1
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Wang Y, Li S, Shi Y, Lv S, Zhu C, Xu C, Zhang B, Allan AC, Grierson D, Chen K. The R2R3 MYB Ruby1 is activated by two cold responsive ethylene response factors, via the retrotransposon in its promoter, to positively regulate anthocyanin biosynthesis in citrus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38922743 DOI: 10.1111/tpj.16866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/07/2024] [Accepted: 04/08/2024] [Indexed: 06/28/2024]
Abstract
Anthocyanins are natural pigments and dietary antioxidants that play multiple biological roles in plants and are important in animal and human nutrition. Low temperature (LT) promotes anthocyanin biosynthesis in many species including blood orange. A retrotransposon in the promoter of Ruby1, which encodes an R2R3 MYB transcription factor, controls cold-induced anthocyanin accumulation in blood orange flesh. However, the specific mechanism remains unclear. In this study, we characterized two LT-induced ETHYLENE RESPONSE FACTORS (CsERF054 and CsERF061). Both CsERF054 and CsERF061 can activate the expression of CsRuby1 by directly binding to a DRE/CRT cis-element within the retrotransposon in the promoter of CsRuby1, thereby positively regulating anthocyanin biosynthesis. Further investigation indicated that CsERF061 also forms a protein complex with CsRuby1 to co-activate the expression of anthocyanin biosynthetic genes, providing a dual mechanism for the upregulation of the anthocyanin pathway. These results provide insights into how LT mediates anthocyanin biosynthesis and increase the understanding of the regulatory network of anthocyanin biosynthesis in blood orange.
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Affiliation(s)
- Yuxin Wang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Shaojia Li
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Yanna Shi
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Shouzheng Lv
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Changqing Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Changjie Xu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Bo Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
| | - Andrew C Allan
- New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Donald Grierson
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Kunsong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, P.R. China
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2
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Yue L, He J, Gan T, Jiu S, Khalil-Ur-Rehman M, Liu K, Bai M, Yang G, Xu Y. Regulatory Mechanism of Proanthocyanidins in Grape Peels Using vvi-miR828a and Its Target Gene VvMYBPA1. PLANTS (BASEL, SWITZERLAND) 2024; 13:1688. [PMID: 38931120 PMCID: PMC11207263 DOI: 10.3390/plants13121688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
Anthocyanins and proanthocyanidins are considered to be essential secondary metabolites in grapes and are used to regulate metabolic processes, while miRNAs are involved in their synthesis of anthocyanins and proanthocyanidins to regulate metabolic processes. The present research work was carried out to investigate the underlying regulatory mechanism of target genes in the grape cultivars 'Italia' and 'Benitaka'. miRNA and transnscriptomic sequencing technology were employed to characterize both the profiles of miRNAs and the transcripts of grape peels at 10 and 11 weeks post flowering (10 wpf and 11 wpf). The results revealed that the expression level of vvi-miR828a in 'Italia' at 10 and 11 wpf was significantly higher than that in 'Benitaka'. miRNA-seq analysis predicted MYBPA1 to be the target gene of vvi-miR828a. In transcriptome analysis, the expression level of the VvMYBPA1 gene in 'Benitaka' was significantly higher than that in 'Italia'; in addition, the TPM values (expression levels) of VvMYBPA1 and miR828a also showed an evident negative correlation. The determination of the proanthocyanidin (PA) content in 'Italia' and 'Benitaka' peels at 11 wpf demonstrated that the PA content of 'Benitaka' was significantly higher than that of 'Italia'. The outcomes of RT-qRCR analysis exhibited that the expression levels of the VdPAL, VdCHS, VdCHI, VdDFR, VdMYB5b, VdANR, and VdMYBPA1 genes related anthocyanin and proanthocyanidin pathways were reduced, while the expression levels of all of the above genes were increased after the transient expression of the VvMYBPA1 vector into grape leaves. The results of the transient overexpression experiment of vvi-miR828a before the veraison period of strawberry fruits showed that vvi-miR828a can significantly slow down the coloration of strawberries. The vvi-miR828a negatively regulates the accumulation of proanthocyanidins in grape fruits by inhibiting the expression of VvMYBPA1.
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Affiliation(s)
- Lingqi Yue
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Jingjing He
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Tian Gan
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | | | - Kunyu Liu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Miao Bai
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Guoshun Yang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Yanshuai Xu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
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3
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Cai Y, Liang Y, Shi H, Cui J, Prakash S, Zhang J, Anaokar S, Chai J, Schwender J, Lu C, Yu XH, Shanklin J. Creating yellow seed Camelina sativa with enhanced oil accumulation by CRISPR-mediated disruption of Transparent Testa 8. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38859598 DOI: 10.1111/pbi.14403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/26/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024]
Abstract
Camelina (Camelina sativa L.), a hexaploid member of the Brassicaceae family, is an emerging oilseed crop being developed to meet the increasing demand for plant oils as biofuel feedstocks. In other Brassicas, high oil content can be associated with a yellow seed phenotype, which is unknown for camelina. We sought to create yellow seed camelina using CRISPR/Cas9 technology to disrupt its Transparent Testa 8 (TT8) transcription factor genes and to evaluate the resulting seed phenotype. We identified three TT8 genes, one in each of the three camelina subgenomes, and obtained independent CsTT8 lines containing frameshift edits. Disruption of TT8 caused seed coat colour to change from brown to yellow reflecting their reduced flavonoid accumulation of up to 44%, and the loss of a well-organized seed coat mucilage layer. Transcriptomic analysis of CsTT8-edited seeds revealed significantly increased expression of the lipid-related transcription factors LEC1, LEC2, FUS3, and WRI1 and their downstream fatty acid synthesis-related targets. These changes caused metabolic remodelling with increased fatty acid synthesis rates and corresponding increases in total fatty acid (TFA) accumulation from 32.4% to as high as 38.0% of seed weight, and TAG yield by more than 21% without significant changes in starch or protein levels compared to parental line. These data highlight the effectiveness of CRISPR in creating novel enhanced-oil germplasm in camelina. The resulting lines may directly contribute to future net-zero carbon energy production or be combined with other traits to produce desired lipid-derived bioproducts at high yields.
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Affiliation(s)
- Yuanheng Cai
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Yuanxue Liang
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Hai Shi
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Jodie Cui
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Shreyas Prakash
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Jianhui Zhang
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Sanket Anaokar
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Jin Chai
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Jorg Schwender
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Xiao-Hong Yu
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - John Shanklin
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
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4
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Banerjee S, Agarwal P, Choudhury SR, Roy S. MYB4, a member of R2R3-subfamily of MYB transcription factor functions as a repressor of key genes involved in flavonoid biosynthesis and repair of UV-B induced DNA double strand breaks in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108698. [PMID: 38714132 DOI: 10.1016/j.plaphy.2024.108698] [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: 11/10/2023] [Revised: 03/31/2024] [Accepted: 05/01/2024] [Indexed: 05/09/2024]
Abstract
Plants accumulate flavonoids as part of UV-B acclimation, while a high level of UV-B irradiation induces DNA damage and leads to genome instability. Here, we show that MYB4, a member of the R2R3-subfamily of MYB transcription factor plays important role in regulating plant response to UV-B exposure through the direct repression of the key genes involved in flavonoids biosynthesis and repair of DNA double-strand breaks (DSBs). Our results demonstrate that MYB4 inhibits seed germination and seedling establishment in Arabidopsis following UV-B exposure. Phenotype analyses of atmyb4-1 single mutant line along with uvr8-6/atmyb4-1, cop1-6/atmyb4-1, and hy5-215/atmyb4-1 double mutants indicate that MYB4 functions downstream of UVR8 mediated signaling pathway and negatively affects UV-B acclimation and cotyledon expansion. Our results indicate that MYB4 acts as transcriptional repressor of two key flavonoid biosynthesis genes, including 4CL and FLS, via directly binding to their promoter, thus reducing flavonoid accumulation. On the other hand, AtMYB4 overexpression leads to higher accumulation level of DSBs along with repressed expression of several key DSB repair genes, including AtATM, AtKU70, AtLIG4, AtXRCC4, AtBRCA1, AtSOG1, AtRAD51, and AtRAD54, respectively. Our results further suggest that MYB4 protein represses the expression of two crucial DSB repair genes, AtKU70 and AtXRCC4 through direct binding with their promoters. Together, our results indicate that MYB4 functions as an important coordinator to regulate plant response to UV-B through transcriptional regulation of key genes involved in flavonoids biosynthesis and repair of UV-B induced DNA damage.
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Affiliation(s)
- Samrat Banerjee
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, West Bengal, 713104, India
| | - Puja Agarwal
- Constituent College in Purnea University, Purnia, 854301, Bihar, India
| | - Swarup Roy Choudhury
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, West Bengal, 713104, India.
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5
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Xia Z, Fan W, Liu D, Chen Y, Lv J, Xu M, Zhang M, Ren Z, Chen X, Wang X, Li L, Zhu P, Liu C, Song Z, Huang C, Wang X, Wang S, Zhao A. Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content. HORTICULTURE RESEARCH 2024; 11:uhae120. [PMID: 38919559 PMCID: PMC11197311 DOI: 10.1093/hr/uhae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/14/2024] [Indexed: 06/27/2024]
Abstract
Understanding the intricate regulatory mechanisms underlying the anthocyanin content (AC) in fruits and vegetables is crucial for advanced biotechnological customization. In this study, we generated high-quality haplotype-resolved genome assemblies for two mulberry cultivars: the high-AC 'Zhongsang5801' (ZS5801) and the low-AC 'Zhenzhubai' (ZZB). Additionally, we conducted a comprehensive analysis of genes associated with AC production. Through genome-wide association studies (GWAS) on 112 mulberry fruits, we identified MaVHAG3, which encodes a vacuolar-type H+-ATPase G3 subunit, as a key gene linked to purple pigmentation. To gain deeper insights into the genetic and molecular processes underlying high AC, we compared the genomes of ZS5801 and ZZB, along with fruit transcriptome data across five developmental stages, and quantified the accumulation of metabolic substances. Compared to ZZB, ZS5801 exhibited significantly more differentially expressed genes (DEGs) related to anthocyanin metabolism and higher levels of anthocyanins and flavonoids. Comparative analyses revealed expansions and contractions in the flavonol synthase (FLS) and dihydroflavonol 4-reductase (DFR) genes, resulting in altered carbon flow. Co-expression analysis demonstrated that ZS5801 displayed more significant alterations in genes involved in late-stage AC regulation compared to ZZB, particularly during the phase stage. In summary, our findings provide valuable insights into the regulation of mulberry fruit AC, offering genetic resources to enhance cultivars with higher AC traits.
