- Lydia Pui Ying Lam
- Graduate School of Engineering Science, Akita University, Tegata Gakuen-machi 1-1, Akita City, Akita 010-0852, Japan
| | - Andy C W Lui
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Laura E Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
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9
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Gong J, Wang Y, Xue C, Wu L, Sheng S, Wang M, Peng J, Cao S. Regulation of blue infertile flower pigmentation by WD40 transcription factor HmWDR68 in Hydrangea macrophylla 'forever summer'. Mol Biol Rep 2024; 51:328. [PMID: 38393428 DOI: 10.1007/s11033-024-09287-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND WD40 transcription factors are crucial in plant growth and developmental, significantly impacting plant growth regulation. This study investigates the WD40 transcription factor HmWDR68's role in developing the distinctive blue infertile flower colors in Hydrangea macrophylla 'Forever Summer'. METHODS AND RESULTS The HmWDR68 gene was isolated by PCR, revealing an open reading frame of 1026 base pairs, which encodes 341 amino acids. Characterized by four WD40 motifs, HmWDR68 is a member of the WD40 family. Phylogenetic analysis indicates that HmWDR68 shares high homology with PsWD40 in Camellia sinensis and CsWD40 in Paeonia suffruticosa, both of which are integral in anthocyanin synthesis regulation. Quantitative real-time PCR (qRT-PCR) analysis demonstrated that HmWDR68 expression in the blue infertile flowers of 'Forever Summer' hydrangea was significantly higher compared to other tissues and organs. Additionally, in various hydrangea varieties with differently colored infertile flowers, HmWDR68 expression was markedly elevated in comparison to other hydrangea varieties, correlating with the development of blue infertile flowers. Pearson correlation analysis revealed a significant association between HmWDR68 expression and the concentration of delphinidin 3-O-glucoside, as well as key genes involved in anthocyanin biosynthesis (HmF3H, HmC3'5'H, HmDFR, and HmANS) in the blue infertile flowers of 'Forever Summer' hydrangea (P < 0.01). CONCLUSION These findings suggest HmWDR68 may specifically regulate blue infertile flower formation in hydrangea by enhancing delphinidin-3-O-glucoside synthesis, modulating expression of HmF3H, HmC3'5'H, HmDFR and HmANS. This study provides insights into HmWDR68's role in hydrangea's blue flowers development, offering a foundation for further research in this field.
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Affiliation(s)
- Jingyi Gong
- College of Life Science and Technology, Central South University of Forestry & Technology, Changsha, Hunan, 410004, China
| | - Yu Wang
- College of Forestry, Central South University of Forestry & Technology, Changsha, Hunan, 410004, China
| | - Chao Xue
- College of Life Science and Technology, Central South University of Forestry & Technology, Changsha, Hunan, 410004, China
| | - Linshi Wu
- Hunan Botanical Garden, Changsha, Hunan, 410000, China
| | - Song Sheng
- College of Forestry, Central South University of Forestry & Technology, Changsha, Hunan, 410004, China
| | - Meng Wang
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650000, China
| | - Jiqing Peng
- College of Life Science and Technology, Central South University of Forestry & Technology, Changsha, Hunan, 410004, China.
| | - Shoujin Cao
- College of Forestry, Central South University of Forestry & Technology, Changsha, Hunan, 410004, China.
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10
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Zhou Y, Xu Y, Zhu GF, Tan J, Lin J, Huang L, Ye Y, Liu J. Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves. Int J Mol Sci 2024; 25:605. [PMID: 38203776 PMCID: PMC10779550 DOI: 10.3390/ijms25010605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Leaf color is a key ornamental characteristic of cultivated caladium (Caladium × hortulanum Birdsey), a plant with diverse leaf colors. However, the genetic improvement of leaf color in cultivated caladium is hindered by the limited understanding of leaf color diversity and regulation. In this study, the chlorophyll and anthocyanin content of 137 germplasm resources were measured to explore the diversity and mechanism of leaf color formation in cultivated caladium. Association analysis of EST-SSR markers and pigment traits was performed, as well as metabolomics and transcriptomics analysis of a red leaf variety and its white leaf mutant. We found significant differences in chlorophyll and anthocyanin content among different color groups of cultivated caladium, and identified three, eight, three, and seven EST-SSR loci significantly associated with chlorophyll-a, chlorophyll-b, total chlorophyll and total anthocyanins content, respectively. The results further revealed that the white leaf mutation was caused by the down-regulation of various anthocyanins (such as cyanidin-3-O-rutinoside, quercetin-3-O-glucoside, and others). This change in concentration is likely due to the down-regulation of key genes (four PAL, four CHS, six CHI, eight F3H, one F3'H, one FLS, one LAR, four DFR, one ANS and two UFGT) involved in anthocyanin biosynthesis. Concurrently, the up-regulation of certain genes (one FLS and one LAR) that divert the anthocyanin precursors to other pathways was noted. Additionally, a significant change in the expression of numerous transcription factors (12 NAC, 12 bZIP, 23 ERF, 23 bHLH, 19 MYB_related, etc.) was observed. These results revealed the genetic and metabolic basis of leaf color diversity and change in cultivated caladium, and provided valuable information for molecular marker-assisted selection and breeding of leaf color in this ornamental plant.
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Affiliation(s)
- Yiwei Zhou
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Y.Z.)
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangzhou 510642, China
| | - Yechun Xu
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Y.Z.)
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangzhou 510642, China
| | - Gen-Fa Zhu
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Y.Z.)
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangzhou 510642, China
| | - Jianjun Tan
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Y.Z.)
| | - Jingyi Lin
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Y.Z.)
| | - Lishan Huang
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Y.Z.)
| | - Yuanjun Ye
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangzhou 510642, China
| | - Jinmei Liu
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Y.Z.)
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11
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Stone BW, Wessinger CA. Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression. Mol Biol Evol 2024; 41:msae007. [PMID: 38232726 PMCID: PMC10826641 DOI: 10.1093/molbev/msae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations versus preexisting variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie the parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.
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Affiliation(s)
- Benjamin W Stone
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| | - Carolyn A Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
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12
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Stone BW, Wessinger CA. Ecological diversification in an adaptive radiation of plants: the role of de novo mutation and introgression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565185. [PMID: 37961506 PMCID: PMC10635055 DOI: 10.1101/2023.11.01.565185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations vs. pre-existing variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.
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Affiliation(s)
- Benjamin W. Stone
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| | - Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
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13
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Gayathiri E, Prakash P, Pandiaraj S, Ramasubburayan R, Gaur A, Sekar M, Viswanathan D, Govindasamy R. Investigating the ecological implications of nanomaterials: Unveiling plants' notable responses to nano-pollution. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108261. [PMID: 38096734 DOI: 10.1016/j.plaphy.2023.108261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 02/15/2024]
Abstract
The rapid advancement of nanotechnology has led to unprecedented innovations; however, it is crucial to analyze its environmental impacts carefully. This review thoroughly examines the complex relationship between plants and nanomaterials, highlighting their significant impact on ecological sustainability and ecosystem well-being. This study investigated the response of plants to nano-pollution stress, revealing the complex regulation of defense-related genes and proteins, and highlighting the sophisticated defense mechanisms in nature. Phytohormones play a crucial role in the complex molecular communication network that regulates plant responses to exposure to nanomaterials. The interaction between plants and nano-pollution influences plants' complex defense strategies. This reveals the interconnectedness of systems of nature. Nevertheless, these findings have implications beyond the plant domain. The incorporation of hyperaccumulator plants into pollution mitigation strategies has the potential to create more environmentally sustainable urban landscapes and improve overall environmental resilience. By utilizing these exceptional plants, we can create a future in which cities serve as centers of both innovation and ecological balance. Further investigation is necessary to explore the long-term presence of nanoparticles in the environment, their ability to induce genetic changes in plants over multiple generations, and their overall impact on ecosystems. In conclusion, this review summarizes significant scientific discoveries with broad implications beyond the confines of laboratories. This highlights the importance of understanding the interactions between plants and nanomaterials within the wider scope of environmental health. By considering these insights, we initiated a path towards the responsible utilization of nanomaterials, environmentally friendly management of pollution, and interdisciplinary exploration. We have the responsibility to balance scientific advancement and environmental preservation to create a sustainable future that combines nature's wisdom with human innovation.
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Affiliation(s)
- Ekambaram Gayathiri
- Department of Plant Biology and Plant Biotechnology, Guru Nanak College (Autonomous), Chennai 600042, Tamil Nadu India
| | - Palanisamy Prakash
- Department of Botany, Periyar University, Periyar Palkalai Nagar, Salem 636011, Tamil Nadu, India
| | - Saravanan Pandiaraj
- Department of Self-Development Skills, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ramasamy Ramasubburayan
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Arti Gaur
- Department of Life Sciences, Parul Institute of Applied Sciences, Parul University, Vadodara-390025, Gujarat, India
| | - Malathy Sekar
- Department of Botany, PG and Research Department of Botany Government Arts College for Men, (autonomous), Nandanam, Chennai 35, Tamilnadu, India
| | - Dhivya Viswanathan
- Centre for Nanobioscience, Department of Orthodontics, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai-600077, Tamilnadu, India
| | - Rajakumar Govindasamy
- Centre for Nanobioscience, Department of Orthodontics, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai-600077, Tamilnadu, India.
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14
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Zhao X, Li Y, Zhang MM, He X, Ahmad S, Lan S, Liu ZJ. Research advances on the gene regulation of floral development and color in orchids. Gene 2023; 888:147751. [PMID: 37657689 DOI: 10.1016/j.gene.2023.147751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/08/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023]
Abstract
Orchidaceae is one of the largest monocotyledon families and contributes significantly to worldwide biodiversity, with value in the fields of landscaping, medicine, and ecology. The diverse phenotypes and vibrant colors of orchid floral organs make them excellent research objects for investigating flower development and pigmentation. In recent years, a number of orchid genomes have been published, laying the molecular foundation for revealing flower development and color presentation. In this article, we review transcription factors, the structural genes responsible for the floral pigment synthesis pathways, the molecular mechanisms of flower morphogenesis, and the potential relationship between flower type and flower color. This study provides a theoretical reference for the research on molecular mechanisms related to flower morphogenesis and color presentation, genetic improvement, and new variety creation in orchids.
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Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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15
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Pei T, Zhu S, Liao W, Fang Y, Liu J, Kong Y, Yan M, Cui M, Zhao Q. Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis. HORTICULTURE RESEARCH 2023; 10:uhad235. [PMID: 38156283 PMCID: PMC10753160 DOI: 10.1093/hr/uhad235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/01/2023] [Indexed: 12/30/2023]
Abstract
Scutellaria baicalensis Georgi, a member of the Lamiaceae family, is a widely utilized medicinal plant. The flavones extracted from S. baicalensis contribute to numerous health benefits, including anti-inflammatory, antiviral, and anti-tumor activities. However, the incomplete genome assembly hinders biological studies on S. baicalensis. This study presents the first telomere-to-telomere (T2T) gap-free genome assembly of S. baicalensis through the integration of Pacbio HiFi, Nanopore ultra-long and Hi-C technologies. A total of 384.59 Mb of genome size with a contig N50 of 42.44 Mb was obtained, and all sequences were anchored into nine pseudochromosomes without any gap or mismatch. In addition, we analysed the major cyanidin- and delphinidin-based anthocyanins involved in the determination of blue-purple flower using a widely-targeted metabolome approach. Based on the genome-wide identification of Cytochrome P450 (CYP450) gene family, three genes (SbFBH1, 2, and 5) encoding flavonoid 3'-hydroxylases (F3'Hs) and one gene (SbFBH7) encoding flavonoid 3'5'-hydroxylase (F3'5'H) were found to hydroxylate the B-ring of flavonoids. Our studies enrich the genomic information available for the Lamiaceae family and provide a toolkit for discovering CYP450 genes involved in the flavonoid decoration.
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Affiliation(s)
- Tianlin Pei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sanming Zhu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Weizhi Liao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yumin Fang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Mengying Cui
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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16
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Zhao X, Wu Y, Zhang X, Tian F, Yu F, Li X, Huang D. Association Analysis of Transcriptome and Targeted Metabolites Identifies Key Genes Involved in Iris germanica Anthocyanin Biosynthesis. Int J Mol Sci 2023; 24:16462. [PMID: 38003651 PMCID: PMC10671556 DOI: 10.3390/ijms242216462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
The anthocyanin biosynthetic pathway is the main pathway regulating floral coloration in Iris germanica, a well-known ornamental plant. We investigated the transcriptome profiles and targeted metabolites to elucidate the relationship between genes and metabolites in anthocyanin biosynthesis in the bitone flower cultivar 'Clarence', which has a deep blue outer perianth and nearly white inner perianth. In this study, delphinidin-, pelargonidin-, and cyanidin-based anthocyanins were detected in the flowers. The content of delphinidin-based anthocyanins increased with the development of the flower. At full bloom (stage 3), delphinidin-based anthocyanins accounted for most of the total anthocyanin metabolites, whereas the content of pelargonidin- and cyanidin-based anthocyanins was relatively low. Based on functional annotations, a number of novel genes in the anthocyanin pathway were identified, which included early biosynthetic genes IgCHS, IgCHI, and IgF3H and late biosynthetic genes Ig F3'5'H, IgANS, and IgDFR. The expression of key structural genes encoding enzymes, such as IgF3H, Ig F3'5'H, IgANS, and IgDFR, was significantly upregulated in the outer perianth compared to the inner perianth. In addition, most structural genes exhibited their highest expression at the half-color stage rather than at the full-bloom stage, which indicates that these genes function ahead of anthocyanins synthesis. Moreover, transcription factors (TFs) of plant R2R3-myeloblastosis (R2R3-MYB) related to the regulation of anthocyanin biosynthesis were identified. Among 56 R2R3-MYB genes, 2 members belonged to subgroup 4, with them regulating the expression of late biosynthetic genes in the anthocyanin biosynthetic pathway, and 4 members belonged to subgroup 7, with them regulating the expression of early biosynthetic genes in the anthocyanin biosynthetic pathway. Quantitative real-time PCR (qRT-PCR) analysis was used to validate the data of RNA sequencing (RNA-Seq). The relative expression profiles of most candidate genes were consistent with the FPKM of RNA-seq. This study identified the key structural genes encoding enzymes and TFs that affect anthocyanin biosynthesis, which provides a basis and reference for the regulation of plant anthocyanin biosynthesis in I. germanica.
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Affiliation(s)
| | | | | | | | | | | | - Dazhuang Huang
- Department of Landscape Architecture, Hebei Agricultural University, 2596 Lekai South Street, Baoding 071001, China; (X.Z.); (Y.W.); (X.Z.); (F.T.); (F.Y.); (X.L.)
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17
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Partap M, Verma V, Thakur M, Bhargava B. Designing of future ornamental crops: a biotechnological driven perspective. HORTICULTURE RESEARCH 2023; 10:uhad192. [PMID: 38023473 PMCID: PMC10681008 DOI: 10.1093/hr/uhad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/14/2023] [Indexed: 12/01/2023]
Abstract
With a basis in human appreciation of beauty and aesthetic values, the new era of ornamental crops is based on implementing innovative technologies and transforming symbols into tangible assets. Recent advances in plant biotechnology have attracted considerable scientific and industrial interest, particularly in terms of modifying desired plant traits and developing future ornamental crops. By utilizing omics approaches, genomic data, genetic engineering, and gene editing tools, scientists have successively explored the underlying molecular mechanism and potential gene(s) behind trait regulation such as floral induction, plant architecture, stress resistance, plasticity, adaptation, and phytoremediation in ornamental crop species. These signs of progress lay a theoretical and practical foundation for designing and enhancing the efficiency of ornamental plants for a wide range of applications. In this review, we briefly summarized the existing literature and advances in biotechnological approaches for the improvement of vital traits in ornamental plants. The future ornamental plants, such as light-emitting plants, biotic/abiotic stress detectors, and pollution abatement, and the introduction of new ornamental varieties via domestication of wild species are also discussed.
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Affiliation(s)
- Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
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18
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Gao J, Dou Y, Wang X, Zhang D, Wei M, Li Y. Transcriptome analysis reveals the mechanism for blue-light-induced biosynthesis of delphinidin derivatives in harvested purple pepper fruit. FRONTIERS IN PLANT SCIENCE 2023; 14:1289120. [PMID: 37965026 PMCID: PMC10640979 DOI: 10.3389/fpls.2023.1289120] [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: 09/05/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023]
Abstract
Anthocyanins are the main pigments that affect the color and quality of purple-fruited sweet pepper (Capsicum annuum). Our previous study indicated that blue light can induce anthocyanin accumulation in purple pepper. In view of its underlying mechanism that is unclear, here, anthocyanin content was determined, and transcriptome analysis was performed on pepper fruits harvested from different light treatments. As a result, among the identified anthocyanin metabolites, the levels of delphinidin (Dp) glycosides, including Dp-3-O-rhamnoside, Dp-3-O-rutinoside, and Dp-3-O-glucoside, were highly accumulated in blue-light-treated fruit, which are mainly responsible for the appearance color of purple pepper. Correlation between anthocyanin content and transcriptomic analysis indicated a total of 1,619 upregulated genes were found, of which six structural and 12 transcription factor (TF) genes were involved in the anthocyanin biosynthetic pathway. Structural gene, for instance, CaUFGT as well as TFs such as CaMYC2-like and CaERF113, which were highly expressed under blue light and presented similar expression patterns consistent with Dp glycoside accumulation, may be candidate genes for anthocyanin synthesis in response to blue-light signal.
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Affiliation(s)
- Jinhui Gao
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yuwei Dou
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Xiaotong Wang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Dalong Zhang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture, Tai’an, Shandong, China
| | - Min Wei
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture, Tai’an, Shandong, China
| | - Yan Li
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture, Tai’an, Shandong, China
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19
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Sun Y, Hu P, Jiang Y, Li J, Chang J, Zhang H, Shao H, Zhou Y. Integrated Metabolome and Transcriptome Analysis of Petal Anthocyanin Accumulation Mechanism in Gloriosa superba 'Rothschildiana' during Different Flower Development Stages. Int J Mol Sci 2023; 24:15034. [PMID: 37894715 PMCID: PMC10606226 DOI: 10.3390/ijms242015034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Flower color is a key ornamental trait in plants. The petals of Gloriosa superba 'Rothschildiana' petals undergo a color transformation from yellow to red during their development, but the molecular mechanism of this process remains unexplored. This study examines the anthocyanin profiles and gene expression patterns of 'Rothschildiana' petals across four developmental stages: bud (S1), initial opening (S2), half opening (S3), and full opening stage (S4). A total of 59 anthocyanins were identified with significant increases in cyanidin-3,5-O-diglucoside, cyanidin-3-O-glucoside, pelargonidin-3-O-glucoside, and pelargonidin-3,5-O-diglucoside levels observed during petal maturation. Transcriptome analysis revealed 46 differentially expressed genes implicated in flavonoid and anthocyanin biosynthesis. Additionally, three gene modules were found to be associated with anthocyanin accumulation throughout flower development. Expression levels of genes associated with auxin, abscisic acid, brassinosteroid signaling, and transcription factors such as NACs and WRKYs underwent significant changes and exhibited strong correlations with several flavonoid and anthocyanin biosynthetic genes in these modules. These findings offer novel insights into the molecular underpinnings of flower color variation and lay the groundwork for the improvement of G. superba.