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Affiliation(s)
- Zhongqiang Xia
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Wei Fan
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Duanyang Liu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Yuane Chen
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Jing Lv
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Mengxia Xu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Meirong Zhang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Zuzhao Ren
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Xuefei Chen
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Xiujuan Wang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Liang Li
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Panpan Zhu
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China
| | - Zhiguang Song
- Chongqing Sericulture Science and Technology Research Institute, Chongqing.400715, China
| | - Chuanshu Huang
- Chongqing Sericulture Science and Technology Research Institute, Chongqing.400715, China
| | - Xiling Wang
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Shuchang Wang
- Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 570100, China
| | - Aichun Zhao
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
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6
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Zhang W, Wu J, He J, Liu C, Yi W, Xie J, Wu Y, Xie T, Ma J, Zhong Z, Yang M, Chen C, Luan A, He Y. AcMYB266, a key regulator of the red coloration in pineapple peel: a case of subfunctionalization in tandem duplicated genes. HORTICULTURE RESEARCH 2024; 11:uhae116. [PMID: 38919552 PMCID: PMC11197299 DOI: 10.1093/hr/uhae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/09/2024] [Indexed: 06/27/2024]
Abstract
Red fruit peel is an attractive target for pineapple breeding. Various pineapple accessions with distinct red coloration patterns exist; however, the precise molecular mechanism accounting for these differences remains unknown, which hinders the pineapple breeding process from combining high fruit quality with red peel. In this study, we characterized a transcription factor, AcMYB266, which is preferentially expressed in pineapple peel and positively regulates anthocyanin accumulation. Transgenic pineapple, Arabidopsis, and tobacco plants overexpressing AcMYB266 exhibited significant anthocyanin accumulation. Conversely, transient silencing of this gene led to decreased anthocyanin accumulation in pineapple red bracts. In-depth analysis indicated that variations of AcMYB266 sequences in the promoter instead of the protein-coding region seem to contribute to different red coloration patterns in peels of three representative pineapple varieties. In addition, we found that AcMYB266 was located in a cluster of four MYB genes exclusive to and conserved in Ananas species. Of this cluster, each was proved to regulate anthocyanin synthesis in different pineapple tissues, illustrating an interesting case of gene subfunctionalization after tandem duplication. In summary, we have characterized AcMYB266 as a key regulator of pineapple red fruit peel and identified an MYB cluster whose members were subfunctionalized to specifically regulate the red coloration of different pineapple tissues. The present study will assist in establishing a theoretical mechanism for pineapple breeding for red fruit peel and provide an interesting case for the investigation of gene subfunctionalization in plants.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crop in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, No. 483, Wushan Road, Wushan Street, Tianhe District, Guangzhou, Guangdong, 510642, China
| | - Jing Wu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crop in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, No. 483, Wushan Road, Wushan Street, Tianhe District, Guangzhou, Guangdong, 510642, China
| | - Junhu He
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/National Key Laboratory for Tropical Crop Breeding, Yazhouwan Technology City, Sanya, Hainan, 572024, China/Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs/Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, No.4, Xueyuan Road, Longhua District, Haikou, Hainan, 571101, China
| | - Chaoyang Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crop in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, No. 483, Wushan Road, Wushan Street, Tianhe District, Guangzhou, Guangdong, 510642, China
| | - Wen Yi
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crop in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, No. 483, Wushan Road, Wushan Street, Tianhe District, Guangzhou, Guangdong, 510642, China
| | - Jingyao Xie
- School of Landscape Architecture, Guangdong Eco-Engineering Polytechnic, No. 297, Guangshan 1st Road, Tianhe District, Guangzhou, Guangdong, 510520, China
| | - Ya Wu
- Environment and plant protection institute, Chinese Academy of Tropical Agricultural Sciences, No. 4, Xueyuan Road, Longhua District, Haikou, Hainan, 571101, China
| | - Tao Xie
- Department of Horticulture, Foshan University, No. 18, Jiangwan 1st Road, Chancheng District, Foshan, Guangdong, 528231, China
| | - Jun Ma
- College of Landscape Architecture, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, Sichuan, 610000, China
| | - Ziqin Zhong
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crop in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, No. 483, Wushan Road, Wushan Street, Tianhe District, Guangzhou, Guangdong, 510642, China
| | - Mingzhe Yang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crop in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, No. 483, Wushan Road, Wushan Street, Tianhe District, Guangzhou, Guangdong, 510642, China
| | - Chengjie Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/National Key Laboratory for Tropical Crop Breeding, Yazhouwan Technology City, Sanya, Hainan, 572024, China/Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs/Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, No.4, Xueyuan Road, Longhua District, Haikou, Hainan, 571101, China
| | - Aiping Luan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/National Key Laboratory for Tropical Crop Breeding, Yazhouwan Technology City, Sanya, Hainan, 572024, China/Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs/Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, No.4, Xueyuan Road, Longhua District, Haikou, Hainan, 571101, China
| | - Yehua He
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crop in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, No. 483, Wushan Road, Wushan Street, Tianhe District, Guangzhou, Guangdong, 510642, China
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7
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Yang G, Sun M, Brewer L, Tang Z, Nieuwenhuizen N, Cooney J, Xu S, Sheng J, Andre C, Xue C, Rebstock R, Yang B, Chang W, Liu Y, Li J, Wang R, Qin M, Brendolise C, Allan AC, Espley RV, Lin‐Wang K, Wu J. Allelic variation of BBX24 is a dominant determinant controlling red coloration and dwarfism in pear. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1468-1490. [PMID: 38169146 PMCID: PMC11123420 DOI: 10.1111/pbi.14280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Variation in anthocyanin biosynthesis in pear fruit provides genetic germplasm resources for breeding, while dwarfing is an important agronomic trait, which is beneficial to reduce the management costs and allow for the implementation of high-density cultivation. Here, we combined bulked segregant analysis (BSA), quantitative trait loci (QTL), and structural variation (SV) analysis to identify a 14-bp deletion which caused a frame shift mutation and resulted in the premature translation termination of a B-box (BBX) family of zinc transcription factor, PyBBX24, and its allelic variation termed PyBBX24ΔN14. PyBBX24ΔN14 overexpression promotes anthocyanin biosynthesis in pear, strawberry, Arabidopsis, tobacco, and tomato, while that of PyBBX24 did not. PyBBX24ΔN14 directly activates the transcription of PyUFGT and PyMYB10 through interaction with PyHY5. Moreover, stable overexpression of PyBBX24ΔN14 exhibits a dwarfing phenotype in Arabidopsis, tobacco, and tomato plants. PyBBX24ΔN14 can activate the expression of PyGA2ox8 via directly binding to its promoter, thereby deactivating bioactive GAs and reducing the plant height. However, the nuclear localization signal (NLS) and Valine-Proline (VP) motifs in the C-terminus of PyBBX24 reverse these effects. Interestingly, mutations leading to premature termination of PyBBX24 were also identified in red sports of un-related European pear varieties. We conclude that mutations in PyBBX24 gene link both an increase in pigmentation and a decrease in plant height.
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Affiliation(s)
- Guangyan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Zhongshan Biological Breeding LaboratoryNanjingJiangsuChina
| | - Manyi Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Zhongshan Biological Breeding LaboratoryNanjingJiangsuChina
| | - Lester Brewer
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Zikai Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Niels Nieuwenhuizen
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Janine Cooney
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Shaozhuo Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Jiawen Sheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Christelle Andre
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Cheng Xue
- State Key Laboratory of Crop Biology, College of Horticulture Science and EngineeringShandong Agricultural UniversityTai'anChina
| | - Ria Rebstock
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Bo Yang
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Wenjing Chang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yueyuan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Jiaming Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Zhongshan Biological Breeding LaboratoryNanjingJiangsuChina
| | - Runze Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Mengfan Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Cyril Brendolise
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Andrew C. Allan
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Richard V. Espley
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Kui Lin‐Wang
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | - Jun Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Zhongshan Biological Breeding LaboratoryNanjingJiangsuChina
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8
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Zhang X, Yu L, Zhang M, Wu T, Song T, Yao Y, Zhang J, Tian J. MdWER interacts with MdERF109 and MdJAZ2 to mediate methyl jasmonate- and light-induced anthocyanin biosynthesis in apple fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1327-1342. [PMID: 38319946 DOI: 10.1111/tpj.16671] [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: 07/25/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 02/08/2024]
Abstract
Anthocyanin generation in apples (Malus domestica) and the pigmentation that results from it may be caused by irradiation and through administration of methyl jasmonate (MeJA). However, their regulatory interrelationships associated with fruit coloration are not well defined. To determine whether MdERF109, a transcription factor (TF) involved in light-mediated coloration and anthocyanin biosynthesis, has synergistic effects with other proteins, we performed a yeast two-hybrid assessment and identified another TF, MdWER. MdWER was induced by MeJA treatment, and although overexpression of MdWER alone did not promote anthocyanin accumulation co-overexpression with MdERF109 resulted in significantly increase in anthocyanin biosynthesis. MdWER may form a protein complex with MdERF109 to promote anthocyanin accumulation by enhancing combinations between the proteins and their corresponding genes. In addition, MdWER, as a MeJA responsive protein, interacts with the anthocyanin repressor MdJAZ2. Transient co-expression in apple fruit and protein interaction assays allowed us to conclude that MdERF109 and MdJAZ2 interact with MdWER and take part in the production of anthocyanins upon MeJA treatment and irradiation. Our findings validate a role for the MdERF109-MdWER-MdJAZ2 module in anthocyanin biosynthesis and uncover a novel mechanism for how light and MeJA signals are coordinated anthocyanin biosynthesis in apple fruit.
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Affiliation(s)
- Xi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Lujia Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Mengjiao Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Tingting Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Ji Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
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9
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Falcioni R, Antunes WC, Berti de Oliveira R, Chicati ML, Demattê JAM, Nanni MR. Hyperspectral and Chlorophyll Fluorescence Analyses of Comparative Leaf Surfaces Reveal Cellular Influences on Leaf Optical Properties in Tradescantia Plants. Cells 2024; 13:952. [PMID: 38891083 PMCID: PMC11171972 DOI: 10.3390/cells13110952] [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: 04/23/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The differential effects of cellular and ultrastructural characteristics on the optical properties of adaxial and abaxial leaf surfaces in the genus Tradescantia highlight the intricate relationships between cellular arrangement and pigment distribution in the plant cells. We examined hyperspectral and chlorophyll a fluorescence (ChlF) kinetics using spectroradiometers and optical and electron microscopy techniques. The leaves were analysed for their spectral properties and cellular makeup. The biochemical compounds were measured and correlated with the biophysical and ultrastructural features. The main findings showed that the top and bottom leaf surfaces had different amounts and patterns of pigments, especially anthocyanins, flavonoids, total phenolics, chlorophyll-carotenoids, and cell and organelle structures, as revealed by the hyperspectral vegetation index (HVI). These differences were further elucidated by the correlation coefficients, which influence the optical signatures of the leaves. Additionally, ChlF kinetics varied between leaf surfaces, correlating with VIS-NIR-SWIR bands through distinct cellular structures and pigment concentrations in the hypodermis cells. We confirmed that the unique optical properties of each leaf surface arise not only from pigmentation but also from complex cellular arrangements and structural adaptations. Some of the factors that affect how leaves reflect light are the arrangement of chloroplasts, thylakoid membranes, vacuoles, and the relative size of the cells themselves. These findings improve our knowledge of the biophysical and biochemical reasons for leaf optical diversity, and indicate possible implications for photosynthetic efficiency and stress adaptation under different environmental conditions in the mesophyll cells of Tradescantia plants.
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Affiliation(s)
- Renan Falcioni
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (W.C.A.); (R.B.d.O.); (M.L.C.); (M.R.N.)
| | - Werner Camargos Antunes
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (W.C.A.); (R.B.d.O.); (M.L.C.); (M.R.N.)
| | - Roney Berti de Oliveira
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (W.C.A.); (R.B.d.O.); (M.L.C.); (M.R.N.)
| | - Marcelo Luiz Chicati
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (W.C.A.); (R.B.d.O.); (M.L.C.); (M.R.N.)
| | - José Alexandre M. Demattê
- Department of Soil Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Av. Pádua Dias, 11, Piracicaba 13418-260, São Paulo, Brazil;
| | - Marcos Rafael Nanni
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (W.C.A.); (R.B.d.O.); (M.L.C.); (M.R.N.)
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10
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Thapa M, Liu L, Barkla BJ, Kretzschmar T, Rogiers SY, Rose TJ. Accumulation patterns of anthocyanin and γ-oryzanol during black rice grain development. PLoS One 2024; 19:e0302745. [PMID: 38776277 PMCID: PMC11111080 DOI: 10.1371/journal.pone.0302745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 04/11/2024] [Indexed: 05/24/2024] Open
Abstract
Pigmented rice, especially black rice, is gaining popularity as it is rich in antioxidants such as anthocyanins and γ-oryzanol. At present, knowledge about temporal control of biosynthesis and accumulation of antioxidants during grain development is limited. To address this, the accumulation patterns of anthocyanins and γ-oryzanol were assessed in two distinct black rice genotypes over the course of grain development, and the expression of known regulatory genes for anthocyanin biosynthesis was examined. The results indicated that total γ-oryzanol content increased continuously throughout grain development, while total anthocyanins peaked at dough stage (15 to 21 days after flowering) followed by a decline until grain maturity in both genotypes. However, the rate of decrease in anthocyanin content differed between genotypes, and a more prominent decline in cyanidin 3-O-glucoside (C3G) relative to peonidin 3-O-glucoside (P3G) was observed for both. Anthocyanin content was closely linked with the expression of key regulatory genes in the MBW (MYB-bHLH-WD40) complex. This improved knowledge of the genotype-specific biosynthesis (anthocyanins only) and accumulation patterns of anthocyanins and γ-oryzanol can inform subsequent research efforts to increase concentrations of these key antioxidants in black rice grains.
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Affiliation(s)
- Manisha Thapa
- Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Lei Liu
- Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Bronwyn J. Barkla
- Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Tobias Kretzschmar
- Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Suzy Y. Rogiers
- NSW Department of Primary Industries, Wollongbar, New South Wales, Australia
| | - Terry J. Rose
- Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
- Centre for Organics Research, Southern Cross University, Lismore, New South Wales, Australia
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11
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Lv S, Tang X, Jiang L, Zhang J, Sun B, Liu Q, Mao X, Yu H, Chen P, Chen W, Fan Z, Li C. OsLSC6 Regulates Leaf Sheath Color and Cold Tolerance in Rice Revealed by Metabolite Genome Wide Association Study. RICE (NEW YORK, N.Y.) 2024; 17:34. [PMID: 38739288 DOI: 10.1186/s12284-024-00713-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/08/2024] [Indexed: 05/14/2024]
Abstract
Plant metabolites including anthocyanins play an important role in the growth of plants, as well as in regulating biotic and abiotic stress responses to the environment. Here we report comprehensive profiling of 3315 metabolites and a further metabolic-based genome-wide association study (mGWAS) based on 292,485 SNPs obtained from 311 rice accessions, including 160 wild and 151 cultivars. We identified hundreds of common variants affecting a large number of secondary metabolites with large effects at high throughput. Finally, we identified a novel gene namely OsLSC6 (Oryza sativa leaf sheath color 6), which encoded a UDP 3-O-glucosyltransferase and involved in the anthocyanin biosynthesis of Cyanidin-3-Galc (sd1825) responsible for leaf sheath color, and resulted in significant different accumulation of sd1825 between wild (purple) and cultivars (green). The results of knockout transgenic experiments showed that OsLSC6 regulated the biosynthesis and accumulation of sd1825, controlled the purple leaf sheath. Our further research revealed that OsLSC6 also confers resistance to cold stress during the seedling stage in rice. And we identified that a SNP in OsLSC6 was responsible for the leaf sheath color and chilling tolerance, supporting the importance of OsLSC6 in plant adaption. Our study could not only demonstrate that OsLSC6 is a vital regulator during anthocyanin biosynthesis and abiotic stress responses, but also provide a powerful complementary tool based on metabolites-to-genes analysis by mGWAS for functional gene identification andpromising candidate in future rice breeding and improvement.
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Affiliation(s)
- Shuwei Lv
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Xuan Tang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Pingli Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China.
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12
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Kim G, Cho H, Kim S. Identification of a candidate gene for the I locus determining the dominant white bulb color in onion (Allium cepa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:118. [PMID: 38709404 DOI: 10.1007/s00122-024-04626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/14/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE Through a map-based cloning approach, a gene coding for an R2R3-MYB transcription factor was identified as a causal gene for the I locus controlling the dominant white bulb color in onion. White bulb colors in onion (Allium cepa L.) are determined by either the C or I loci. The causal gene for the C locus was previously isolated, but the gene responsible for the I locus has not been identified yet. To identify candidate genes for the I locus, an approximately 7-Mb genomic DNA region harboring the I locus was obtained from onion and bunching onion (A. fistulosum) whole genome sequences using two tightly linked molecular markers. Within this interval, the AcMYB1 gene, known as a positive regulator of anthocyanin production, was identified. No polymorphic sequences were found between white and red AcMYB1 alleles in the 4,860-bp full-length genomic DNA sequences. However, a 4,838-bp LTR-retrotransposon was identified in the white allele, in the 79-bp upstream coding region from the stop codon. The insertion of this LTR-retrotransposon created a premature stop codon, resulting in the replacement of 26 amino acids with seven different residues. A molecular marker was developed based on the insertion of this LTR-retrotransposon to genotype the I locus. A perfect linkage between bulb color phenotypes and marker genotypes was observed among 5,303 individuals of segregating populations. The transcription of AcMYB1 appeared to be normal in both red and white onions, but the transcription of CHS-A, which encodes chalcone synthase and is involved in the first step of the anthocyanin biosynthesis pathway, was inactivated in the white onions. Taken together, an aberrant AcMYB1 protein produced from the mutant allele might be responsible for the dominant white bulb color in onions.
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Affiliation(s)
- Geonjoong Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Heejung Cho
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Sunggil Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea.
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13
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Zuo D, Yan Y, Ma J, Zhao P. Genome-Wide Analysis of Transcription Factor R2R3-MYB Gene Family and Gene Expression Profiles during Anthocyanin Synthesis in Common Walnut ( Juglans regia L.). Genes (Basel) 2024; 15:587. [PMID: 38790216 PMCID: PMC11121633 DOI: 10.3390/genes15050587] [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: 03/21/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
The R2R3-MYB gene family, encoding plant transcriptional regulators, participates in many metabolic pathways of plant physiology and development, including flavonoid metabolism and anthocyanin synthesis. This study proceeded as follows: the JrR2R3-MYB gene family was analyzed genome-wide, and the family members were identified and characterized using the high-quality walnut reference genome "Chandler 2.0". All 204 JrR2R3-MYBs were established and categorized into 30 subgroups via phylogenetic analysis. JrR2R3-MYBs were unevenly distributed over 16 chromosomes. Most JrR2R3-MYBs had similar structures and conservative motifs. The cis-acting elements exhibit multiple functions of JrR2R3-MYBs such as light response, metabolite response, and stress response. We found that the expansion of JrR2R3-MYBs was mainly caused by WGD or segmental duplication events. Ka/Ks analysis indicated that these genes were in a state of negative purifying selection. Transcriptome results suggested that JrR2R3-MYBs were widely entangled in the process of walnut organ development and differentially expressed in different colored varieties of walnuts. Subsequently, we identified 17 differentially expressed JrR2R3-MYBs, 9 of which may regulate anthocyanin biosynthesis based on the results of a phylogenetic analysis. These genes were present in greater expression levels in 'Zijing' leaves than in 'Lvling' leaves, as revealed by the results of qRT-PCR experiments. These results contributed to the elucidation of the functions of JrR2R3-MYBs in walnut coloration. Collectively, this work provides a foundation for exploring the functional characteristics of the JrR2R3-MYBs in walnuts and improving the nutritional value and appearance quality of walnuts.
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Affiliation(s)
| | | | | | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (D.Z.); (Y.Y.); (J.M.)
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14
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Liu X, Zhao T, Yuan L, Qiu F, Tang Y, Li D, Zhang F, Zeng L, Yang C, Nagdy MM, Htun ZLL, Lan X, Chen M, Liao Z, Li Y. A Fruit-Expressed MYB Transcription Factor Regulates Anthocyanin Biosynthesis in Atropa belladonna. Int J Mol Sci 2024; 25:4963. [PMID: 38732182 PMCID: PMC11084770 DOI: 10.3390/ijms25094963] [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: 04/05/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Anthocyanins are water-soluble flavonoid pigments that play a crucial role in plant growth and metabolism. They serve as attractants for animals by providing plants with red, blue, and purple pigments, facilitating pollination and seed dispersal. The fruits of solanaceous plants, tomato (Solanum lycopersicum) and eggplant (Solanum melongena), primarily accumulate anthocyanins in the fruit peels, while the ripe fruits of Atropa belladonna (Ab) have a dark purple flesh due to anthocyanin accumulation. In this study, an R2R3-MYB transcription factor (TF), AbMYB1, was identified through association analysis of gene expression and anthocyanin accumulation in different tissues of A. belladonna. Its role in regulating anthocyanin biosynthesis was investigated through gene overexpression and RNA interference (RNAi). Overexpression of AbMYB1 significantly enhanced the expression of anthocyanin biosynthesis genes, such as AbF3H, AbF3'5'H, AbDFR, AbANS, and Ab3GT, leading to increased anthocyanin production. Conversely, RNAi-mediated suppression of AbMYB1 resulted in decreased expression of most anthocyanin biosynthesis genes, as well as reduced anthocyanin contents in A. belladonna. Overall, AbMYB1 was identified as a fruit-expressed R2R3-MYB TF that positively regulated anthocyanin biosynthesis in A. belladonna. This study provides valuable insights into the regulation of anthocyanin biosynthesis in Solanaceae plants, laying the foundation for understanding anthocyanin accumulation especially in the whole fruits of solanaceous plants.
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Affiliation(s)
- Xiaoqiang Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Tengfei Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Lina Yuan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Fei Qiu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Yueli Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Dan Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Fangyuan Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Lingjiang Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Chunxian Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Mohammad Mahmoud Nagdy
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (M.M.N.); (M.C.)
- Department of Medicinal and Aromatic Plants Research, National Research Centre, Cairo 12311, Egypt
| | - Zun Lai Lai Htun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
- Department of Botany, University of Magway, Magway 04012, Myanmar
| | - Xiaozhong Lan
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Xizang Agriculture and Animal Husbandry University, Nyingchi 860000, China;
| | - Min Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (M.M.N.); (M.C.)
| | - Zhihua Liao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
| | - Yan Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; (X.L.); (T.Z.); (L.Y.); (F.Q.); (Y.T.); (D.L.); (F.Z.); (L.Z.); (C.Y.); (Z.L.L.H.)
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15
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Bulgakov VP. Chromatin modifications and memory in regulation of stress-related polyphenols: finding new ways to control flavonoid biosynthesis. Crit Rev Biotechnol 2024:1-17. [PMID: 38697923 DOI: 10.1080/07388551.2024.2336529] [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: 10/04/2023] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
The influence of epigenetic factors on plant defense responses and the balance between growth and defense is becoming a central area in plant biology. It is believed that the biosynthesis of secondary metabolites can be regulated by epigenetic factors, but this is not associated with the formation of a "memory" to the previous biosynthetic status. This review shows that some epigenetic effects can result in epigenetic memory, which opens up new areas of research in secondary metabolites, in particular flavonoids. Plant-controlled chromatin modifications can lead to the generation of stress memory, a phenomenon through which information regarding past stress cues is retained, resulting in a modified response to recurring stress. How deeply are the mechanisms of chromatin modification and memory generation involved in the control of flavonoid biosynthesis? This article collects available information from the literature and interactome databases to address this issue. Visualization of the interaction of chromatin-modifying proteins with the flavonoid biosynthetic machinery is presented. Chromatin modifiers and "bookmarks" that may be involved in the regulation of flavonoid biosynthesis through memory have been identified. Through different mechanisms of chromatin modification, plants can harmonize flavonoid metabolism with: stress responses, developmental programs, light-dependent processes, flowering, and longevity programs. The available information points to the possibility of developing chromatin-modifying technologies to control flavonoid biosynthesis.
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Affiliation(s)
- Victor P Bulgakov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
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16
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Zhang C, Sha Y, Wang Q, Liu J, Zhang P, Cheng S, Qin P. Integrative metabolome and transcriptome profiling provide insights into elucidation of the synthetic mechanisms of phenolic compounds in Yunnan hulled wheat (Triticum aestivum ssp. yunnanense King). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4109-4127. [PMID: 38308467 DOI: 10.1002/jsfa.13293] [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: 08/23/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Yunnan hulled wheat grains (YHWs) have abundant phenolic compounds (PCs). However, a systematic elucidation of the phenolic characteristics and molecular basis in YHWs is currently lacking. The aim of the study, for the first time, was to conduct metabolomic and transcriptomic analyses of YHWs at different developmental stages. RESULTS A total of five phenolic metabolite classes (phenolic acids, flavonoids, quinones, lignans and coumarins, and tannins) and 361 PCs were identified, with flavonoids and phenolic acids being the most abundant components. The relative abundance of the identified PCs showed a dynamic decreasing pattern with grain development, and the most significant differences in accumulation were between the enlargement and mature stage, which is consistent with the gene regulation patterns of the corresponding phenolic biosynthesis pathway. Through co-expression and co-network analysis, PAL, HCT, CCR, F3H, CHS, CHI and bZIP were identified and predicted as candidate key enzymes and transcription factors. CONCLUSION The results broaden our understanding of PC accumulation in wheat whole grains, especially the differential transfer between immature and mature grains. The identified PCs and potential regulatory factors provide important information for future in-depth research on the biosynthesis of PCs and the improvement of wheat nutritional quality. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Chuanli Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- College of Tropical Crops, Yunnan Agricultural University, Kunming, China
| | - Yun Sha
- Agricultural Technology Extension Station of Lincang, Lincang, China
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Shunhe Cheng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Jiangshu Lixiahe Institue of Agriculture Science, Yangzhou, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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17
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Gou Y, Jing Y, Song J, Nagdy MM, Peng C, Zeng L, Chen M, Lan X, Htun ZLL, Liao Z, Li Y. A novel bHLH gene responsive to low nitrogen positively regulates the biosynthesis of medicinal tropane alkaloids in Atropa belladonna. Int J Biol Macromol 2024; 266:131012. [PMID: 38522709 DOI: 10.1016/j.ijbiomac.2024.131012] [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: 01/11/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Medicinal tropane alkaloids (TAs), including hyoscyamine, anisodamine and scopolamine, are essential anticholinergic drugs specifically produced in several solanaceous plants. Atropa belladonna is one of the most important medicinal plants that produces TAs. Therefore, it is necessary to cultivate new A. belladonna germplasm with the high content of TAs. Here, we found that the levels of TAs were elevated under low nitrogen (LN) condition, and identified a LN-responsive bHLH transcription factor (TF) of A. belladonna (named LNIR) regulating the biosynthesis of TAs. The expression level of LNIR was highest in secondary roots where TAs are synthesized specifically, and was significantly induced by LN. Further research revealed that LNIR directly activated the transcription of hyoscyamine 6β-hydroxylase gene (H6H) by binding to its promoter, which converts hyoscyamine into anisodamine and subsequently epoxidizes anisodamine to form scopolamine. Overexpression of LNIR upregulated the expression levels of TA biosynthesis genes and consequently led to the increased production of TAs. In summary, we functionally identified a LN-responsive bHLH gene that facilitated the development of A. belladonna with high-yield TAs under the decreased usage of nitrogen fertilizer.
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Affiliation(s)
- Yuqin Gou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yanming Jing
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiaxin Song
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Mohammad Mahmoud Nagdy
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; Department of Medicinal and Aromatic Plants Research, National Research Centre, 12311 Dokki, Cairo, Egypt
| | - Chao Peng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lingjiang Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Min Chen
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Centre, The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Xizang Characteristic Agricultural and Animal Husbandry Resources, Tibet Agriculture and Animal Husbandry College, Nyingchi of Xizang 860000, China
| | - Zun Lai Lai Htun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China; Department of Botany, University of Magway, Magway 04012, Myanmar
| | - Zhihua Liao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Yan Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China.