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Affiliation(s)
- Yue Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; (Y.S.); (P.H.); (Y.J.); (J.L.); (J.C.); (H.Z.)
| | - Pinli Hu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; (Y.S.); (P.H.); (Y.J.); (J.L.); (J.C.); (H.Z.)
| | - Yanan Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; (Y.S.); (P.H.); (Y.J.); (J.L.); (J.C.); (H.Z.)
| | - Jun Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; (Y.S.); (P.H.); (Y.J.); (J.L.); (J.C.); (H.Z.)
| | - Jiaxing Chang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; (Y.S.); (P.H.); (Y.J.); (J.L.); (J.C.); (H.Z.)
| | - Huihui Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; (Y.S.); (P.H.); (Y.J.); (J.L.); (J.C.); (H.Z.)
| | - Haojing Shao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; (Y.S.); (P.H.); (Y.J.); (J.L.); (J.C.); (H.Z.)
| | - Yiwei Zhou
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Ma L, Jia W, Duan Q, Du W, Li X, Cui G, Wang X, Wang J. Heterologous Expression of Platycodon grandiflorus PgF3'5'H Modifies Flower Color Pigmentation in Tobacco. Genes (Basel) 2023; 14:1920. [PMID: 37895269 PMCID: PMC10606865 DOI: 10.3390/genes14101920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
Flavonoid-3',5'-hydroxylase (F3'5'H) is the key enzyme for the biosynthesis of delphinidin-based anthocyanins, which are generally required for purple or blue flowers. Previously, we isolated a full-length cDNA of PgF3'5'H from Platycodon grandiflorus, which shared the highest homology with Campanula medium F3'5'H. In this study, PgF3'5'H was subcloned into a plant over-expression vector and transformed into tobacco via Agrobacterium tumefaciens to investigate its catalytic function. Positive transgenic tobacco T0 plants were obtained by hygromycin resistance screening and PCR detection. PgF3'5'H showed a higher expression level in all PgF3'5'H transgenic tobacco plants than in control plants. Under the drive of the cauliflower mosaic virus (CaMV) 35S promoter, the over-expressed PgF3'5'H produced dihydromyricetin (DHM) and some new anthocyanin pigments (including delphinidin, petunidin, peonidin, and malvidin derivatives), and increased dihydrokaempferol (DHK), taxifolin, tridactyl, cyanidin derivatives, and pelargonidin derivatives in PgF3'5'H transgenic tobacco plants by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis, resulting in a dramatic color alteration from light pink to magenta. These results indicate that PgF3'5'H products have F3'5'H enzyme activity. In addition, PgF3'5'H transfer alters flavonoid pigment synthesis and accumulation in tobacco. Thus, PgF3'5'H may be considered a candidate gene for gene engineering to enhance anthocyanin accumulation and the molecular breeding project for blue flowers.
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Affiliation(s)
| | | | | | | | | | | | | | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Key Lab of Yunnan Flower Breeding, National Engineering Research Center For Ornamental Horticulture, Kunming 650205, China; (L.M.); (X.L.)
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21
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Yang M, Wan S, Chen J, Chen W, Wang Y, Li W, Wang M, Guan R. Mutation to a cytochrome P 450 -like gene alters the leaf color by affecting the heme and chlorophyll biosynthesis pathways in Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:432-445. [PMID: 37421327 DOI: 10.1111/tpj.16382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/04/2023] [Accepted: 07/04/2023] [Indexed: 07/10/2023]
Abstract
The regulated biosynthesis of chlorophyll is important because of its effects on plant photosynthesis and dry biomass production. In this study, a map-based cloning approach was used to isolate the cytochrome P450 -like gene BnaC08g34840D (BnCDE1) from a chlorophyll-deficient mutant (cde1) of Brassica napus obtained by ethyl methanesulfonate (EMS) mutagenization. Sequence analyses revealed that BnaC08g34840D in the cde1 mutant (BnCDE1I320T ) encodes a substitution at amino acid 320 (Ile320Thr) in the conserved region. The over-expression of BnCDE1I320T in ZS11 (i.e., gene-mapping parent with green leaves) recapitulated a yellow-green leaf phenotype. The CRISPR/Cas9 genome-editing system was used to design two single-guide RNAs (sgRNAs) targeting BnCDE1I320T in the cde1 mutant. The knockout of BnCDE1I320T in the cde1 mutant via a gene-editing method restored normal leaf coloration (i.e., green leaves). These results indicate that the substitution in BnaC08g34840D alters the leaf color. Physiological analyses showed that the over-expression of BnCDE1I320T leads to decreases in the number of chloroplasts per mesophyll cell and in the contents of the intermediates of the chlorophyll biosynthesis pathway in leaves, while it increases heme biosynthesis, thereby lowering the photosynthetic efficiency of the cde1 mutant. The Ile320Thr mutation in the highly conserved region of BnaC08g34840D inhibited chlorophyll biosynthesis and disrupted the balance between heme and chlorophyll biosynthesis. Our findings may further reveal how the proper balance between the chlorophyll and heme biosynthesis pathways is maintained.
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Affiliation(s)
- Mao Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shubei Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenjing Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yangming Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiyan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Meihong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongzhan Guan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
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22
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Li J, Jiang S, Yang G, Xu Y, Li L, Yang F. RNA-sequencing analysis reveals novel genes involved in the different peel color formation in eggplant. HORTICULTURE RESEARCH 2023; 10:uhad181. [PMID: 37885819 PMCID: PMC10599318 DOI: 10.1093/hr/uhad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/26/2023] [Indexed: 10/28/2023]
Abstract
Eggplant (Solanum melongena L.) is a highly nutritious vegetable. Here, the molecular mechanism of color formation in eggplants was determined using six eggplant cultivars with different peel colors and two SmMYB113-overexpressing transgenic eggplants with a purple peel and pulp. Significant differentially expressed genes (DEGs) were identified by RNA-sequencing analysis using the following criteria: log2(sample1/sample2) ≥ 0.75 and q-value ≤ 0.05. Two analytical strategies were used to identify genes related to the different peel color according to the peel color, flavonoids content, delphinidins/flavonoids ratio, and the content of anthocyanins. Finally, 27 novel genes were identified to be related to the color difference among eggplant peels and 32 novel genes were identified to be related to anthocyanin biosynthesis and regulated by SmMYB113. Venn analysis revealed that SmCytb5, SmGST, SmMATE, SmASAT3, and SmF3'5'M were shared among both sets of novel genes. Transient expression assay in tobacco suggested that these five genes were not sufficient for inducing anthocyanin biosynthesis alone, but they play important roles in anthocyanin accumulation in eggplant peels. Yeast one-hybrid, electrophoretic mobility shift assay and dual-luciferase assays indicated that the expression of the five genes could be directly activated by SmMYB113 protein. Finally, a regulatory model for the mechanism of color formation in eggplant was proposed. Overall, the results of this study provide useful information that enhances our understanding of the molecular mechanism underlying the different color formation in eggplant.
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Affiliation(s)
- Jing Li
- College of Horticulture Science and Engineering, Shandong Agricultural University/State Key Laboratory of Crop Biology, Tai’an, Shandong 271018, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture and Rural Affairs, Tai’an, Shandong 271018, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Senlin Jiang
- College of Horticulture Science and Engineering, Shandong Agricultural University/State Key Laboratory of Crop Biology, Tai’an, Shandong 271018, China
| | - Guobin Yang
- College of Horticulture Science and Engineering, Shandong Agricultural University/State Key Laboratory of Crop Biology, Tai’an, Shandong 271018, China
| | - Yanwei Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University/State Key Laboratory of Crop Biology, Tai’an, Shandong 271018, China
| | - Lujun Li
- College of Horticulture Science and Engineering, Shandong Agricultural University/State Key Laboratory of Crop Biology, Tai’an, Shandong 271018, China
| | - Fengjuan Yang
- College of Horticulture Science and Engineering, Shandong Agricultural University/State Key Laboratory of Crop Biology, Tai’an, Shandong 271018, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture and Rural Affairs, Tai’an, Shandong 271018, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, Tai’an, Shandong 271018, China
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Li Y, Zhao X, Zhang MM, He X, Huang Y, Ahmad S, Liu ZJ, Lan S. Genome-based identification of the CYP75 gene family in Orchidaceae and its expression patterns in Cymbidium goeringii. FRONTIERS IN PLANT SCIENCE 2023; 14:1243828. [PMID: 37828920 PMCID: PMC10564990 DOI: 10.3389/fpls.2023.1243828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
With a great diversity of species, Orchidaceae stands out as an essential component of plant biodiversity, making it a primary resource for studying angiosperms evolution and genomics. This study focuses on 13 published orchid genomes to identify and analyze the CYP75 gene family belonging to the cytochrome P450 superfamily, which is closely related to flavonoid biosynthetic enzymes and pigment regulation. We found 72 CYP75s in the 13 orchid genomes and further classified them into two classes: CYP75A and CYP75B subfamily, the former synthesizes blue anthocyanins, while the latter is involved in the production of red anthocyanins. Furthermore, the amount of CYP75Bs (53/72) greatly exceeds the amount of CYP75As (19/72) in orchids. Our findings suggest that CYP75B genes have a more important evolutionary role, as red plants are more common in nature than blue plants. We also discovered unique conserved motifs in each subfamily that serve as specific recognition features (motif 19 belong to CYP75A; motif 17 belong to CYP75B). Two diverse-colored varieties of C. goeringii were selected for qRT-PCR experiments. The expression of CgCYP75B1 was significantly higher in the purple-red variant compared to the yellow-green variant, while CgCYP75A1 showed no significant difference. Based on transcriptomic expression analysis, CYP75Bs are more highly expressed than CYP75As in floral organs, especially in colorful petals and lips. These results provide valuable information for future studies on CYP75s in orchids and other angiosperms.
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Affiliation(s)
- Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Huang
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Admini stration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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Zhu Z, Zeng X, Shi X, Ma J, Liu X, Li Q. Transcription and Metabolic Profiling Analysis of Three Discolorations in a Day of Hibiscus mutabilis. BIOLOGY 2023; 12:1115. [PMID: 37626999 PMCID: PMC10452391 DOI: 10.3390/biology12081115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
In this study, we used combined transcriptomics and metabolomics to analyze the H. mutabilis cultivar's genetic and physiological mechanisms during three flower color transition periods (from white to pink, then from pink to red) within the span of one day. As a result, 186 genes were found to be significantly increased with the deepening of the H. mutabilis flower color; these genes were mainly involved in the expression of peroxidase 30, zinc finger protein, phosphate transporter PHO1, etc. In contrast, 298 genes were significantly downregulated with the deepening of H. mutabilis flower color, including those involved in the expression of probable O-methyltransferase 3, copper binding protein 9, and heat stress transcription factor A-6b. Some genes showed differential expression strategies as the flower color gradually darkened. We further detected 19 metabolites that gradually increased with the deepening of the H. mutabilis flower color, including L-isoleucine, palmitic acid, L-methionine, and (+)-7-isonitrobenzene. The content of the metabolite hexadecanedioate decreased with the deepening of the H. mutabilis flower color. Combined transcriptomics and metabolomics revealed that the metabolic pathways, including those related to anthocyanin biosynthesis, cysteine and methionine metabolism, and sulfur metabolism, appear to be closely related to H. mutabilis flower color transition. This study served as the first report on the genetic and physiological mechanisms of short-term H. mutabilis flower color transition and will promote the molecular breeding of ornamental cultivars of H. mutabilis.