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18
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Zhao X, Feng Y, Ke D, Teng Y, Yuan Z. Comparative transcriptomic and metabolomic profiles reveal fruit peel color variation in two red pomegranate cultivars. PLANT MOLECULAR BIOLOGY 2024; 114:51. [PMID: 38691187 DOI: 10.1007/s11103-024-01446-9] [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: 07/20/2023] [Accepted: 03/23/2024] [Indexed: 05/03/2024]
Abstract
Pomegranate (Punica granatum L.) which belongs to family Lythraceae, is one of the most important fruit crops of many tropical and subtropical regions. A high variability in fruit color is observed among different pomegranate accessions, which arises from the qualitative and quantitative differences in anthocyanins. However, the mechanism of fruit color variation is still not fully elucidated. In the present study, we investigated the red color mutation between a red-skinned pomegranate 'Hongbaoshi' and a purple-red-skinned cultivar 'Moshiliu', by using transcriptomic and metabolomic approaches. A total of 51 anthocyanins were identified from fruit peels, among which 3-glucoside and 3,5-diglucoside of cyanidin (Cy), delphinidin (Dp), and pelargonidin (Pg) were dominant. High proportion of Pg in early stages of 'Hongbaoshi' but high Dp in late stages of 'Moshiliu' were characterized. The unique high levels of Cy and Dp anthocyanins accumulating from early developmental stages accounted for the purple-red phenotype of 'Moshiliu'. Transcriptomic analysis revealed an early down-regulated and late up-regulated of anthocyanin-related structure genes in 'Moshiliu' compared with 'Hongbaoshi'. Alao, ANR was specially expressed in 'Hongbaoshi', with extremely low expression levels in 'Moshiliu'. For transcription factors R2R3-MYB, the profiles demonstrated a much higher transcription levels of three subgroup (SG) 5 MYBs and a sharp decrease in expression of SG6 MYB LOC116202527 in high-anthocyanin 'Moshiliu'. SG4 MYBs exhibited two entirely different patterns, LOC116203744 and LOC116212505 were down-regulated whereas LOC116205515 and LOC116212778 were up-regulated in 'Moshiliu' pomegranate. The results indicate that specific SG members of the MYB family might promote the peel coloration in different manners and play important roles in color mutation in pomegranate.
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Affiliation(s)
- Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
| | - Yingyi Feng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Ding Ke
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yingfen Teng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
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19
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Huang W, Xu B, Guo W, Huang Z, Li Y, Wu W. De novo genome assembly and population genomics of a shrub tree Barthea barthei (Hance) krass provide insights into the adaptive color variations. FRONTIERS IN PLANT SCIENCE 2024; 15:1365686. [PMID: 38751846 PMCID: PMC11094225 DOI: 10.3389/fpls.2024.1365686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Flower color is a classic example of an ecologically important trait under selection in plants. Understanding the genetic mechanisms underlying shifts in flower color can provide key insights into ecological speciation. In this study, we investigated the genetic basis of flower color divergence in Barthea barthei, a shrub tree species exhibiting natural variation in flower color. We assembled a high-quality genome assembly for B. barthei with a contig N50 of 2.39 Mb and a scaffold N50 of 16.21 Mb. The assembly was annotated with 46,430 protein-coding genes and 1,560 non-coding RNAs. Genome synteny analysis revealed two recent tetraploidization events in B. barthei, estimated to have occurred at approximately 17 and 63 million years ago. These tetraploidization events resulted in massive duplicated gene content, with over 70% of genes retained in collinear blocks. Gene family members of the core regulators of the MBW complex were significantly expanded in B. barthei compared to Arabidopsis, suggesting that these duplications may have provided raw genetic material for the evolution of novel regulatory interactions and the diversification of anthocyanin pigmentation. Transcriptome profiling of B. barthei flowers revealed differential expression of 9 transcription factors related to anthocyanin biosynthesis between the two ecotypes. Six of these differentially expressed transcription factors were identified as high-confidence candidates for adaptive evolution based on positive selection signals. This study provides insights into the genetic basis of flower color divergence and the evolutionary mechanisms underlying ecological adaptation in plants.
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Affiliation(s)
- Weicheng Huang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- South China Botanical Garden, Chinese Academy of Science, Guangzhou, China
| | - Bin Xu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Wei Guo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zecheng Huang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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20
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Wang B, Wen X, Fu B, Wei Y, Song X, Li S, Wang L, Wu Y, Hong Y, Dai S. Genome-Wide Analysis of MYB Gene Family in Chrysanthemum ×morifolium Provides Insights into Flower Color Regulation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1221. [PMID: 38732436 PMCID: PMC11085527 DOI: 10.3390/plants13091221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024]
Abstract
MYBs constitute the second largest transcription factor (TF) superfamily in flowering plants with substantial structural and functional diversity, which have been brought into focus because they affect flower colors by regulating anthocyanin biosynthesis. Up to now, the genomic data of several Chrysanthemum species have been released, which provides us with abundant genomic resources for revealing the evolution of the MYB gene family in Chrysanthemum species. In the present study, comparative analyses of the MYB gene family in six representative species, including C. lavandulifolium, C. seticuspe, C. ×morifolium, Helianthus annuus, Lactuca sativa, and Arabidopsis thaliana, were performed. A total of 1104 MYBs, which were classified into four subfamilies and 35 lineages, were identified in the three Chrysanthemum species (C. lavandulifolium, C. seticuspe, and C. ×morifolium). We found that whole-genome duplication and tandem duplication are the main duplication mechanisms that drove the occurrence of duplicates in CmMYBs (particularly in the R2R3-MYB subfamily) during the evolution of the cultivated chrysanthemums. Sequence structure and selective pressure analyses of the MYB gene family revealed that some of R2R3-MYBs were subjected to positive selection, which are mostly located on the distal telomere segments of the chromosomes and contain motifs 7 and 8. In addition, the gene expression analysis of CmMYBs in different organs and at various capitulum developmental stages of C. ×morifolium indicated that CmMYBS2, CmMYB96, and CmMYB109 might be the negative regulators for anthocyanin biosynthesis. Our results provide the phylogenetic context for research on the genetic and functional evolution of the MYB gene family in Chrysanthemum species and deepen our understanding of the regulatory mechanism of MYB TFs on the flower color of C. ×morifolium.
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Affiliation(s)
- Bohao Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (B.W.)
| | - Xiaohui Wen
- Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China
| | - Boxiao Fu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (B.W.)
| | - Yuanyuan Wei
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (B.W.)
| | - Xiang Song
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (B.W.)
| | - Shuangda Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (B.W.)
| | - Luyao Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (B.W.)
| | - Yanbin Wu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (B.W.)
| | - Yan Hong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (B.W.)
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (B.W.)
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21
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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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22
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Li N, Xu Y, Lu Y. A Regulatory Mechanism on Pathways: Modulating Roles of MYC2 and BBX21 in the Flavonoid Network. PLANTS (BASEL, SWITZERLAND) 2024; 13:1156. [PMID: 38674565 PMCID: PMC11054080 DOI: 10.3390/plants13081156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Genes of metabolic pathways are individually or collectively regulated, often via unclear mechanisms. The anthocyanin pathway, well known for its regulation by the MYB/bHLH/WDR (MBW) complex but less well understood in its connections to MYC2, BBX21, SPL9, PIF3, and HY5, is investigated here for its direct links to the regulators. We show that MYC2 can activate the structural genes of the anthocyanin pathway but also suppress them (except F3'H) in both Arabidopsis and Oryza when a local MBW complex is present. BBX21 or SPL9 can activate all or part of the structural genes, respectively, but the effects can be largely overwritten by the local MBW complex. HY5 primarily influences expressions of the early genes (CHS, CHI, and F3H). TF-TF relationships can be complex here: PIF3, BBX21, or SPL9 can mildly activate MYC2; MYC2 physically interacts with the bHLH (GL3) of the MBW complex and/or competes with strong actions of BBX21 to lessen a stimulus to the anthocyanin pathway. The dual role of MYC2 in regulating the anthocyanin pathway and a similar role of BBX21 in regulating BAN reveal a network-level mechanism, in which pathways are modulated locally and competing interactions between modulators may tone down strong environmental signals before they reach the network.
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Affiliation(s)
- Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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23
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Li J, Wang F, Sayed MA, Shen X, Zhou L, Liu X, Sun X, Chen S, Wu Y, Lu L, Gong S, Iqbal A, Yang Y. Integrated transcriptomic and metabolomic data reveal the cold stress responses molecular mechanisms of two coconut varieties. FRONTIERS IN PLANT SCIENCE 2024; 15:1353352. [PMID: 38689842 PMCID: PMC11058665 DOI: 10.3389/fpls.2024.1353352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Among tropical fruit trees, coconut holds significant edible and economic importance. The natural growth of coconuts faces a challenge in the form of low temperatures, which is a crucial factor among adverse environmental stresses impacting their geographical distribution. Hence, it is essential to enhance our comprehension of the molecular mechanisms through which cold stress influences various coconut varieties. We employed analyses of leaf growth morphology and physiological traits to examine how coconuts respond to low temperatures over 2-hour, 8-hour, 2-day, and 7-day intervals. Additionally, we performed transcriptome and metabolome analyses to identify the molecular and physiological shifts in two coconut varieties displaying distinct sensitivities to the cold stress. As the length of cold stress extended, there was a prominent escalation within the soluble protein (SP), proline (Pro) concentrations, the activity of peroxidase (POD) and superoxide dismutase (SOD) in the leaves. Contrariwise, the activity of glutathione peroxidase (GSH) underwent a substantial reduction during this period. The widespread analysis of metabolome and transcriptome disclosed a nexus of genes and metabolites intricately cold stress were chiefly involved in pathways centered around amino acid, flavonoid, carbohydrate and lipid metabolism. We perceived several stress-responsive metabolites, such as flavonoids, carbohydrates, lipids, and amino acids, which unveiled considerably, lower in the genotype subtle to cold stress. Furthermore, we uncovered pivotal genes in the amino acid biosynthesis, antioxidant system and flavonoid biosynthesis pathway that presented down-regulation in coconut varieties sensitive to cold stress. This study broadly enriches our contemporary perception of the molecular machinery that contributes to altering levels of cold stress tolerance amid coconut genotypes. It also unlocks several unique prospects for exploration in the areas of breeding or engineering, aiming to identifying tolerant and/or sensitive coconut varieties encompassing multi-omics layers in response to cold stress conditions.
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Affiliation(s)
- Jing Li
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Fangyuan Wang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Md. Abu Sayed
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - XiaoJun Shen
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Xiaomei Liu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Xiwei Sun
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Shuangyan Chen
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
- School of Tropical Crops, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yi Wu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Lilan Lu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Shufang Gong
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Amjad Iqbal
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
- Department of Food Science & Technology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yaodong Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
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Wang R, Yang X, Wang T, Li B, Li P, Zhang Q. Integration of Metabolomic and Transcriptomic Analyses Reveals the Molecular Mechanisms of Flower Color Formation in Prunus mume. PLANTS (BASEL, SWITZERLAND) 2024; 13:1077. [PMID: 38674486 PMCID: PMC11054544 DOI: 10.3390/plants13081077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/04/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
Flower color is an important trait that affects the economic value of Prunus mume, a famous ornamental plant in the Rosaceae family. P. mume with purple-red flowers is uniquely charming and highly favored in landscape applications. However, little is known about its flower coloring mechanism, which stands as a critical obstacle on the path to innovative breeding for P. mume flower color. In this study, transcriptomic and targeted metabolomic analyses of purple-red P. mume and white P. mume were performed to elucidate the mechanism of flower color formation. In addition, the expression patterns of key genes were analyzed using an RT-qPCR experiment. The results showed that the differential metabolites were significantly enriched in the flavonoid synthesis pathway. A total of 14 anthocyanins emerged as the pivotal metabolites responsible for the differences in flower color between the two P. mume cultivars, comprising seven cyanidin derivatives, five pelargonium derivatives, and two paeoniflorin derivatives. Moreover, the results clarified that the metabolic pathway determining flower color in purple-red P. mume encompasses two distinct branches: cyanidin and pelargonidin, excluding the delphinidin branch. Additionally, through the integrated analysis of transcriptomic and metabolomic data, we identified 18 key genes responsible for anthocyanin regulation, thereby constructing the gene regulatory network for P. mume anthocyanin synthesis. Among them, ten genes (PmCHI, PmGT2, PmGT5, PmGST3, PmMYB17, PmMYB22, PmMYB23, PmbHLH4, PmbHLH10, and PmbHLH20) related to anthocyanin synthesis were significantly positively correlated with anthocyanin contents, indicating that they may be the key contributors to anthocyanin accumulation. Our investigation contributes a novel perspective to understanding the mechanisms responsible for flower color formation in P. mume. The findings of this study introduce novel strategies for molecular design breeding aimed at manipulating flower color in P. mume.
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Affiliation(s)
- Ruyi Wang
- College of Landscape and Tourism, Hebei Agricultural University, Baoding 071000, China; (R.W.); (X.Y.)
| | - Xin Yang
- College of Landscape and Tourism, Hebei Agricultural University, Baoding 071000, China; (R.W.); (X.Y.)
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Tao Wang
- China National Botanical Garden, Beijing 100089, China
| | - Baohui Li
- College of Landscape and Tourism, Hebei Agricultural University, Baoding 071000, China; (R.W.); (X.Y.)
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Ping Li
- College of Landscape and Tourism, Hebei Agricultural University, Baoding 071000, China; (R.W.); (X.Y.)
| | - Qin Zhang
- College of Landscape and Tourism, Hebei Agricultural University, Baoding 071000, China; (R.W.); (X.Y.)