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Affiliation(s)
- Zhangshun Zhu
- Chengdu Botanical Garden (Chengdu Park Urban Plant Science Research Institute), Chengdu 610083, China; (Z.Z.); (X.Z.); (X.S.); (J.M.)
| | - Xinmei Zeng
- Chengdu Botanical Garden (Chengdu Park Urban Plant Science Research Institute), Chengdu 610083, China; (Z.Z.); (X.Z.); (X.S.); (J.M.)
| | - Xiaoqing Shi
- Chengdu Botanical Garden (Chengdu Park Urban Plant Science Research Institute), Chengdu 610083, China; (Z.Z.); (X.Z.); (X.S.); (J.M.)
| | - Jiao Ma
- Chengdu Botanical Garden (Chengdu Park Urban Plant Science Research Institute), Chengdu 610083, China; (Z.Z.); (X.Z.); (X.S.); (J.M.)
| | - Xiaoli Liu
- Chengdu Botanical Garden (Chengdu Park Urban Plant Science Research Institute), Chengdu 610083, China; (Z.Z.); (X.Z.); (X.S.); (J.M.)
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
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25
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Jiang H, Zhang X, Leng L, Gong D, Zhang X, Liu J, Peng D, Wu Z, Yang Y. A chromosome-scale and haplotype-resolved genome assembly of carnation ( Dianthus caryophyllus) based on high-fidelity sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1230836. [PMID: 37600187 PMCID: PMC10437072 DOI: 10.3389/fpls.2023.1230836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
Dianthus caryophyllus is an economic species often considered excellent cut flowers and is suitable for bouquets and gardens. Here, we assembled the haplotype-resolved genome of D. caryophyllus 'Aili' at the chromosome level for the first time. The total lengths of the two assembled haplotypes of carnation were 584.88 Mb for haplotype genome 1 (hap1) and 578.78 Mb for haplotype genome 2 (hap2), respectively. We predicted a total of 44,098 and 42,425 protein-coding genes, respectively. The remarkable structure variation was identified between two haplotypes. Moreover, we identified 403.80 Mb of transposable elements (TEs) in hap1, which accounted for 69.34% of the genome. In contrast, hap2 had 402.70 Mb of TEs, representing 69.61% of the genome. Long terminal repeats were the predominant transposable elements. Phylogenetic analysis showed that the species differentiation time between carnation and gypsophila was estimated to be ~54.43 MYA. The unique gene families of carnation genomes were identified in 'Aili' and previously published 'Francesco' and 'Scarlet Queen'. The assembled and annotated haplotype-resolved D. caryophyllus genome not only promises to facilitate molecular biology studies but also contributes to genome-level evolutionary studies.
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Affiliation(s)
- Heling Jiang
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoni Zhang
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Luhong Leng
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Desheng Gong
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaohui Zhang
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junyang Liu
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Dan Peng
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Zhiqiang Wu
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yingxue Yang
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Jiang J, Huang H, Gao Q, Li Y, Xiang H, Zeng W, Xu L, Liu X, Li J, Mi Q, Deng L, Yang W, Zhang J, Yang G, Li X. Effects of editing DFR genes on flowers, leaves, and roots of tobacco. BMC PLANT BIOLOGY 2023; 23:349. [PMID: 37407922 DOI: 10.1186/s12870-023-04307-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND DFR is a crucial structural gene in plant flavonoid and polyphenol metabolism, and DFR knockout (DFR-KO) plants may have increased biomass accumulation. It is uncertain whether DFR-KO has comparable effects in tobacco and what the molecular mechanism is. We employed the CRISPR/Cas9 method to generate a knockout homozygous construct and collected samples from various developmental phases for transcriptome and metabolome detection and analysis. RESULTS DFR-KO turned tobacco blossoms white on homozygous tobacco (Nicotiana tabacum) plants with both NtDFR1 and NtDFR2 knockout. RNA-seq investigation of anthesis leaf (LF), anthesis flower (FF), mature leaf (LM), and mature root (RM) variations in wild-type (CK) and DFR-KO lines revealed 2898, 276, 311, and 101 differentially expressed genes (DEGs), respectively. DFR-KO primarily affected leaves during anthesis. According to KEGG and GSEA studies, DFR-KO lines upregulated photosynthetic pathway carbon fixation and downregulated photosystem I and II genes. DFR-KO may diminish tobacco anthesis leaf photosynthetic light reaction but boost dark reaction carbon fixation. DFR-KO lowered the expression of pathway-related genes in LF, such as oxidative phosphorylation and proteasome, while boosting those in the plant-pathogen interaction and MAPK signaling pathways, indicating that it may increase biological stress resistance. DFR-KO greatly boosted the expression of other structural genes involved in phenylpropanoid production in FF, which may account for metabolite accumulation. The metabolome showed that LF overexpressed 8 flavonoid metabolites and FF downregulated 24 flavone metabolites. In DFR-KO LF, proteasome-related genes downregulated 16 amino acid metabolites and reduced free amino acids. Furthermore, the DEG analysis on LM revealed that the impact of DFR-KO on tobacco growth may progressively diminish with time. CONCLUSION The broad impact of DFR-KO on different phases and organs of tobacco development was thoroughly and methodically investigated in this research. DFR-KO decreased catabolism and photosynthetic light reactions in leaves during the flowering stage while increasing carbon fixation and disease resistance pathways. However, the impact of DFR-KO on tobacco growth steadily declined as it grew and matured, and transcriptional and metabolic modifications were consistent. This work offers a fresh insight and theoretical foundation for tobacco breeding and the development of gene-edited strains.
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Affiliation(s)
- Jiarui Jiang
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Haitao Huang
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Qian Gao
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Yong Li
- Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, 210014, Jiangsu Province, China
| | - Haiying Xiang
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Wanli Zeng
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Li Xu
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Xin Liu
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Jing Li
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Qili Mi
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Lele Deng
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Wenwu Yang
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Jianduo Zhang
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Guangyu Yang
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China
| | - Xuemei Li
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, No. 181 Hongjin Road, Kunming, 650000, Yunnan Province, China.
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27
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Kang Y, Choi C, Kim JY, Min KD, Kim C. Optimizing genomic selection of agricultural traits using K-wheat core collection. FRONTIERS IN PLANT SCIENCE 2023; 14:1112297. [PMID: 37389296 PMCID: PMC10303932 DOI: 10.3389/fpls.2023.1112297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/02/2023] [Indexed: 07/01/2023]
Abstract
The agricultural traits that constitute basic plant breeding information are usually quantitative or complex in nature. This quantitative and complex combination of traits complicates the process of selection in breeding. This study examined the potential of genome-wide association studies (GWAS) and genomewide selection (GS) for breeding ten agricultural traits by using genome-wide SNPs. As a first step, a trait-associated candidate marker was identified by GWAS using a genetically diverse 567 Korean (K)-wheat core collection. The accessions were genotyped using an Axiom® 35K wheat DNA chip, and ten agricultural traits were determined (awn color, awn length, culm color, culm length, ear color, ear length, days to heading, days to maturity, leaf length, and leaf width). It is essential to sustain global wheat production by utilizing accessions in wheat breeding. Among the traits associated with awn color and ear color that showed a high positive correlation, a SNP located on chr1B was significantly associated with both traits. Next, GS evaluated the prediction accuracy using six predictive models (G-BLUP, LASSO, BayseA, reproducing kernel Hilbert space, support vector machine (SVM), and random forest) and various training populations (TPs). With the exception of the SVM, all statistical models demonstrated a prediction accuracy of 0.4 or better. For the optimization of the TP, the number of TPs was randomly selected (10%, 30%, 50% and 70%) or divided into three subgroups (CC-sub 1, CC-sub 2 and CC-sub 3) based on the subpopulation structure. Based on subgroup-based TPs, better prediction accuracy was found for awn color, culm color, culm length, ear color, ear length, and leaf width. A variety of Korean wheat cultivars were used for validation to evaluate the prediction ability of populations. Seven out of ten cultivars showed phenotype-consistent results based on genomics-evaluated breeding values (GEBVs) calculated by the reproducing kernel Hilbert space (RKHS) predictive model. Our research provides a basis for improving complex traits in wheat breeding programs through genomics assisted breeding. The results of our research can be used as a basis for improving wheat breeding programs by using genomics-assisted breeding.
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Affiliation(s)
- Yuna Kang
- Department of Crop Science, Chungnam National University, Daejeon, Republic of Korea
| | - Changhyun Choi
- Wheat Research Team, National Institution Crop Sciences, Wanju-gun, Republic of Korea
| | - Jae Yoon Kim
- Department of Plant Resources, Kongju National University, Yesan, Republic of Korea
| | - Kyeong Do Min
- Department of Plant Resources, Kongju National University, Yesan, Republic of Korea
| | - Changsoo Kim
- Department of Crop Science, Chungnam National University, Daejeon, Republic of Korea
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon, Republic of Korea
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Kapoor P, Sharma S, Tiwari A, Kaur S, Kumari A, Sonah H, Goyal A, Krishania M, Garg M. Genome–Transcriptome Transition Approaches to Characterize Anthocyanin Biosynthesis Pathway Genes in Blue, Black and Purple Wheat. Genes (Basel) 2023; 14:genes14040809. [PMID: 37107567 PMCID: PMC10137985 DOI: 10.3390/genes14040809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Colored wheat has gained enormous attention from the scientific community, but the information available on the anthocyanin biosynthetic genes is very minimal. The study involved their genome-wide identification, in silico characterization and differential expression analysis among purple, blue, black and white wheat lines. The recently released wheat genome mining putatively identified eight structural genes in the anthocyanin biosynthesis pathway with a total of 1194 isoforms. Genes showed distinct exon architecture, domain profile, regulatory elements, chromosome emplacement, tissue localization, phylogeny and synteny, indicative of their unique function. RNA sequencing of developing seeds from colored (black, blue and purple) and white wheats identified differential expressions in 97 isoforms. The F3H on group two chromosomes and F3′5′H on 1D chromosomes could be significant influencers in purple and blue color development, respectively. Apart from a role in anthocyanin biosynthesis, these putative structural genes also played an important role in light, drought, low temperature and other defense responses. The information can assist in targeted anthocyanin production in the wheat seed endosperm.
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Wen S, Li N, Song S, Liu N, Ding Y. Comparative Transcriptome and Metabolome Analyses of Broccoli Germplasms with Purple and Green Curds Reveal the Structural Genes and Transitional Regulators Regulating Color Formation. Int J Mol Sci 2023; 24:ijms24076115. [PMID: 37047084 PMCID: PMC10094742 DOI: 10.3390/ijms24076115] [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: 03/06/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Owing to the high anthocyanin content, broccoli varieties with purple curds have become more popular in food inventories, while the genetic mechanisms of anthocyanin biosynthesis pathways remain largely unknown. We bred a pair of near-isogenic lines (NILs), GB767 and PB767, whose curds exhibited green and purple colors, respectively, due to the purple sepals of florets. RNA sequencing and widely targeted metabolic analyses were conducted. Compared with GB767, eighteen anthocyanin biosynthesis-related genes exhibited significantly higher expressions in PB767, and in turn, the expression level of BolMYBL2.1 was attenuated. A comparison of the metabolites in the flavonoid biosynthetic pathways revealed 142 differentially accumulated metabolites, among which higher content of anthocyanins was responsible for the purple color of PB767. Interestingly, the total cyanidin contents were similar between the curds of NILs, whereas total delphinidin contents were increased by more than 170 times in purple curds, presumably due to a non-canonical F3'H/CYP75B gene, BolC02g015480.2J, with elevated expression in PB767. Furthermore, correlation analysis further confirmed that the identified nineteen DEGs were significantly correlated with seven differentially accumulated anthocyanins in PB767. Together, these results identified the metabolic factors and genes that contribute to the purplish curds, which could lay foundations for the breeding programs of purple broccoli.
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Affiliation(s)
- Shaozhe Wen
- Beijing Vegetable Research Center (National Engineering Research Center for Vegetables), Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Ning Li
- Beijing Vegetable Research Center (National Engineering Research Center for Vegetables), Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
- Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Shuhui Song
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Ning Liu
- Beijing Vegetable Research Center (National Engineering Research Center for Vegetables), Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
- Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Yunhua Ding
- Beijing Vegetable Research Center (National Engineering Research Center for Vegetables), Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
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Negi S, Tak H, Madari S, Bhakta S, Ganapathi TR. Functional characterization of 5'-regulatory region of flavonoid 3',5'-hydroxylase-1 gene of banana plants. PROTOPLASMA 2023; 260:391-403. [PMID: 35727420 DOI: 10.1007/s00709-022-01785-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Generation of crops with broad-spectrum tolerance to biotic and abiotic stress conditions depends upon availability of genetic elements suitable for varied situations and diverse genotypes. Here, we characterize the 5'-upstream regulatory region of flavonoid 3'5'-hydroxylase-1 (F3'5'H-1) gene from banana and analyzed its tissue-specific and stress-mediated activation in genetic background of tobacco plants. MusaF3'5'H-1 is a stress-responsive gene as its expression is induced in banana after application of salicylic acid and methyl jasmonate while its transcript levels were drastically reduced in response to drought, high salinity and abscisic acid. PMusaF3'5'H-1 harbours cis-elements associated with stress conditions and those responsible for tissue-specific expression. Transgenic lines harbouring PMusaF3'5'H-1-GUS displays strong GUS expression in guard cells of stomata indicating guard cell preferred activity of PMusaF3'5'H-1 while its activity was undetectable in roots. Drought and high salinity induce strong expression of GUS in transgenic tobacco lines and exposure to abscisic acid, salicylic acid and methyl jasmonate revealed distinct profiles of GUS expression in transgenic lines confirming involvement of F3'5'H-1 in plant stress responses. Fluorescent β-galactosidase assay revealed induction profiles of PMusaF3'5'H-1 at different time points in transgenic lines exposed to salicylic acid and abscisic acid while strong suppression in GUS expression was observed after application of methyl jasmonate. The guard cell preferred activity of PMusaF3'5'H-1 and stress-mediated expression profiles of MusaF3'5'H-1 indicated the suitability of PMusaF3'5'H-1 for generating stress-enduring crops and analyzing guard cell functions.
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Affiliation(s)
- Sanjana Negi
- Department of Biotechnology, University of Mumbai, Mumbai, 400098, India
| | - Himanshu Tak
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India.
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
| | - Steffi Madari
- Department of Biotechnology, University of Mumbai, Mumbai, 400098, India
| | - Subham Bhakta
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - T R Ganapathi
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
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Jiang SH, Wang HH, Zhang R, Yang ZY, He GR, Ming F. Transcriptomic-based analysis to identify candidate genes for blue color rose breeding. PLANT MOLECULAR BIOLOGY 2023; 111:439-454. [PMID: 36913074 DOI: 10.1007/s11103-023-01337-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Analysis of the flower color formation mechanism of 'Rhapsody in Blue' by BF and WF transcriptomes reveals that RhF3'H and RhGT74F2 play a key role in flower color formation. Rosa hybrida has colorful flowers and a high ornamental value. Although rose flowers have a wide range of colors, no blue roses exist in nature, and the reason for this is unclear. In this study, the blue-purple petals (BF) of the rose variety 'Rhapsody in Blue' and the white petals (WF) of its natural mutant were subjected to transcriptome analysis to find genes related to the formation of the blue-purple color. The results showed that the anthocyanin content was significantly higher in BF than in WF. A total of 1077 differentially expressed genes (DEGs) were detected by RNA-Seq analysis, of which 555 were up-regulated and 522 were down-regulated in the WF vs. BF petals. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the DEGs revealed that a single gene up-regulated in BF was related to multiple metabolic pathways including metabolic process, cellular process, protein-containing complex, etc. Additionally, the transcript levels of most of the structural genes related to anthocyanin synthesis were significantly higher in BF than in WF. Selected genes were analyzed by qRT-PCR and the results were highly consistent with the RNA-Seq results. The functions of RhF3'H and RhGT74F2 were verified by transient overexpression analyses, and the results confirmed that both affect the accumulation of anthocyanins in 'Rhapsody in Blue'. We have obtained comprehensive transcriptome data for the rose variety 'Rhapsody in Blue'. Our results provide new insights into the mechanisms underlying rose color formation and even blue rose formation.
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Affiliation(s)
- Sheng-Hang Jiang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Huan-Huan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Ren Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Zhen-Yu Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Guo-Ren He
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Feng Ming
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
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Fan M, Li X, Zhang Y, Yang M, Wu S, Yin H, Liu W, Fan Z, Li J. Novel insight into anthocyanin metabolism and molecular characterization of its key regulators in Camellia sasanqua. PLANT MOLECULAR BIOLOGY 2023; 111:249-262. [PMID: 36371768 DOI: 10.1007/s11103-022-01324-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Flower color is a trait that affects the ornamental value of a plant. Camellia sasanqua is a horticultural plant with rich flower color, but little is known about the regulatory mechanism of color diversity in this plant. Here, the anthocyanin profile of 20 C. sasanqua cultivars revealed and quantified 11 anthocyanin derivatives (five delphinidin-based and six cyanidin-based anthocyanins) for the first time. Cyanidin-3-O-(6-O-(E)-p-coumaroyl)-glucoside was the main contributor to flower base color, and the accumulation of cyanidin and delphinidin derivatives differed in the petals. To further explore the molecular mechanism of color divergence, a transcriptome analysis was performed using C. sasanqua cultivars 'YingYueYe', 'WanXia', 'XueYueHua', and'XiaoMeiGui'. The co-expression network related to differences in delphinidin and cyanidin derivatives accumulation was identified. Eleven candidate genes encoding key enzymes (e.g., F3H, F3'H, and ANS) were involved in anthocyanin biosynthesis. Moreover, 27 transcription factors were screened as regulators of the two types of accumulating anthocyanins. The association was suggested by correlation analysis between the expression levels of the candidate genes and the different camellia cultivars. We concluded that cyanidin and delphinidin derivatives are the major drivers of color diversity in C. sasanqua. This finding provides valuable resources for the study of flower color in C. sasanqua and lays a foundation for genetic modification of anthocyanin biosynthesis.
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Affiliation(s)
- Menglong Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - XinLei Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
| | - Ying Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Meiying Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Si Wu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - HengFu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - WeiXin Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - ZhengQi Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - JiYuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
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Xiong Y, He J, Li M, Du K, Lang H, Gao P, Xie Y. Integrative Analysis of Metabolome and Transcriptome Reveals the Mechanism of Color Formation in Yellow-Fleshed Kiwifruit. Int J Mol Sci 2023; 24:ijms24021573. [PMID: 36675098 PMCID: PMC9867141 DOI: 10.3390/ijms24021573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
During the development of yellow-fleshed kiwifruit (Actinidia chinensis), the flesh appeared light pink at the initial stage, the pink faded at the fastest growth stage, and gradually changed into green. At the maturity stage, it showed bright yellow. In order to analyze the mechanism of flesh color change at the metabolic and gene transcription level, the relationship between color and changes of metabolites and key enzyme genes was studied. In this study, five time points (20 d, 58 d, 97 d, 136 d, and 175 d) of yellow-fleshed kiwifruit were used for flavonoid metabolites detection and transcriptome, and four time points (20 d, 97 d, 136 d, and 175 d) were used for targeted detection of carotenoids. Through the analysis of the content changes of flavonoid metabolites, it was found that the accumulation of pelargonidin and cyanidin and their respective anthocyanin derivatives was related to the pink flesh of young fruit, but not to delphinidin and its derivative anthocyanins. A total of 140 flavonoid compounds were detected in the flesh, among which anthocyanin and 76% of the flavonoid compounds had the highest content at 20 d, and began to decrease significantly at 58 d until 175 d, resulting in the pale-pink fading of the flesh. At the mature stage of fruit development (175 d), the degradation of chlorophyll and the increase of carotenoids jointly led to the change of flesh color from green to yellow, in addition to chlorophyll degradation. In kiwifruit flesh, 10 carotenoids were detected, with none of them being linear carotenoids. During the whole development process of kiwifruit, the content of β-carotene was always higher than that of α-carotene. In addition, β-cryptoxanthin was the most-accumulated pigment in the kiwifruit at 175 d. Through transcriptome analysis of kiwifruit flesh, seven key transcription factors for flavonoid biosynthesis and ten key transcription factors for carotenoid synthesis were screened. This study was the first to analyze the effect of flavonoid accumulation on the pink color of yellow-fleshed kiwifruit. The high proportion of β-cryptoxanthin in yellow-fleshed kiwifruit was preliminarily found. This provides information on metabolite accumulation for further revealing the pink color of yellow-fleshed kiwifruit, and also provides a new direction for the study of carotenoid biosynthesis and regulation in yellow-fleshed kiwifruit.