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25
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Ye XX, Chen YQ, Wu JS, Zhong HQ, Lin B, Huang ML, Fan RH. Biochemical and Transcriptome Analysis Reveals Pigment Biosynthesis Influenced Chlorina Leaf Formation in Anoectochilus roxburghii (Wall.) Lindl. Biochem Genet 2024; 62:1040-1054. [PMID: 37528284 DOI: 10.1007/s10528-023-10432-7] [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: 09/29/2022] [Accepted: 06/15/2023] [Indexed: 08/03/2023]
Abstract
Anoectochilus roxburghii (Wall.) Lindl is a perennial herb of the Orchidaceae family; a yellow-green mutant and a yellow mutant were obtained from the wild type, thereby providing good material for the study of leaf color variation. Pigment content analysis revealed that chlorophyll, carotenoids, and anthocyanin were lower in the yellow-green and yellow mutants than in the wild type. Transcriptome analysis of the yellow mutant and wild type revealed that 78,712 unigenes were obtained, and 599 differentially expressed genes (120 upregulated and 479 downregulated) were identified. Using the Kyoto Encyclopedia of Genes and Genomes pathway analysis, candidate genes involved in the anthocyanin biosynthetic pathway (five unigenes) and the chlorophyll metabolic pathway (two unigenes) were identified. Meanwhile, the low expression of the chlorophyll and anthocyanin biosynthetic genes resulted in the absence of chlorophylls and anthocyanins in the yellow mutant. This study provides a basis for similar research in other closely related species.
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Affiliation(s)
- Xiu-Xian Ye
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Yi-Quan Chen
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Jian-She Wu
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Huai-Qin Zhong
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Bing Lin
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Min-Ling Huang
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China.
| | - Rong-Hui Fan
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China.
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26
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Ma R, Huang W, Hu Q, Tian G, An J, Fang T, Liu J, Hou J, Zhao M, Sun L. Tandemly duplicated MYB genes are functionally diverged in the regulation of anthocyanin biosynthesis in soybean. PLANT PHYSIOLOGY 2024; 194:2549-2563. [PMID: 38235827 DOI: 10.1093/plphys/kiae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/13/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
Gene duplications have long been recognized as a driving force in the evolution of genes, giving rise to novel functions. The soybean (Glycine max) genome is characterized by a large number of duplicated genes. However, the extent and mechanisms of functional divergence among these duplicated genes in soybean remain poorly understood. In this study, we revealed that 4 MYB genes (GmMYBA5, GmMYBA2, GmMYBA1, and Glyma.09g235000)-presumably generated by tandem duplication specifically in the Phaseoleae lineage-exhibited a stronger purifying selection in soybean compared to common bean (Phaseolus vulgaris). To gain insights into the diverse functions of these tandemly duplicated MYB genes in anthocyanin biosynthesis, we examined the expression, transcriptional activity, induced metabolites, and evolutionary history of these 4 MYB genes. Our data revealed that Glyma.09g235000 is a pseudogene, while the remaining 3 MYB genes exhibit strong transcriptional activation activity, promoting anthocyanin biosynthesis in different soybean tissues. GmMYBA5, GmMYBA2, and GmMYBA1 induced anthocyanin accumulation by upregulating the expression of anthocyanin pathway-related genes. Notably, GmMYBA5 showed a lower capacity for gene induction compared to GmMYBA2 and GmMYBA1. Metabolomics analysis further demonstrated that GmMYBA5 induced distinct anthocyanin accumulation in Nicotiana benthamiana leaves and soybean hairy roots compared to GmMYBA2 and GmMYBA1, suggesting their functional divergence leading to the accumulation of different metabolites accumulation following gene duplication. Together, our data provide evidence of functional divergence within the MYB gene cluster following tandem duplication, which sheds light on the potential evolutionary directions of gene duplications during legume evolution.
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Affiliation(s)
- Ruirui Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Wenxuan Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Quan Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Guo Tian
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie An
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ting Fang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jia Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jingjing Hou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lianjun Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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Gu C, Pei MS, Guo ZH, Wu L, Qi KJ, Wang XP, Liu H, Liu Z, Lang Z, Zhang S. Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism. Genome Biol 2024; 25:70. [PMID: 38486226 PMCID: PMC10938805 DOI: 10.1186/s13059-024-03200-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here, we systematically investigate the metabolic landscape and regulatory network involved. RESULTS We generate an association database consisting of 439 metabolites and 14,399 genes to elucidate the gene regulatory network of pear flesh metabolism. Interestingly, we detect increased DNA methylation in the promoters of most genes within the database during pear flesh development. Application of a DNA methylation inhibitor to the developing fruit represses chlorophyll degradation in the pericarp and promotes xanthophyll, β-carotene, and abscisic acid (ABA) accumulation in the flesh. We find the gradual increase in ABA production during pear flesh development is correlated with the expression of several carotenoid pathway genes and multiple transcription factors. Of these transcription factors, the zinc finger protein PbZFP1 is identified as a positive mediator of ABA biosynthesis in pear flesh. Most ABA pathway genes and transcription factors are modified by DNA methylation in the promoters, although some are induced by the DNA methylation inhibitor. These results suggest that DNA methylation inhibits ABA accumulation, which may delay fruit ripening. CONCLUSION Our findings provide insights into epigenetic regulation of metabolic regulatory networks during pear flesh development, particularly with regard to DNA methylation.
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Affiliation(s)
- Chao Gu
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mao-Song Pei
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Hua Guo
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lei Wu
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai-Jie Qi
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue-Ping Wang
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong Liu
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Zhaobo Lang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Shaoling Zhang
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Ma S, Zhou H, Ren T, Yu ER, Feng B, Wang J, Zhang C, Zhou C, Li Y. Integrated transcriptome and metabolome analysis revealed that HaMYB1 modulates anthocyanin accumulation to deepen sunflower flower color. PLANT CELL REPORTS 2024; 43:74. [PMID: 38379014 PMCID: PMC10879246 DOI: 10.1007/s00299-023-03098-3] [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: 08/22/2023] [Accepted: 09/25/2023] [Indexed: 02/22/2024]
Abstract
KEY MESSAGE HanMYB1 was found to play positive roles in the modulation of anthocyanins metabolism based on the integrative analysis of different color cultivars and the related molecular genetic analyses. As a high value ornamental and edible crop with various colors, sunflowers (Helianthus annuus L.) provide an ideal system to understand the formation of flower color. Anthocyanins are major pigments in higher plants, which is associated with development of flower colors and ability of oxidation resistance. Here, we performed an integrative analysis of the transcriptome and flavonoid metabolome in five sunflower cultivars with different flower colors. According to differentially expressed genes and differentially accumulated flavonoids, these cultivars could be grouped into yellow and red. The results showed that more anthocyanins were accumulated in the red group flowers, especially the chrysanthemin. Some anthocyanins biosynthesis-related genes like UFGT (UDP-glycose flavonoid glycosyltransferase) also expressed more in the red group flowers. A MYB transcriptional factor, HanMYB1, was found to play vital positive roles in the modulation of anthocyanins metabolism by the integrative analysis. Overexpressed HanMYB1 in tobacco could deepen the flower color, increase the accumulation of anthocyanins and directly active the express of UFGT genes. Our findings indicated that the MYB transcriptional factors provide new insight into the dynamic regulation of the anthocyanin biosynthesis in facilitating sunflower color formation and anthocyanin accumulation.
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Affiliation(s)
- Siqi Ma
- Marine Agriculture Research Center/Key Laboratory of Synthetic Biology of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Hanlin Zhou
- Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement/Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Tingting Ren
- Marine Agriculture Research Center/Key Laboratory of Synthetic Biology of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Er-Ru Yu
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Science, Guiyang, 550006, China
| | - Bin Feng
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Science, Guiyang, 550006, China
| | - Juying Wang
- Technical Innovation Center for Comprehensive Utilization of Saline-Alkali Land in Huangsanjiao Agricultural High-Tech, Dongying, 257000, China
| | - Chengsheng Zhang
- Marine Agriculture Research Center/Key Laboratory of Synthetic Biology of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Chao Zhou
- Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement/Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
| | - Yiqiang Li
- Marine Agriculture Research Center/Key Laboratory of Synthetic Biology of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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29
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Kim JM, Lee JW, Seo JS, Ha BK, Kwon SJ. Differentially Expressed Genes Related to Isoflavone Biosynthesis in a Soybean Mutant Revealed by a Comparative Transcriptomic Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:584. [PMID: 38475431 DOI: 10.3390/plants13050584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Soybean [Glycine max (L.) Merr.] isoflavones, which are secondary metabolites with various functions, are included in food, cosmetics, and medicine. However, the molecular mechanisms regulating the glycosylation and malonylation of isoflavone glycoconjugates remain unclear. In this study, we conducted an RNA-seq analysis to compare soybean genotypes with different isoflavone contents, including Danbaek and Hwanggeum (low-isoflavone cultivars) as well as DB-088 (high-isoflavone mutant). The transcriptome analysis yielded over 278 million clean reads, representing 39,156 transcripts. The analysis of differentially expressed genes (DEGs) detected 2654 up-regulated and 1805 down-regulated genes between the low- and high-isoflavone genotypes. The putative functions of these 4459 DEGs were annotated on the basis of GO and KEGG pathway enrichment analyses. These DEGs were further analyzed to compare the expression patterns of the genes involved in the biosynthesis of secondary metabolites and the genes encoding transcription factors. The examination of the relative expression levels of 70 isoflavone biosynthetic genes revealed the HID, IFS, UGT, and MAT expression levels were significantly up/down-regulated depending on the genotype and seed developmental stage. These expression patterns were confirmed by quantitative real-time PCR. Moreover, a gene co-expression analysis detected potential protein-protein interactions, suggestive of common functions. The study findings provide valuable insights into the structural genes responsible for isoflavone biosynthesis and accumulation in soybean seeds.
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Affiliation(s)
- Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jeong Woo Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji Su Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
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Hu Y, Zhao H, Xue L, Nie N, Zhang H, Zhao N, He S, Liu Q, Gao S, Zhai H. IbMYC2 Contributes to Salt and Drought Stress Tolerance via Modulating Anthocyanin Accumulation and ROS-Scavenging System in Sweet Potato. Int J Mol Sci 2024; 25:2096. [PMID: 38396773 PMCID: PMC10889443 DOI: 10.3390/ijms25042096] [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: 12/28/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Basic helix-loop-helix (bHLH) transcription factors extensively affect various physiological processes in plant metabolism, growth, and abiotic stress. However, the regulation mechanism of bHLH transcription factors in balancing anthocyanin biosynthesis and abiotic stress in sweet potato (Ipomoea batata (L.) Lam.) remains unclear. Previously, transcriptome analysis revealed the genes that were differentially expressed among the purple-fleshed sweet potato cultivar 'Jingshu 6' and its anthocyanin-rich mutant 'JS6-5'. Here, we selected one of these potential genes, IbMYC2, which belongs to the bHLH transcription factor family, for subsequent analyses. The expression of IbMYC2 in the JS6-5 storage roots is almost four-fold higher than Jingshu 6 and significantly induced by hydrogen peroxide (H2O2), methyl jasmonate (MeJA), NaCl, and polyethylene glycol (PEG)6000. Overexpression of IbMYC2 significantly enhances anthocyanin production and exhibits a certain antioxidant capacity, thereby improving salt and drought tolerance. In contrast, reducing IbMYC2 expression increases its susceptibility. Our data showed that IbMYC2 could elevate the expression of anthocyanin synthesis pathway genes by binding to IbCHI and IbDFR promoters. Additionally, overexpressing IbMYC2 activates genes encoding reactive oxygen species (ROS)-scavenging and proline synthesis enzymes under salt and drought conditions. Taken together, these results demonstrate that the IbMYC2 gene exercises a significant impact on crop quality and stress resistance.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (Y.H.); (H.Z.); (L.X.); (N.N.); (H.Z.); (N.Z.); (S.H.); (Q.L.)
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (Y.H.); (H.Z.); (L.X.); (N.N.); (H.Z.); (N.Z.); (S.H.); (Q.L.)
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31
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Zhang L, Zhang J, Wei B, Li Y, Fang X, Zhong Y, Wang L. Transcription factor MdNAC33 is involved in ALA-induced anthocyanin accumulation in apples. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111949. [PMID: 38065304 DOI: 10.1016/j.plantsci.2023.111949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
5-Aminolevulinic acid (ALA), as a new natural plant growth regulator, has a significant function in promoting anthocyanin accumulation in many species of fruits. However, the mechanisms underlying remain obscure. In a transcriptome study of our group, it was found that many transcription factors (TFs) including NACs responsive to ALA treatment during anthocyanin accumulation. In the present study, we found a NAC of apple, MdNAC33 was coordinatively expressed with anthocyanin accumulation after ALA treatment in the apple fruits and leaves, suggesting that this TF may be involved in anthocyanin accumulation induced by ALA. We found that the MdNAC33 protein was localized in the nucleus and exhibited strong transcriptional activity in both yeast cells and plants, where its C-terminal contributed to the transcriptional activity. Functional analysis showed that overexpression of MdNAC33 promoted the accumulation of anthocyanin, while the silencing vector of MdNAC33 (RNAi) significantly impaired the anthocyanin accumulation induced by ALA. Yeast one-hybrid (Y1H), luciferase assay and electrophoretic mobility shift assay (EMSA) indicated that MdNAC33 could bind to promoters of MdbHLH3, MdDFR and MdANS to activate the gene expressions. In addition, MdNAC33 specifically interacts with MdMYB1, a positive regulator of anthocyanin biosynthesis, which was then in turn binding to its target genes MdUFGT and MdGSTF12, to promote anthocyanin accumulation in apples. Taken together, our data indicate that MdNAC33 plays multiple roles in ALA-induced anthocyanin biosynthesis. It provides new insights into the mechanisms of anthocyanin accumulation induced by ALA.