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Affiliation(s)
- Yun Xiong
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Junya He
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Mingzhang Li
- Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu 610065, China
| | - Kui Du
- Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu 610065, China
| | - Hangyu Lang
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Ping Gao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yue Xie
- Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu 610065, China
- Correspondence:
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Zhang X, Wang J, Li P, Sun C, Dong W. Integrative metabolome and transcriptome analyses reveals the black fruit coloring mechanism of Crataegus maximowiczii C. K. Schneid. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:111-121. [PMID: 36399912 DOI: 10.1016/j.plaphy.2022.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Crataegus is an economically important plant due to its medicinal and health-promoting properties. Flavonoids are the main functional components of Crataegus fruit. Fruits of naturally pollinated Crataegus maximowiczii possess an extraordinary black skin and are rich in anthocyanins and other flavonoids. However, the composition of anthocyanins and the overall molecular mechanism of anthocyanin biosynthesis in C. maximowiczii fruits have not been fully elucidated. In this study, the metabolome and transcriptome of C. maximowiczii fruits with black and red skin were analyzed. The results revealed that the differential metabolites and genes were enriched in the anthocyanin biosynthesis pathways in C. maximowiczii fruits. In total, 52 differentially accumulated flavonoid metabolites, 12 differentially accumulated anthocyanins and 22 differentially expressed genes were identified. After weighted gene coexpression network analysis, two modules were found to be highly interrelated with the accumulation of anthocyanin components. The coexpression networks of these two modules were used to identify key candidate transcription factors associated with anthocyanin biosynthesis, such as MYB5, MYB113, bHLH60, ERF105, bZIP44, NAC082, and WRKY11. The results revealed that cyanidin-based anthocyanins were the main pigments responsible for the black coloration of C. maximowiczii fruits. Based on these differentially accumulated anthocyanins and key genes, genetic and metabolic regulatory networks of anthocyanin biosynthesis were also proposed. Overall, this study elucidates the molecular basis of the formation of black color in C. maximowiczii fruits, and provides an intensive study on anthocyanin biosynthesis in C. maximowiczii for comprehensive utilization.
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Affiliation(s)
- Xiao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jian Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Peihao Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Chao Sun
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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Qin S, Liu Y, Cui B, Cheng J, Liu S, Liu H. Isolation and functional diversification of dihydroflavonol 4-Reductase gene HvDFR from Hosta ventricosa indicate its role in driving anthocyanin accumulation. PLANT SIGNALING & BEHAVIOR 2022; 17:2010389. [PMID: 34951328 PMCID: PMC8967398 DOI: 10.1080/15592324.2021.2010389] [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: 10/11/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 06/14/2023]
Abstract
Anthocyanins are natural colorants are synthesized in a branch of the flavonoid pathway. Dihydroflavonol-4reductase (DFR) catalyzes dihydroflavonoids into anthocyanins biosynthesis, which is a key regulatory enzyme of anthocyanin biosynthesis in plants. Hosta ventricosa is an ornamental plant with elegant flowers and rich colorful leaves. How the function of HvDFR contributes to the anthocyanins biosynthesis is still unknown. In this study, the DFR homolog was identified from H. ventricosa and sequence analysis showed that HvDFR possessed the conserved NADPH binding and catalytic domains. A phylogenetic analysis showed that HvDFR was close to the clade formed with MaDFR and HoDFR in Asparagaceae. Gene expression analysis revealed that HvDFR was constitutive expressed in all tissues and expressed highly in flower as well as was positively correlated with anthocyanin content. In addition, the subcellular location of HvDFR showed that is in the nucleus and cell membrane. Overexpression of HvDFR in transgenic tobacco lines enhanced the anthocyanins accumulation along with the key genes upregulated, such as F3H, F3'H, ANS, and UFGT. Our results indicated a functional activity of the HvDFR, which provide an insight into the regulation of anthocyanins content in H. ventricosa.
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Affiliation(s)
- Shijie Qin
- College of Life Sciences, Jilin Agricultural University, Changchun, P.R. China
| | - Yitong Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, P.R. China
| | - Baiqi Cui
- College of Life Sciences, Jilin Agricultural University, Changchun, P.R. China
| | - Jianlin Cheng
- College of Life Sciences, Jilin Agricultural University, Changchun, P.R. China
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, P.R. China
| | - Hongzhang Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, P.R. China
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Zhu L, Wen J, Ma Q, Yan K, Du Y, Chen Z, Lu X, Ren J, Wang Y, Li S, Li Q. Transcriptome profiling provides insights into leaf color changes in two Acer palmatum genotypes. BMC PLANT BIOLOGY 2022; 22:589. [PMID: 36526968 PMCID: PMC9756493 DOI: 10.1186/s12870-022-03979-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ornamental trees with seasonally-dependent leaf color, such as Acer palmatum, have gained worldwide popularity. Leaf color is a main determinant of the ornamental and economic value of A. palmatum. However, the molecular mechanisms responsible for leaf color changes remain unclear. RESULTS We chose A. palmatum cultivars with yellow ('Jinling Huangfeng') and red ('Jinling Danfeng') leaves as the ideal material for studying the complex metabolic networks responsible for variations in leaf coloration. The 24 libraries obtained from four different time points in the growth of 'Jinling Huangfeng' and 'Jinling Danfeng' was subjected to Illumina high-throughput sequencing. We observed that the difference in cyanidin and delphinidin content is the primary reason behind the varying coloration of the leaves. Transcriptomic analyses revealed 225,684 unigenes, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes (DEGs) confirmed that they were involved in 'anthocyanin biosynthesis.' Eighteen structural genes involved in anthocyanin biosynthesis were thought to be related to anthocyanin accumulation, whereas 46 MYBs, 33 basic helix-loop-helixs (bHLHs), and 29 WD40s were presumed to be involved in regulating anthocyanin biosynthesis. Based on weighted gene co-expression network analysis (WGCNA), three candidate genes (ApRHOMBOID, ApMAPK, and ApUNE10) were screened in the significant association module with a correlation coefficient (r2) of 0.86. CONCLUSION In this study, the leaf color changes of two A. palmatum genotypes were analyzed. These findings provide novel insights into variations in leaf coloration and suggest pathways for targeted genetic improvements in A. palmatum.
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Affiliation(s)
- Lu Zhu
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, 210014 Nanjing, Jiangsu China
| | - Jing Wen
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, 210014 Nanjing, Jiangsu China
| | - Qiuyue Ma
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, 210014 Nanjing, Jiangsu China
| | - Kunyuan Yan
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, 210014 Nanjing, Jiangsu China
| | - Yiming Du
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, 210014 Nanjing, Jiangsu China
| | - Zhu Chen
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, 40 Nongke South Road, 230031 Hefei, Anhui China
| | - Xiaoyu Lu
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, 40 Nongke South Road, 230031 Hefei, Anhui China
| | - Jie Ren
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, 40 Nongke South Road, 230031 Hefei, Anhui China
| | - Yuelan Wang
- Chenshi Maples Nursery, 313308 Longba Village, Huzhou, Zhejiang China
| | - Shushun Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, 210014 Nanjing, Jiangsu China
| | - Qianzhong Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, 210014 Nanjing, Jiangsu China
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Comparative Transcriptome Analysis Unveils the Molecular Mechanism Underlying Sepal Colour Changes under Acidic pH Substratum in Hydrangea macrophylla. Int J Mol Sci 2022; 23:ijms232315428. [PMID: 36499756 PMCID: PMC9739076 DOI: 10.3390/ijms232315428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The hydrangea (Hydrangea macrophylla (Thunb). Ser.), an ornamental plant, has good marketing potential and is known for its capacity to change the colour of its inflorescence depending on the pH of the cultivation media. The molecular mechanisms causing these changes are still uncertain. In the present study, transcriptome and targeted metabolic profiling were used to identify molecular changes in the RNAome of hydrangea plants cultured at two different pH levels. De novo assembly yielded 186,477 unigenes. Transcriptomic datasets provided a comprehensive and systemic overview of the dynamic networks of the gene expression underlying flower colour formation in hydrangeas. Weighted analyses of gene co-expression network identified candidate genes and hub genes from the modules linked closely to the hyper accumulation of Al3+ during different stages of flower development. F3'5'H, ANS, FLS, CHS, UA3GT, CHI, DFR, and F3H were enhanced significantly in the modules. In addition, MYB, bHLH, PAL6, PAL9, and WD40 were identified as hub genes. Thus, a hypothesis elucidating the colour change in the flowers of Al3+-treated plants was established. This study identified many potential key regulators of flower pigmentation, providing novel insights into the molecular networks in hydrangea flowers.
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Hübner K. Put the Blue Genes on. CHEM UNSERER ZEIT 2022. [DOI: 10.1002/ciuz.202200018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Qian J, Jiang L, Qing H, Chen J, Wan Z, Xu M, Fu J, Zhang C. ZeMYB9 regulates cyanidin synthesis by activating the expression of flavonoid 3'-hydroxylase gene in Zinnia elegans. FRONTIERS IN PLANT SCIENCE 2022; 13:981086. [PMID: 36330274 PMCID: PMC9623174 DOI: 10.3389/fpls.2022.981086] [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: 06/29/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Petal color in Zinnia elegans is characterized mainly by anthocyanin accumulation. The difference in the content of anthocyanins, especially cyanidins, affects petal coloration in Z. elegans, but the underlying regulatory mechanism remains elusive. Here, we report one R2R3-MYB transcription factor from subgroup 6, ZeMYB9, acting as a positive regulator of anthocyanin accumulation in Z. elegans. Up-regulated expression of ZeMYB9 and flavonoid 3'-hydroxylase gene (ZeF3'H) was detected in the cultivar with higher cyanidin content. ZeMYB9 could specifically activate the promoter of ZeF3'H, and over-expression of ZeMYB9 induces much greater anthocyanin accumulation and higher expression level of anthocyanin biosynthetic genes in both petunia and tobacco. And then, ZeMYB9 was demonstrated to interact with ZeGL3, a bHLH transcription factor belonging to IIIf subgroup. Promoter activity of ZeF3'H was significantly promoted by co-expressing ZeMYB9 and ZeGL3 compared with expressing ZeMYB9 alone. Moreover, transient co-expression of ZeMYB9 and ZeGL3 induced anthocyanin accumulation in tobacco leaves. Our results suggest that ZeMYB9 could enhance cyanidin synthesis and regulate petal color in Z. elegans though activating the expression of ZeF3'H, by itself or interacting with ZeGL3.
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Affiliation(s)
- Jieyu Qian
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Lingli Jiang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Hongsheng Qing
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Jiahong Chen
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Ziyun Wan
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Menghan Xu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Jianxin Fu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Chao Zhang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, China
- School of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, China
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40
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Haghi R, Ahmadikhah A, Fazeli A, Shariati V. Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole-genome resequencing. THE PLANT GENOME 2022; 15:e20224. [PMID: 35703064 DOI: 10.1002/tpg2.20224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/16/2022] [Indexed: 06/15/2023]
Abstract
Anthocyanin pigment as a phenolic secondary metabolite is accumulated in areal organs of some rice cultivars. Despite several research attempts, the majority of genomic regions and candidate genes for purple-colored stem (Ps) resulting from anthocyanin pigmentation of rice leaf sheath have not been identified. A genome-wide association study (GWAS) and whole-genome resequencing (WGR) analysis was applied for genetic dissection of anthocyanin pigmentation of rice stem. Using GWAS, the genomic regions (on chromosomes 2, 4, and 6) tagged to eight single-nucleotide polymorphisms (SNPs) were identified to be significantly associated with purple stem, and in the vicinity of GWAS signals, 19 genes were highlighted as putative candidate genes. To narrow down the genomic regions more highly associated to the trait, a WGR study on recombinant inbred lines (RIL) with opposite phenotypes was conducted. After defining the DNA variation between reference genome, maternal parent and the two sister lines, a narrow genomic region on the short arm of chromosome 6 (4.7-6.2 Mbp interval) was identified to be highly associated with anthocyanin pigmentation of rice stem. In the interval, a few candidate genes with probable role in anthocyanin biosynthesis and accumulation were identified, which included five structural genes involved in the known pathways [one chalcone isomerase (CHI), two glycosyl transferases, and two UDP-flavonoid-3-O-glucosyl (UFGT) transferases] and two transcription factors [one basic helix-loop-helix (bHLH)- and one myeloblastosis (MYB)-coding genes]. The identified candidate genes can be used in breeding programs of rice or other Gramineae species for anthocyanin accumulation in areal organs.
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Affiliation(s)
- Reza Haghi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Dep. of Agronomy and Plant Breeding, Faculty of Agriculture, Ilam Univ., Ilam, Iran
| | - Asadollah Ahmadikhah
- Dep. of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
| | - Arash Fazeli
- Dep. of Agronomy and Plant Breeding, Faculty of Agriculture, Ilam Univ., Ilam, Iran
| | - Vahid Shariati
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Zhou T, Sun J, Zhai Y, Gao C, Ruhsam M, Wang X. Transcriptome profiles of yellowish-white and fuchsia colored flowers in the Rheum palmatum complex reveal genes related to color polymorphism. PLANT MOLECULAR BIOLOGY 2022; 110:187-197. [PMID: 35943640 DOI: 10.1007/s11103-022-01299-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Flower color variation is ubiquitous in many plant species, and several studies have been conducted to elucidate the underlying molecular mechanism. There are two flower color variants (yellowish-white and fuchsia) in the Rheum palmatum complex, however, few studies have investigated this phenomenon. Here, we used transcriptome sequencing of the two color variants to shed light on the molecular and biochemical basis for these color morphs. Comparison of the two transcriptomes identified 9641 differentially expressed unigenes (DEGs), including 6477 up-regulated and 3163 down-regulated genes. Functional analyses indicated that several DEGs were related to the anthocyanin biosynthesis pathway, and the expression profiles of these DEGs were coincident with the qRT-PCR validation results, indicating that expression levels of structural genes have a profound effect on the color variation in the R. palmatum complex. Our results suggested that the interaction of transcription factors (MYB, bHLH and WRKY) also regulated the anthocyanin biosynthesis in the R. palmatum complex. Estimation of selection pressures using the dN/dS ratio showed that 1106 pairs of orthologous genes have undergone positive selection. Of these positively selected genes, 21 were involved in the anthocyanin biosynthetic pathway, indicating that they may encode the proteins for structural alteration and affect flower color in the R. palmatum complex.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jiangyan Sun
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yunyan Zhai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenxi Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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Li C, Yang J, Yang K, Wu H, Chen H, Wu Q, Zhao H. Tartary buckwheat FtF3'H1 as a metabolic branch switch to increase anthocyanin content in transgenic plant. FRONTIERS IN PLANT SCIENCE 2022; 13:959698. [PMID: 36092410 PMCID: PMC9452690 DOI: 10.3389/fpls.2022.959698] [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: 06/02/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Tartary buckwheat (TB) is a pseudocereal rich in flavonoids, mainly including flavonols and anthocyanins. The flavonoid 3'-hydroxylase (F3'H) is a key enzyme in flavonoid biosynthesis and is encoded by two copies in TB genome. However, its biological function and effects on flavonol and anthocyanin synthesis in TB have not been well validated yet. In this study, we cloned the full-length FtF3'H1 gene highly expressed in all tissues (compared with FtF3'H2) according to TB flowering transcriptome data. The corresponding FtF3'H1 protein contains 534 amino acids with the molecular properties of the typical plant F3'H and belongs to the CYP75B family. During the flowering stage, the FtF3'H1 expression was highest in flowers, and its expression pattern showed a significant and positive correlation with the total flavonoids (R 2 > 0.95). The overexpression of FtF3'H1 in Arabidopsis thaliana, Nicotiana tabacum and TB hairy roots resulted in a significant increase in anthocyanin contents (p < 0.05) but a decrease in rutin (p < 0.05). The average anthocyanin contents were 2.94 mg/g (fresh weight, FW) in A. thaliana (about 135% increase), 1.18 mg/g (FW) in tobacco (about 17% increase), and 1.56 mg/g (FW) TB hairy roots (about 44% increase), and the rutin contents were dropped to about 53.85, 14.99, 46.31%, respectively. However, the expression of genes involved in anthocyanin (DFRs and ANSs) and flavonol (FLSs) synthesis pathways were significantly upregulated (p < 0.05). In particular, the expression level of DFR, a key enzyme that enters the anthocyanin branch, was upregulated thousand-fold in A. thaliana and in N. tabacum. These results might be attributed to FtF3'H1 protein with a higher substrate preference for anthocyanin synthesis substrates. Altogether, we identified the basic biochemical activity of FtF3'H1 in vivo and investigated its involvement in anthocyanin and flavonol metabolism in plant.
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43
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Li Y, Zhou Y, Chen H, Chen C, Liu Z, Han C, Wu Q, Yu F. Transcriptomic Analyses Reveal Key Genes Involved in Pigment Biosynthesis Related to Leaf Color Change of Liquidambar formosana Hance. Molecules 2022; 27:molecules27175433. [PMID: 36080201 PMCID: PMC9457658 DOI: 10.3390/molecules27175433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Liquidambar formosana Hance has a highly ornamental value as an important urban greening tree species with bright and beautiful leaf color. To gain insights into the physiological and molecular mechanisms of L. formosana leaf color change, the leaves of three different clones were sampled every ten days from October 13, 2019, five times in total, which are S1, S2, S3, S4 and S5. Transcriptome sequencing was performed at S1 and S4. The chlorophyll content of the three clones decreased significantly, while the anthocyanins content of the three clones increased significantly in the coloring stage. The anthocyanins content of clone 2 was far more than that of the other two clones throughout the period of leaf color change. The transcriptome analysis showed that six DEGs related to anthocyanins biosynthesis, including CHS (chalcone synthase), CHI (chalcone isomerase), F3′H (flavonoid 3′-hydroxylase), DFR (dihydroflavonol 4-reductase), ANS (anthocyanidin synthase) and FLS (flavonol synthase), were found in three clones. Clone 2 has another three DEGs related to anthocyanins biosynthesis, including PAL (Phenylalanine ammonia-lyase), F3′5′H (flavonoid 3′,5′-hydroxylase) and UFGT (flavonoid 3-O-glucosyltransferase). We lay a foundation for understanding the molecular regulation mechanism of the formation of leaf color by exploring valuable genes, which is helpful for L. formosana breeding.
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Affiliation(s)
- Yanjun Li
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Yang Zhou
- Faculty of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Chen Chen
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Zemao Liu
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Chao Han
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Qikui Wu
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Faculty of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Fangyuan Yu
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
- Correspondence:
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Ke L, Yu D, Zheng H, Xu Y, Wu Y, Jiao J, Wang X, Mei J, Cai F, Zhao Y, Sun J, Zhang X, Sun Y. Function deficiency of GhOMT1 causes anthocyanidins over-accumulation and diversifies fibre colours in cotton (Gossypium hirsutum). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1546-1560. [PMID: 35503731 PMCID: PMC9342615 DOI: 10.1111/pbi.13832] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/23/2022] [Indexed: 05/25/2023]
Abstract
Naturally coloured cotton (NCC) fibres need little or no dyeing process in textile industry to low-carbon emission and are environment-friendly. Proanthocyanidins (PAs) and their derivatives were considered as the main components causing fibre coloration and made NCCs very popular and healthy, but the monotonous fibre colours greatly limit the wide application of NCCs. Here a G. hirsutum empurpled mutant (HS2) caused by T-DNA insertion is found to enhance the anthocyanidins biosynthesis and accumulate anthocyanidins in the whole plant. HPLC and LC/MS-ESI analysis confirmed the anthocyanidins methylation and peonidin, petunidin and malvidin formation are blocked. The deficiency of GhOMT1 in HS2 was associated with the activation of the anthocyanidin biosynthesis and the altered components of anthocyanidins. The transcripts of key genes in anthocyanidin biosynthesis pathway are significantly up-regulated in HS2, while transcripts of the genes for transport and decoration were at similar levels as in WT. To investigate the potential mechanism of GhOMT1 deficiency in cotton fibre coloration, HS2 mutant was crossed with NCCs. Surprisingly, offsprings of HS2 and NCCs enhanced PAs biosynthesis and increased PAs levels in their fibres from the accumulated anthocyanidins through up-regulated GhANR and GhLAR. As expected, multiple novel lines with improved fibre colours including orange red and navy blue were produced in their generations. Based on this work, a new strategy for breeding diversified NCCs was brought out by promoting PA biosynthesis. This work will help shed light on mechanisms of PA biosynthesis and bring out potential molecular breeding strategy to increase PA levels in NCCs.