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Affiliation(s)
- Liuzi Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiangting Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bo Wei
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yage Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiang Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Zhong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Liangju Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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32
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Aruwa CE, Sabiu S. Adipose tissue inflammation linked to obesity: A review of current understanding, therapies and relevance of phyto-therapeutics. Heliyon 2024; 10:e23114. [PMID: 38163110 PMCID: PMC10755291 DOI: 10.1016/j.heliyon.2023.e23114] [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: 07/18/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Obesity is a current global challenge affecting all ages and is characterized by the up-regulated secretion of bioactive factors/pathways which result in adipose tissue inflammation (ATI). Current obesity therapies are mainly focused on lifestyle (diet/nutrition) changes. This is because many chemosynthetic anti-obesogenic medications cause adverse effects like diarrhoea, dyspepsia, and faecal incontinence, among others. As such, it is necessary to appraise the efficacies and mechanisms of action of safer, natural alternatives like plant-sourced compounds, extracts [extractable phenol (EP) and macromolecular antioxidant (MA) extracts], and anti-inflammatory peptides, among others, with a view to providing a unique approach to obesity care. These natural alternatives may constitute potent therapies for ATI linked to obesity. The potential of MA compounds (analysed for the first time in this review) and extracts in ATI and obesity management is elucidated upon, while also highlighting research gaps and future prospects. Furthermore, immune cells, signalling pathways, genes, and adipocyte cytokines play key roles in ATI responses and are targeted in certain therapies. As a result, this review gives an in-depth appraisal of ATI linked to obesity, its causes, mechanisms, and effects of past, present, and future therapies for reversal and alleviation of ATI. Achieving a significant decrease in morbidity and mortality rates attributed to ATI linked to obesity and related comorbidities is possible as research improves our understanding over time.
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Affiliation(s)
- Christiana Eleojo Aruwa
- Department of Biotechnology and Food Science, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
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Kim J, Jang H, Huh SM, Cho A, Yim B, Jeong SH, Kim H, Yu HJ, Mun JH. Effect of structural variation in the promoter region of RsMYB1.1 on the skin color of radish taproot. FRONTIERS IN PLANT SCIENCE 2024; 14:1327009. [PMID: 38264015 PMCID: PMC10804855 DOI: 10.3389/fpls.2023.1327009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024]
Abstract
Accumulation of anthocyanins in the taproot of radish is an agronomic trait beneficial for human health. Several genetic loci are related to a red skin or flesh color of radish, however, the functional divergence of candidate genes between non-red and red radishes has not been investigated. Here, we report that a novel genetic locus on the R2 chromosome, where RsMYB1.1 is located, is associated with the red color of the skin of radish taproot. A genome-wide association study (GWAS) of 66 non-red-skinned (nR) and 34 red-skinned (R) radish accessions identified three nonsynonymous single nucleotide polymorphisms (SNPs) in the third exon of RsMYB1.1. Although the genotypes of SNP loci differed between the nR and R radishes, no functional difference in the RsMYB1.1 proteins of nR and R radishes in their physical interaction with RsTT8 was detected by yeast-two hybrid assay or in anthocyanin accumulation in tobacco and radish leaves coexpressing RsMYB1.1 and RsTT8. By contrast, insertion- or deletion-based GWAS revealed that one large AT-rich low-complexity sequence of 1.3-2 kb was inserted in the promoter region of RsMYB1.1 in the nR radishes (RsMYB1.1nR), whereas the R radishes had no such insertion; this represents a presence/absence variation (PAV). This insertion sequence (RsIS) was radish specific and distributed among the nine chromosomes of Raphanus genomes. Despite the extremely low transcription level of RsMYB1.1nR in the nR radishes, the inactive RsMYB1.1nR promoter could be functionally restored by deletion of the RsIS. The results of a transient expression assay using radish root sections suggested that the RsIS negatively regulates the expression of RsMYB1.1nR, resulting in the downregulation of anthocyanin biosynthesis genes, including RsCHS, RsDFR, and RsANS, in the nR radishes. This work provides the first evidence of the involvement of PAV in an agronomic trait of radish.
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Affiliation(s)
- Jiin Kim
- Department of Life Sciences, Institute of Convergence Science & Technology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Hoyeol Jang
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
| | - Sun Mi Huh
- Department of Life Sciences, Institute of Convergence Science & Technology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Ara Cho
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Bomi Yim
- Department of Life Sciences, Institute of Convergence Science & Technology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Seung-Hoon Jeong
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
| | - Hee-Ju Yu
- Department of Life Sciences, Institute of Convergence Science & Technology, The Catholic University of Korea, Bucheon, Republic of Korea
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Jeong-Hwan Mun
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
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Zeng HT, Zheng T, Tang Q, Xu H, Chen M. Integrative metabolome and transcriptome analyses reveal the coloration mechanism in Camellia oleifera petals with different color. BMC PLANT BIOLOGY 2024; 24:19. [PMID: 38166635 PMCID: PMC10759395 DOI: 10.1186/s12870-023-04699-6] [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: 08/31/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Camellia olelfera petals are colorful, and have high ornamental value. However, the color formation mechanism of C. olelfera petals with different color is still unclear. In our study, WGCNA method was applied to integrate metabolites and transcriptomes to investigate the coloration mechanism of four C. olelfera cultivars with different petal colors. RESULTS Here, a total of 372 flavonoids were identified (including 27 anthocyanins), and 13 anthocyanins were significantly differentially accumulated in C. olelfera petals. Among them, cyanidin-3-O-(6''-O-p-Coumaroyl) glucoside was the main color constituent in pink petals, cyanidin-3-O-glucoside, cyanidin-3-O-galactoside, cyanidin-3-O-rutinoside, and cyanidin-3-O-(6''-O-malonyl) glucoside were the main contributors to candy pink petals, and peonidin-3-O-glucoside was the important color substance responsible for the red petals of C. oleifera. Furthermore, six structural genes (Co4CL1, CoF3H1, CoF3'H, CoANS, CoUGT75C1-4, and CoUGT75C1-5), three MYBs (CoMYB1, CoMYB4, and CoMYB44-3), three bHLHs (CobHLH30, CobHLH 77, and CobHLH 79-1), and two WRKYs (CoWRKY7 and CoWRKY22) could be identified candidate genes related to anthocyanins biosynthesis and accumulation, and lead to the pink and red phenotypes. The regulatory network of differentially accumulated anthocyanins and the anthocyanins related genes in C. olelfera petals were established. CONCLUSIONS These findings elucidate the molecular basis of the coloration mechanisms of pink and red color in C. olelfera petals, and provided valuable target genes for future improvement of petals color in C. olelfera.
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Affiliation(s)
- Hai-Tao Zeng
- College of Biology Science and Engineering, Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Shaanxi University of Technology, Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong, 723001, Shaanxi, China
| | - Tao Zheng
- College of Biology Science and Engineering, Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Shaanxi University of Technology, Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong, 723001, Shaanxi, China.
| | - Qi Tang
- College of Biology Science and Engineering, Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Shaanxi University of Technology, Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong, 723001, Shaanxi, China
| | - Hao Xu
- College of Biology Science and Engineering, Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Shaanxi University of Technology, Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong, 723001, Shaanxi, China
| | - Mengjiao Chen
- College of Biology Science and Engineering, Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Shaanxi University of Technology, Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong, 723001, Shaanxi, China
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Jiang W, Jiang Q, Shui Z, An P, Shi S, Liu T, Zhang H, Huang S, Jing B, Xiao E, Quan L, Liu J, Wang Z. HaMYBA-HabHLH1 regulatory complex and HaMYBF fine-tune red flower coloration in the corolla of sunflower (Helianthus annuus L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111901. [PMID: 37865209 DOI: 10.1016/j.plantsci.2023.111901] [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: 07/14/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
Sunflowers are well-known ornamental plants, while sunflowers with red corolla are rare and the mechanisms underlying red coloration remain unclear. Here, a comprehensive analysis of metabolomics and transcriptomics on flavonoid pathway was performed to investigate the molecular mechanisms underlying the differential color formation between red sunflower Pc103 and two yellow sunflowers (Yr17 and Y35). Targeted metabolomic analysis revealed higher anthocyanin levels but lower flavonol content in Pc103 compared to the yellow cultivars. RNA-sequencing and phylogenetic analysis identified multiple genes involved in the flavonoid pathway, including series of structural genes and three MYB and bHLH genes. Specifically, HaMYBA and HabHLH1 were up-regulated in Pc103, whereas HaMYBF exhibited reduced expression. HaMYBA was found to interact with HabHLH1 in vivo and in vitro, while HaMYBF does not. Transient expression analysis further revealed that HabHLH1 and HaMYBA cooperatively regulate increased expression of dihydroflavonol 4-reductase (DFR), leading to anthocyanin accumulation. On the other hand, ectopic expression of HaMYBF independently modulates flavonol synthase (FLS) expression, but hindered anthocyanin production. Collectively, our findings suggest that the up-regulation of HaMYBA and HabHLH1, as well as the down-regulation of HaMYBF, contribute to the red coloration in Pc103. It offers a theoretical basis for improving sunflower color through genetic engineering.
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Affiliation(s)
- Wenhui Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China; Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen 518120, China
| | - Qinqin Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Zhijie Shui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Peipei An
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Shandang Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Tianxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Hanbing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Shuyi Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Bing Jing
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Enshi Xiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Li Quan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Jixia Liu
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia 750002, China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China.
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Huang H, Zhao L, Zhang B, Huang W, Zhang Z, An B. Integrated analysis of the metabolome and transcriptome provides insights into anthocyanin biosynthesis of cashew apple. Food Res Int 2024; 175:113711. [PMID: 38129034 DOI: 10.1016/j.foodres.2023.113711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
The cashew apple remains an underutilized agricultural product despite its abundance as a by-product of cashew nut production. Anthocyanins are water-soluble pigments responsible for red, purple, and blue hues in plant tissues and have various health-promoting properties. To investigate the anthocyanin biosynthesis in cashew apples, fruits with varying peel colors from three cultivars were subjected to integrative analyses with metabolomics and transcriptomics. Through a UPLC-ESI-MS/MS-based targeted metabolomics analysis, a total of 26 distinct anthocyanin compounds were identified in the fruits of the three cashew cultivars. Subsequent quantification revealed that Pelargonidin-3-O-galactoside, Petunidin-3-O-arabinoside, and Cyanidin-3-O-galactoside were the primary contributors responsible for the red pigmentation in cashew apple peels. Following transcriptomic analysis showed that the expression levels of anthocyanin biosynthetic genes were predominantly higher in the red cashew apples as compared to the other two cultivars. Moreover, correlation analysis revealed that eight potential transcription factors implicated in the regulation of anthocyanin biosynthesis. Among these, four transcription factors exhibited positive correlations with both anthocyanin contents and anthocyanin biosynthetic gene expression, while the remaining four transcription factors displayed negative correlations. These findings provide a comprehensive understanding of the molecular basis of anthocyanin biosynthesis in cashew apple peels.
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Affiliation(s)
- Haijie Huang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory of Crop Gene Resources and Germplasm Creation in South China, Ministry of Agriculture and Rural Affairs & National Cultivar Improvement Center of Tropical Fruit Tree, Haikou, 571101, People's Republic of China.
| | - Li Zhao
- Tropical Biodiversity and Bioresource Utilization Laboratory, Qiongtai Normal University, Haikou 570100, People's Republic of China
| | - Bei Zhang
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, People's Republic of China
| | - Weijian Huang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory of Crop Gene Resources and Germplasm Creation in South China, Ministry of Agriculture and Rural Affairs & National Cultivar Improvement Center of Tropical Fruit Tree, Haikou, 571101, People's Republic of China
| | - Zhongrun Zhang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory of Crop Gene Resources and Germplasm Creation in South China, Ministry of Agriculture and Rural Affairs & National Cultivar Improvement Center of Tropical Fruit Tree, Haikou, 571101, People's Republic of China
| | - Bang An
- Sanya Nanfan Research Institute of Hainan University, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, People's Republic of China.
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37
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Yang Z, Lin M, Yang X, Wu D, Chen K. Comprehensive analysis of transcriptome and metabolome provides insights into the stress response mechanisms of apple fruit to postharvest impact damage. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 7:100176. [PMID: 37457816 PMCID: PMC10344661 DOI: 10.1016/j.fochms.2023.100176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/06/2023] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
An integrated analysis of the transcriptome and metabolome was conducted to investigate the underlying mechanisms of apple fruit response to impact damage stress. During the post-damage storage, a total of 124 differentially expressed genes (DEGs) were identified, which were mainly annotated in 13 pathways, including phenylpropanoid biosynthesis. Besides, 175 differentially expressed metabolites (DEMs), including 142 up-regulated and 33 down-regulated metabolites, exhibited significant alteration after impact damage. The DEGs and DEMs were simultaneously annotated in 7 metabolic pathways, including flavonoid biosynthesis. Key genes in the volatile esters and flavonoid biosynthesis pathways were revealed, which may play a crucial role in the coping mechanisms of apple fruit under impact damage stress. Moreover, 13 ABC transporters were significantly upregulated, indicating that ABC transporters may contribute to the transportation of secondary metabolites associated with response to impact damage stress. The results may elucidate the comprehension of metabolic networks and molecular mechanisms in apple fruits that have undergone impact damage.
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Affiliation(s)
- Zhichao Yang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Menghua Lin
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
| | - Xiangzheng Yang
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- Jinan Fruit Research Institute, All China Federation of Supply and Marketing Cooperatives, Jinan 250014, PR China
| | - Di Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- Zhejiang University Zhongyuan Institute, Zhengzhou 450000, PR China
| | - Kunsong Chen
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
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Zhang Y, Wang L, Kong X, Chen Z, Zhong S, Li X, Shan R, You X, Wei K, Chen C. Integrated Analysis of Metabolome and Transcriptome Revealed Different Regulatory Networks of Metabolic Flux in Tea Plants [ Camellia sinensis (L.) O. Kuntze] with Varied Leaf Colors. Int J Mol Sci 2023; 25:242. [PMID: 38203412 PMCID: PMC10779186 DOI: 10.3390/ijms25010242] [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: 11/15/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Leaf color variations in tea plants were widely considered due to their attractive phenotypes and characteristic flavors. The molecular mechanism of color formation was extensively investigated. But few studies focused on the transformation process of leaf color change. In this study, four strains of 'Baijiguan' F1 half-sib generation with similar genetic backgrounds but different colors were used as materials, including Green (G), Yellow-Green (Y-G), Yellow (Y), and Yellow-Red (Y-R). The results of broadly targeted metabolomics showed that 47 metabolites were differentially accumulated in etiolated leaves (Y-G, Y, and Y-R) as compared with G. Among them, lipids were the main downregulated primary metabolites in etiolated leaves, which were closely linked with the thylakoid membrane and chloroplast structure. Flavones and flavonols were the dominant upregulated secondary metabolites in etiolated leaves, which might be a repair strategy for reducing the negative effects of dysfunctional chloroplasts. Further integrated analysis with the transcriptome indicated different variation mechanisms of leaf phenotype in Y-G, Y, and Y-R. The leaf color formation of Y-G and Y was largely determined by the increased content of eriodictyol-7-O-neohesperidoside and the enhanced activities of its modification process, while the color formation of Y-R depended on the increased contents of apigenin derivates and the vigorous processes of their transportation and transcription factor regulation. The key candidate genes, including UDPG, HCT, CsGSTF1, AN1/CsMYB75, and bHLH62, might play important roles in the flavonoid pathway.
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Affiliation(s)
- Yazhen Zhang
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China; (Y.Z.); (X.K.); (Z.C.); (S.Z.); (X.L.); (R.S.); (X.Y.)
| | - Liyuan Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou 310008, China;
| | - Xiangrui Kong
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China; (Y.Z.); (X.K.); (Z.C.); (S.Z.); (X.L.); (R.S.); (X.Y.)
| | - Zhihui Chen
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China; (Y.Z.); (X.K.); (Z.C.); (S.Z.); (X.L.); (R.S.); (X.Y.)
| | - Sitong Zhong
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China; (Y.Z.); (X.K.); (Z.C.); (S.Z.); (X.L.); (R.S.); (X.Y.)
| | - Xinlei Li
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China; (Y.Z.); (X.K.); (Z.C.); (S.Z.); (X.L.); (R.S.); (X.Y.)
| | - Ruiyang Shan
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China; (Y.Z.); (X.K.); (Z.C.); (S.Z.); (X.L.); (R.S.); (X.Y.)
| | - Xiaomei You
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China; (Y.Z.); (X.K.); (Z.C.); (S.Z.); (X.L.); (R.S.); (X.Y.)
| | - Kang Wei
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou 310008, China;
| | - Changsong Chen
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China; (Y.Z.); (X.K.); (Z.C.); (S.Z.); (X.L.); (R.S.); (X.Y.)
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Chen Y, Ling Q, Li X, Ma Q, Tang S, Yuanzhi P, Liu QL, Jia Y, Yong X, Jiang B. Transcriptome analysis during axillary bud growth in chrysanthemum ( chrysanthemum× morifolium). PeerJ 2023; 11:e16436. [PMID: 38111658 PMCID: PMC10726743 DOI: 10.7717/peerj.16436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/19/2023] [Indexed: 12/20/2023] Open
Abstract
The chrysanthemum DgLsL gene, homologous with tomato Ls, is one of the earliest expressed genes controlling axillary meristem initiation. In this study, the wild-type chrysanthemum (CW) and DgLsL-overexpressed line 15 (C15) were used to investigate the regulatory mechanism of axillary bud development in chrysanthemum. Transcriptome sequencing was carried out to detect the differentially expressed genes of the axillary buds 0 h, 24 h and 48 h after decapitation. The phenotypic results showed that the number of axillary buds of C15 was significantly higher than CW. A total of 9,224 DEGs were identified in C15-0 vs. CW-0, 10,622 DEGs in C15-24 vs. CW-24, and 8,929 DEGs in C15-48 vs. CW-48.GO and KEGG pathway enrichment analyses showed that the genes of the flavonoid, phenylpropanoids and plant hormone pathways appeared to be differentially expressed, indicating their important roles in axillary bud germination. DgLsL reduces GA content in axillary buds by promoting GA2ox expression.These results confirmed previous studies on axillary bud germination and growth, and revealed the important roles of genes involved in plant hormone biosynthesis and signal transduction, aiding in the study of the gene patterns involved in axillary bud germination and growth.
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Affiliation(s)
- Yijun Chen
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Qin Ling
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Xin Li
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Qiqi Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - ShaoKang Tang
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Pan Yuanzhi
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Qing-lin Liu
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Yin Jia
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Xue Yong
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Beibei Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
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Yang W, Jiang T, Wang Y, Wang X, Wang R. Combined Transcriptomics and Metabolomics Analysis Reveals the Effect of Selenium Fertilization on Lycium barbarum Fruit. Molecules 2023; 28:8088. [PMID: 38138577 PMCID: PMC10745541 DOI: 10.3390/molecules28248088] [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: 09/17/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
As a beneficial nutrient and essential trace element, selenium plays a significant role in plant growth functions and human protein biosynthesis. Plant selenium enrichment is mainly obtained from both natural soil and exogenous selenium supplementation, while human beings consume selenium-enriched foods for the purposes of selenium supplementation. In this study, different types of selenium fertilizers were sprayed onto Lycium barbarum in Ningxia, and transcriptomics and metabolomics techniques were used to explore the effects of selenium on the fruit differentials and differential genes in Lycium barbarum. Taking the "Ning Qiyi No.1" wolfberry as the research object, sodium selenite, nano-selenium, and organic selenium were sprayed at a concentration of 100 mg·L-1 three times from the first fruiting period to the harvesting period, with a control treatment comprising the spraying of clear water. We determined the major metabolites and differential genes of the amino acids and derivatives, flavonoids, and alkaloids in ripe wolfberries. We found that spraying selenium significantly enhanced the Lycium barbarum metabolic differentiators; the most effective spray was the organic selenium, with 129 major metabolic differentiators and 10 common metabolic pathways screened after spraying. Nano-selenium was the next best fertilizer we screened, with 111 major metabolic differentiators, the same number as organic selenium in terms of differential genes and common metabolite pathways. Sodium selenite was the least effective of the three, with only 59 of its major metabolic differentials screened, but its differential genes and metabolites were enriched for five common pathways.
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Affiliation(s)
- Wenqin Yang
- College of Agronomy, Ningxia University, Yinchuan 750021, China; (W.Y.); (T.J.); (Y.W.)
| | - Tingting Jiang
- College of Agronomy, Ningxia University, Yinchuan 750021, China; (W.Y.); (T.J.); (Y.W.)
| | - Yaqi Wang
- College of Agronomy, Ningxia University, Yinchuan 750021, China; (W.Y.); (T.J.); (Y.W.)
| | - Xiaojing Wang
- Ningxia Research Institute of Quality Standards and Testing Technology of Agricultural Products, Yinchuan 750001, China
| | - Rui Wang
- College of Agronomy, Ningxia University, Yinchuan 750021, China; (W.Y.); (T.J.); (Y.W.)
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Liang MH, Li XY. Involvement of Transcription Factors and Regulatory Proteins in the Regulation of Carotenoid Accumulation in Plants and Algae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18660-18673. [PMID: 38053506 DOI: 10.1021/acs.jafc.3c05662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Carotenoids are essential for photosynthesis and photoprotection in photosynthetic organisms, which are widely used in food coloring, feed additives, nutraceuticals, cosmetics, and pharmaceuticals. Carotenoid biofortification in crop plants or algae has been considered as a sustainable strategy to improve human nutrition and health. However, the regulatory mechanisms of carotenoid accumulation are still not systematic and particularly scarce in algae. This article focuses on the regulatory mechanisms of carotenoid accumulation in plants and algae through regulatory factors (transcription factors and regulatory proteins), demonstrating the complexity of homeostasis regulation of carotenoids, mainly including transcriptional regulation as the primary mechanism, subsequent post-translational regulation, and cross-linking with other metabolic processes. Different organs of plants and different plant/algal species usually have specific regulatory mechanisms for the biosynthesis, storage, and degradation of carotenoids in response to the environmental and developmental signals. In plants and algae, regulators such as MYB, bHLH, MADS, bZIP, AP2/ERF, WRKY, and orange proteins can be involved in the regulation of carotenoid metabolism. And many more regulators, regulatory networks, and mechanisms need to be explored. Our paper will provide a basis for multitarget or multipathway engineering for carotenoid biofortification in plants and algae.
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Affiliation(s)
- Ming-Hua Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xian-Yi Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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Li J, Wu K, Li L, Ma G, Fang L, Zeng S. Identification of HpMYB1 inducing anthocyanin accumulation in Hippeastrum Hybridum tepals by RNA-seq. BMC PLANT BIOLOGY 2023; 23:594. [PMID: 38012575 PMCID: PMC10683291 DOI: 10.1186/s12870-023-04582-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Cultivated Hippeastrum × hybridum is a popular ornamental plant with large and colorful flowers, long flowering duration, and high commercial value. As its main ornamental feature, its flower color is related to the anthocyanin content in the tepals. However, the molecular regulatory mechanisms of anthocyanin biosynthesis in H. × hybridum have not yet been elucidated. RESULTS In the present study, 12 cDNA libraries of four stages of H.× hybridum 'Royal Velvet' tepal development were used for RNA-seq, obtaining 79.83 gigabases (GB) of clean data. The data were assembled into 148,453 unigenes, and 11,262 differentially expressed genes were identified. Forty key enzymes participating in anthocyanin biosynthesis were investigated, and the results showed that most of the anthocyanin structural genes were expressed at low levels in S1 and were markedly upregulated in S2 and S3. The expression profiles of 12 selected genes were verified by qRT-PCR. Furthermore, the R2R3-MYB transcription factor (TF), HpMYB1, involved in the regulation of anthocyanin biosynthesis was identified by sequence, expression pattern, and subcellular localization analyses. Its overexpression in tobacco significantly increased the anthocyanin levels in various tissues and activated anthocyanin-related genes. CONCLUSIONS Using RNA-seq technology, we successfully identified a potential R2R3-MYB gene, HpMYB1, that regulates anthocyanin biosynthesis in H.× hybridum 'Royal Velvet'. Our findings provide basic transcript information and valuable transcriptome data for further identification of key genes involved in anthocyanin biosynthesis and can be applied in the artificial breeding of new H. × hybridum cultivars with enhanced ornamental value.
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Affiliation(s)
- Ji Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Kunlin Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Lin Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Guohua Ma
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Lin Fang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
| | - Songjun Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, 510650, Guangzhou, China.
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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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Hua Y, Dai B, Luo Y, Ding Y. Integrated analysis of multiple metabolome and transcriptome revealed the accumulation of flavonoids and associated molecular regulation mechanisms in Rubus chingii Hu at different developmental stages. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108085. [PMID: 37847976 DOI: 10.1016/j.plaphy.2023.108085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/04/2023] [Accepted: 10/08/2023] [Indexed: 10/19/2023]
Abstract
The traditional Chinese herb Rubus chingii Hu (R. chingii) is widely used in clinical practice due to its beneficial effects. Flavonoids are the important class of pharmacological substances in R. chingii, however, the molecular mechanism underlying the differences in active flavonoid contents in R. chingii at different developmental stages remain poorly understood. In this experiment, we selected four developmental stages (GG, GY, YR, RR) of R. chingii as the research material. We studied the untargeted and targeted metabolic profiles of flavonoids in different periods of R. chingii, combining full-length and comparative transcriptome analyses. Functional analyses were conducted on genes implicated in flavonoid differences. GG and RR displayed relatively higher and lower contents of flavonols, flavones, flavanols, flavanones, and isoflavonoid, respectively. RNA-seq analyses showed structural genes such as RcPAL, RcC4H, Rc4CL, RcCHS, RcCHI, RcF3H, RcF3'H, and RcFLS in flavonoid biosynthesis pathway were upregulated in GG, which were essential for the accumulation flavanones, flavones, and flavonols (effective components). qRT-PCR analyses investigated that six structural genes RcCHI, RcF3H, 2 RcCHS, and 2 Rc4CL, two TFs RcMYB308 and RcMYB123 had a consistent expression pattern with which in transcriptome. Also, an interaction network showed that the RcMYB308 could positively regulate Ka3R, Qu, Qu3G, AS, Hy, Ti through RcF3H. Furthermore, Subcellular localization analysis revealed that RcMYB308 was localization to the nucleus. In tobacco, RcMYB308 was overexpressed, resulting in higher flavonoids, RcF3H, RcF3'H, RcCHI, and RcFLS. RcMYB308 upregulated RcF3H in dual-luciferase assays. These results provide new insights for further understanding the molecular mechanism regulating flavonol biosynthesis in R. chingii fruit, and also provide a potential MYB regulator for molecular breeding of R. chingii.