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Affiliation(s)
- Liping Ke
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Dongliang Yu
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Hongli Zheng
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Yihan Xu
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Yuqing Wu
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Junye Jiao
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Xiaoli Wang
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Jun Mei
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Fangfang Cai
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Yanyan Zhao
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Jie Sun
- College of AgricultureThe Key Laboratory of Oasis Eco‐AgricultureShihezi UniversityShiheziChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yuqiang Sun
- Plant Genomics & Molecular Improvement of Colored Fiber LaboratoryCollege of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
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45
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Alternative Splicing and Its Roles in Plant Metabolism. Int J Mol Sci 2022; 23:ijms23137355. [PMID: 35806361 PMCID: PMC9266299 DOI: 10.3390/ijms23137355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/02/2023] Open
Abstract
Plant metabolism, including primary metabolism such as tricarboxylic acid cycle, glycolysis, shikimate and amino acid pathways as well as specialized metabolism such as biosynthesis of phenolics, alkaloids and saponins, contributes to plant survival, growth, development and interactions with the environment. To this end, these metabolic processes are tightly and finely regulated transcriptionally, post-transcriptionally, translationally and post-translationally in response to different growth and developmental stages as well as the constantly changing environment. In this review, we summarize and describe the current knowledge of the regulation of plant metabolism by alternative splicing, a post-transcriptional regulatory mechanism that generates multiple protein isoforms from a single gene by using alternative splice sites during splicing. Numerous genes in plant metabolism have been shown to be alternatively spliced under different developmental stages and stress conditions. In particular, alternative splicing serves as a regulatory mechanism to fine-tune plant metabolism by altering biochemical activities, interaction and subcellular localization of proteins encoded by splice isoforms of various genes.
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46
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Ruan H, Shi X, Gao L, Rashid A, Li Y, Lei T, Dai X, Xia T, Wang Y. Functional analysis of the dihydroflavonol 4-reductase family of Camellia sinensis: exploiting key amino acids to reconstruct reduction activity. HORTICULTURE RESEARCH 2022; 9:uhac098. [PMID: 35795397 PMCID: PMC9250652 DOI: 10.1093/hr/uhac098] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/15/2022] [Indexed: 05/28/2023]
Abstract
Anthocyanins and proanthocyanidins (PAs) are important types of flavonoids, plant secondary metabolites with a wide range of industrial and pharmaceutical applications. DFR (dihydroflavonol 4-reductase) is a pivotal enzyme that plays an important role in the flavonoid pathway. Here, four CsDFR genes were isolated from Camellia sinensis, and their overexpression was analyzed in vitro and in vivo. Based on transcription and metabolic analyses, CsDFR expression was closely consistent with catechins and PAs accumulation. Moreover, enzyme activity analyses revealed that the two recombinant proteins CsDFRa and CsDFRc exhibited DFR activity, converting dihydroflavonols into leucoanthocyanins in vitro, but CsDFRb1 and CsDFRb3 did not. CsDFRa and CsDFRc overexpression in AtDFR mutants (tt3) revealed that CsDFRs are involved in the biosynthesis of anthocyanins and PAs, as CsDFRa and CsDFRc restored not only the purple petiole phenotype but also the seed coat color. Site-directed mutagenesis revealed that the two amino acid residues S117 and T123 of CsDFRa play a prominent role in controlling DFR reductase activity. Enzymatic assays indicated that CsDFRa and CsDFRc exhibited a higher affinity for DHQ and DHK, respectively, whereas CsDFRb1N120S and CsDFRb1C126T exhibited a higher affinity for DHM. Our findings comprehensively characterize the DFRs from C. sinensis and shed light on their critical role in metabolic engineering.
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Affiliation(s)
- Haixiang Ruan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xingxing Shi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- College of Tea Science, Guizhou University, Guiyang Guizhou 550025, China
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Arif Rashid
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yan Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ting Lei
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xinlong Dai
- College of Tea Science, Guizhou University, Guiyang Guizhou 550025, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yunsheng Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
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Chen D, Yang Y, Niu G, Shan X, Zhang X, Jiang H, Liu L, Wen Z, Ge X, Zhao Q, Yao X, Sun D. Metabolic and RNA sequencing analysis of cauliflower curds with different types of pigmentation. AOB PLANTS 2022; 14:plac001. [PMID: 35414860 PMCID: PMC8994856 DOI: 10.1093/aobpla/plac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Cauliflower (Brassica oleracea var. botrytis) is a popular vegetable worldwide due to its delicious taste, high nutritional value and anti-cancer properties. Cauliflower normally produces white curds, and natural spontaneous mutations lead to the production of orange, purple or green curds. However, some white cauliflowers show uneven purple pigmentation in their curds, which seriously affects the appearance quality and economic value of this crop. The underlying mechanism is still unclear. In this study, we performed comparative transcriptional and metabolic profiling analysis of light orange, white and purplish cauliflower curds. Metabolite analysis revealed that the pigments conferring purple colouration were delphinin and cyanin. Transcriptome analysis showed that the anthocyanin metabolism-related structural genes DFR, ANS and UGT and the transcription factor genes PAP2, TT8, GL3, EGL3 and TTG1 were upregulated in purplish versus white curds. These findings shed light on the formation of purplish curds, which could facilitate the breeding of purely white or red cauliflower.
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Affiliation(s)
- Daozong Chen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou 341000, China
| | - Yingxia Yang
- Tianjin Academy of Agricultural Sciences, The State Key Laboratory of Vegetable Germplasm Innovation, The Tianjin Key Laboratory of Vegetable Genetics and Breeding, Tianjin 300384, China
| | - Guobao Niu
- Tianjin Academy of Agricultural Sciences, The State Key Laboratory of Vegetable Germplasm Innovation, The Tianjin Key Laboratory of Vegetable Genetics and Breeding, Tianjin 300384, China
| | - Xiaozheng Shan
- Tianjin Academy of Agricultural Sciences, The State Key Laboratory of Vegetable Germplasm Innovation, The Tianjin Key Laboratory of Vegetable Genetics and Breeding, Tianjin 300384, China
| | - Xiaoli Zhang
- Tianjin Academy of Agricultural Sciences, The State Key Laboratory of Vegetable Germplasm Innovation, The Tianjin Key Laboratory of Vegetable Genetics and Breeding, Tianjin 300384, China
| | - Hanmin Jiang
- Tianjin Academy of Agricultural Sciences, The State Key Laboratory of Vegetable Germplasm Innovation, The Tianjin Key Laboratory of Vegetable Genetics and Breeding, Tianjin 300384, China
| | - Lili Liu
- Tianjin Academy of Agricultural Sciences, The State Key Laboratory of Vegetable Germplasm Innovation, The Tianjin Key Laboratory of Vegetable Genetics and Breeding, Tianjin 300384, China
| | - Zhenghua Wen
- Tianjin Academy of Agricultural Sciences, The State Key Laboratory of Vegetable Germplasm Innovation, The Tianjin Key Laboratory of Vegetable Genetics and Breeding, Tianjin 300384, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiancheng Zhao
- Tianjin Huierjia Seeds Industry Technology Co., Ltd, Tianjin 300392, China
| | - Xingwei Yao
- Tianjin Academy of Agricultural Sciences, The State Key Laboratory of Vegetable Germplasm Innovation, The Tianjin Key Laboratory of Vegetable Genetics and Breeding, Tianjin 300384, China
| | - Deling Sun
- Tianjin Academy of Agricultural Sciences, The State Key Laboratory of Vegetable Germplasm Innovation, The Tianjin Key Laboratory of Vegetable Genetics and Breeding, Tianjin 300384, China
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Wong DCJ, Perkins J, Peakall R. Anthocyanin and Flavonol Glycoside Metabolic Pathways Underpin Floral Color Mimicry and Contrast in a Sexually Deceptive Orchid. FRONTIERS IN PLANT SCIENCE 2022; 13:860997. [PMID: 35401591 PMCID: PMC8983864 DOI: 10.3389/fpls.2022.860997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/17/2022] [Indexed: 06/10/2023]
Abstract
Sexually deceptive plants secure pollination by luring specific male insects as pollinators using a combination of olfactory, visual, and morphological mimicry. Flower color is a key component to this attraction, but its chemical and genetic basis remains poorly understood. Chiloglottis trapeziformis is a sexually deceptive orchid which has predominantly dull green-red flowers except for the central black callus projecting from the labellum lamina. The callus mimics the female of the pollinator and the stark color contrast between the black callus and dull green or red lamina is thought to enhance the visibility of the mimic. The goal of this study was to investigate the chemical composition and genetic regulation of temporal and spatial color patterns leading to visual mimicry, by integrating targeted metabolite profiling and transcriptomic analysis. Even at the very young bud stage, high levels of anthocyanins were detected in the dark callus, with peak accumulation by the mature bud stage. In contrast, anthocyanin levels in the lamina peaked as the buds opened and became reddish-green. Coordinated upregulation of multiple genes, including dihydroflavonol reductase and leucoanthocyanidin dioxygenase, and the downregulation of flavonol synthase genes (FLS) in the callus at the very young bud stage underpins the initial high anthocyanin levels. Conversely, within the lamina, upregulated FLS genes promote flavonol glycoside over anthocyanin production, with the downstream upregulation of flavonoid O-methyltransferase genes further contributing to the accumulation of methylated flavonol glycosides, whose levels peaked in the mature bud stage. Finally, the peak anthocyanin content of the reddish-green lamina of the open flower is underpinned by small increases in gene expression levels and/or differential upregulation in the lamina in select anthocyanin genes while FLS patterns showed little change. Differential expression of candidate genes involved in specific transport, vacuolar acidification, and photosynthetic pathways may also assist in maintaining the distinct callus and contrasting lamina color from the earliest bud stage through to the mature flower. Our findings highlight that flower color in this sexually deceptive orchid is achieved by complex tissue-specific coordinated regulation of genes and biochemical pathways across multiple developmental stages.
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Albert NW, Lafferty DJ, Moss SMA, Davies KM. Flavonoids – flowers, fruit, forage and the future. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2034654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Declan J. Lafferty
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Sarah M. A. Moss
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Kevin M. Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
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50
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High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids. Sci Rep 2022; 12:3346. [PMID: 35228611 PMCID: PMC8885740 DOI: 10.1038/s41598-022-07318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/11/2022] [Indexed: 11/26/2022] Open
Abstract
Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.
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