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Affiliation(s)
- Yujiao Hua
- Department of Clinical Pharmacy, Affiliated Hospital of Jiangnan University, Wuxi, 214000, China.
| | - Bingyi Dai
- Otolaryngology Head and Neck Surgery, Affiliated Hospital of Jiangnan University, Wuxi, 214000, China.
| | - Yiyuan Luo
- Zhejiang Pharmaceutical College, Ningbo, 315500, China.
| | - Yongjuan Ding
- Department of Clinical Pharmacy, Affiliated Hospital of Jiangnan University, Wuxi, 214000, China.
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Lim SH, Kim DH, Lee JY. Molecular mechanism controlling anthocyanin composition and content in radish plants with different root colors. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108091. [PMID: 37864927 DOI: 10.1016/j.plaphy.2023.108091] [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: 06/01/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
Radish (Raphanus sativus) roots exhibit various colors that reflect their anthocyanin compositions and contents. However, the details of the mechanism linking the expression of anthocyanin biosynthesis and their transcriptional regulators to anthocyanin composition in radish roots remained unknown. Here, we characterized the role of the anthocyanin biosynthetic enzyme flavonoid 3'-hydroxylase (RsF3'H), together with the R2R3 MYB transcription factor (TF) RsMYB1 and the basic helix-loop-helix (bHLH) TF TRANSPARENT TESTA 8 (RsTT8), in four radish plants with different root colors: white (W), deep red (DR), dark purple (DP), and dark greyish purple (DGP). The DR plant contained heterozygous for RsF3'H with low expression level and accumulated a large amount of pelargonidin, resulting in deep red color. While, the DP and DGP plants accumulated the cyanidin due to the higher expression level of functional RsF3'H. Notably, RsMYB1 and RsTT8 transcripts were abundant in all pigmented roots, but not in white roots. To investigate the differential expression of RsMYB1 and RsTT8, we compared the sequences of their promoter regions among the four radish plants, revealing variations in the numbers of cis-elements and in promoter architecture. Promoter activation assays demonstrated that variation in the RsMYB1 and RsTT8 promoters may contribute to the expression level of these genes, and RsMYB1 can activate its own expression as well as promote the RsTT8 expression. These results suggested that RsF3'H plays a vital role in anthocyanin composition and the expression level of both RsMYB1 and RsTT8 are crucial determinants for anthocyanin content in radish roots. Overall, these findings provide insight into the molecular basis of anthocyanin composition and level in radish roots.
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Affiliation(s)
- Sun-Hyung Lim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Republic of Korea; Research Institute of International Technology and Information, Hankyong National University, Anseong, 17579, Republic of Korea.
| | - Da-Hye Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Republic of Korea; Research Institute of International Technology and Information, Hankyong National University, Anseong, 17579, Republic of Korea
| | - Jong-Yeol Lee
- National Academy of Agricultural Science, Rural Development Administration, Jeonju, 54874, Republic of Korea
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Wang Y, Zhou LJ, Song A, Wang Y, Geng Z, Zhao K, Jiang J, Chen S, Chen F. Comparative transcriptome analysis and flavonoid profiling of floral mutants reveals CmMYB11 regulating flavonoid biosynthesis in chrysanthemum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111837. [PMID: 37611834 DOI: 10.1016/j.plantsci.2023.111837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Flavonoids, of which the major groups are flavones, flavonols, and anthocyanins, confer a variety of colors on plants. Bud sports with variation of floral colors occur occasionally during chrysanthemum cultivation. Although it has been reported that methylation at the promoter of CmMYB6 was related to anthocyanin contents, the regulatory networks of flavonoid biosynthesis still remain largely unknown in mutation of chrysanthemum. We compared phenotypes, pigment composition and transcriptomes in two chrysanthemum cultivars, 'Anastasia Dark Green' and 'Anastasia Pink', and regenerated bud sports of these cultivars with altered floral colors. Increased anthocyanins turned the 'Anastasia Dark Green' mutant red, while decreased anthocyanins turned the 'Anastasia Pink' mutant white. Moreover, total flavonoids were reduced in both mutants. Multiple flavonoid biosynthetic genes and regulatory genes encoding MYBs and bHLHs transcription factors were differentially expressed in pairwise comparisons of transcriptomes in 'Anastasia Dark Green' or 'Anastasia Pink' and their mutants at different flowering stages. Among these regulatory genes, the expression patterns of CmMYB6 and CmbHLH2 correlated to changes of anthocyanin contents, and down-regulation of CmMYB11 correlated to decreased total flavonoid contents in two mutants. CmMYB11 was shown to directly activate the promoter activities of CmCHS2, CmCHI, CmDFR, CmANS, CmFNS, and CmFLS. Furthermore, overexpression of CmMYB11 increased both flavonols and anthocyanins in tobacco petals. Our work provides new insights into regulatory networks involved in flavonoid biosynthesis and coloration in chrysanthemum.
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Affiliation(s)
- Yiguang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Li-Jie Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Yuxi Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Zhiqiang Geng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Kunkun Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China.
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Zhang Z, Zhou D, Li S, Pan J, Liang J, Wu X, Wu XN, Krall L, Zhu G. Multiomics Analysis Reveals the Chemical and Genetic Bases of Pigmented Potato Tuber. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16402-16416. [PMID: 37856829 DOI: 10.1021/acs.jafc.3c04979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Anthocyanins and carotenoids determine the diversity of potato tuber flesh pigmentation; here, the underlying chemical and genetic bases were elucidated by multiomics analyses. A total of 31 anthocyanins and 30 carotenoids were quantified in five differently pigmented tubers. Cyanidin and pelargonidin derivatives determined the redness, while malvidin, petunidin, and delphinidin derivatives contributed to purpleness. Violaxanthin derivatives determined the light-yellow color, while zeaxanthin and antheraxanthin derivatives further enhanced the deep-yellow deposition. Integrated transcriptome and proteome analyses identified that F3'5'H highly enhanced anthocyanin biosynthesis in purple flesh and was responsible for metabolic divergence between red and purple samples. BCH2 significantly enhanced carotenoid biosynthesis in yellow samples and along with ZEP, NCED1, and CCD1 genes determined metabolic divergence between light and deep-yellow samples. The weighted correlation network analysis constructed a regulatory network revealing the central role of AN1 in regulating anthocyanin biosynthesis, and 10 new transcription factors related to anthocyanin and carotenoid metabolism regulation were identified. Our findings provide targeted genes controlling tuber pigmentation, which will be meaningful for the genetic manipulation of tuber quality improvement.
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Affiliation(s)
- Zhong Zhang
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
- 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, Guangdong 518120, China
| | - Dao Zhou
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Shalan Li
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Jun Pan
- 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, Guangdong 518120, China
| | - Jun Liang
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Xi Wu
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Leonard Krall
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Guangtao Zhu
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
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Shan T, Xu J, Zhong X, Zhang J, He B, Tao Y, Wu J. Full-length transcriptome sequencing provides new insights into the complexity of flavonoid biosynthesis in Glechoma longituba. PHYSIOLOGIA PLANTARUM 2023; 175:e14104. [PMID: 38148235 DOI: 10.1111/ppl.14104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/28/2023]
Abstract
Glechoma longituba has been frequently used in treating urolithiasis and cholelithiasis due to the presence of flavonoids, which are its major bioactive constituents. However, research on the molecular background of flavonoid biosynthesis in G. longituba is limited. In this study, we used single-molecule real-time combined with next-generation sequencing technologies to construct the complete transcriptome of G. longituba. We identified 404,648 non-redundant transcripts, including 249,697 coding sequences, 197,811 simple sequence repeats, 174,846 long noncoding RNA, and 176,554 coding RNA. Moreover, we functionally annotated 346,218 isoforms (85.56%) and identified 86,528 differentially expressed genes. We also identified 55 non-redundant full-length isoforms related to the flavonoid biosynthetic pathway. Pearson correlation analysis revealed that the expression levels of some key genes of the flavonoid biosynthesis pathway were significantly positively correlated with the flavonoid metabolites. Furthermore, we performed bioinformatics analysis (sequence and structural) of isoform_47029 (encoding flavanone 3-hydroxylase) and isoform_53692 (encoding flavonol synthase) to evaluate their potential biological functions. Finally, we validated gene expression levels of 12 flavonoid-related key enzyme genes using quantitative real-time PCR. Overall, this study provides full-length transcriptome information on G. longituba for the first time and valuable molecular resources for further research on the medicinal properties of this plant.
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Affiliation(s)
- Tingyu Shan
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Jingyao Xu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Xinxin Zhong
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Jingjing Zhang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Bing He
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
| | - Yijia Tao
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
| | - Jiawen Wu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, China
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Xu P, Li X, Fan J, Tian S, Cao M, Lin A, Gao Q, Xiao K, Wang C, Kuang H, Lian H. An arginine-to-histidine mutation in flavanone-3-hydroxylase results in pink strawberry fruits. PLANT PHYSIOLOGY 2023; 193:1849-1865. [PMID: 37477940 DOI: 10.1093/plphys/kiad424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023]
Abstract
Fruit color is a very important external commodity factor for consumers. Compared to the most typical red octoploid strawberry (Fragaria × ananassa), the pink strawberry often sells for a more expensive price and has a higher economic benefit due to its outstanding color. However, few studies have examined the molecular basis of pink-colored strawberry fruit. Through an EMS mutagenesis of woodland strawberry (Fragaria vesca), we identified a mutant with pink fruits and green petioles. Bulked-segregant analysis sequencing analysis and gene function verification confirmed that the responsible mutation resides in a gene encoding flavanone-3-hydroxylase (F3H) in the anthocyanin synthesis pathway. This nonsynonymous mutation results in an arginine-to-histidine change at position 130 of F3H. Molecular docking experiments showed that the arginine-to-histidine mutation results in a reduction of intermolecular force-hydrogen bonding between the F3H protein and its substrates. Enzymatic experiments showed a greatly reduced ability of the mutated F3H protein to catalyze the conversion of the substrates and hence a blockage of the anthocyanin synthesis pathway. The discovery of a key residue in the F3H gene controlling anthocyanin synthesis provides a clear target of modification for the molecular breeding of strawberry varieties with pink-colored fruits, which may be of great commercial value.
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Affiliation(s)
- Pengbo Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinyu Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junmiao Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuhua Tian
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Minghao Cao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Ecology, Lishui University, Lishui 323000, China
| | - Anqi Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qinhua Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Kun Xiao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Horticultural Science, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Chong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyun Kuang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences 201403, Shanghai, China
| | - Hongli Lian
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Wang A, Liu Y, Li Q, Li X, Zhang X, Kong J, Liu Z, Yang Y, Wang J. FlbZIP12 gene enhances drought tolerance via modulating flavonoid biosynthesis in Fagopyrum leptopodum. FRONTIERS IN PLANT SCIENCE 2023; 14:1279468. [PMID: 37885669 PMCID: PMC10598875 DOI: 10.3389/fpls.2023.1279468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
Karst lands provide a poor substrate to support plant growth, as they are low in nutrients and water content. Common buckwheat (Fagopyrum esculentum) is becoming a popular crop for its gluten-free grains and their high levels of phenolic compounds, but buckwheat yields are affected by high water requirements during grain filling. Here, we describe a wild population of drought-tolerant Fagopyrum leptopodum and its potential for enhancing drought tolerance in cultivated buckwheat. We determined that the expression of a gene encoding a Basic leucine zipper (bZIP) transcription factor, FlbZIP12, from F. leptopodum is induced by abiotic stresses, including treatment with the phytohormone abscisic acid, salt, and polyethylene glycol. In addition, we show that overexpressing FlbZIP12 in Tartary buckwheat (Fagopyrum tataricum) root hairs promoted drought tolerance by increasing the activities of the enzymes superoxide dismutase and catalase, decreasing malondialdehyde content, and upregulating the expression of stress-related genes. Notably, FlbZIP12 overexpression induced the expression of key genes involved in flavonoid biosynthesis. We also determined that FlbZIP12 interacts with protein kinases from the FlSnRK2 family in vitro and in vivo. Taken together, our results provide a theoretical basis for improving drought tolerance in buckwheat via modulating the expression of FlbZIP12 and flavonoid contents.
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Affiliation(s)
- Anhu Wang
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, China
| | - Yu Liu
- Key Laboratory of Bio-resource and Ecoenvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Qiujie Li
- Key Laboratory of Bio-resource and Ecoenvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaoyi Li
- Key Laboratory of Bio-resource and Ecoenvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinrong Zhang
- Key Laboratory of Bio-resource and Ecoenvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiao Kong
- Key Laboratory of Bio-resource and Ecoenvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhibing Liu
- Key Laboratory of Bio-resource and Ecoenvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi Yang
- Key Laboratory of Bio-resource and Ecoenvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianmei Wang
- Key Laboratory of Bio-resource and Ecoenvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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