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Rehman S, Bahadur S, Xia W. Unlocking nature's secrets: The pivotal role of WRKY transcription factors in plant flowering and fruit development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112150. [PMID: 38857658 DOI: 10.1016/j.plantsci.2024.112150] [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: 02/16/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
The WRKY transcription factor family is a key player in the regulatory mechanisms of flowering plants, significantly influencing both their biotic and abiotic response systems as well as being vital to numerous physiological and biological functions. Over the past two decades, the functionality of WRKY proteins has been the subject of extensive research in over 50 plant species, with a strong focus on their roles in responding to various stresses. Despite this extensive research, there remains a notable gap in comprehensive studies aimed at understanding how specific WRKY genes directly influence the timing of flowering and fruit development. This review offers an up-to-date look at WRKY family genes and provides insights into the key genes of WRKY to control flowering, enhance fruit ripening and secondary metabolism synthesis, and maintain fruit quality of various plants, including annuals, perennials, medicinal, and crop plants. The WRKY transcription factors serve as critical regulators within the transcriptional regulatory network, playing a crucial role in the precise enhancement of flowering processes. It is also involved in the up-regulation of fruit ripening was strongly demonstrated by combined transcriptomics and metabolomic investigation. Therefore, we speculated that the WRKY family is known to be a key regulator of flowering and fruiting in plants. This detailed insight will enable the identification of the series of molecular occurrences featuring WRKY proteins throughout the stages of flowering and fruiting.
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Affiliation(s)
- Shazia Rehman
- Sanya Nanfan Research Institution, Hainan University, Sanya, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Saraj Bahadur
- College of Forestry, Hainan University, Haikou 570228, China; College of Life and Health Sciences, Hainan University, Haikou 570228, China.
| | - Wei Xia
- Sanya Nanfan Research Institution, Hainan University, Sanya, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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Parrish SB, Paudel D, Deng Z. Transcriptome analysis of Lantana camara flower petals reveals candidate anthocyanin biosynthesis genes mediating red flower color development. G3 (BETHESDA, MD.) 2023; 14:jkad259. [PMID: 37974306 PMCID: PMC10755171 DOI: 10.1093/g3journal/jkad259] [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: 07/05/2023] [Revised: 07/05/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Flower color plays a crucial role in the appeal and selection of ornamental plants, directly influencing breeding strategies and the broader horticulture industry. Lantana camara, a widely favored flowering shrub, presents a rich palette of flower colors. Yet, the intricate molecular mechanisms governing this color variation in the species have remained largely unidentified. With the aim of filling this gap, this study embarked on a comprehensive de novo transcriptome assembly and differential gene expression analysis across 3 distinct lantana accessions, each showcasing a unique flower color. By harnessing the capabilities of both PacBio and Illumina sequencing platforms, a robust transcriptome assembly, encompassing 123,492 gene clusters and boasting 94.2% BUSCO completeness, was developed. The differential expression analysis unveiled 72,862 unique gene clusters that exhibited varied expression across different flower stages. A pronounced upregulation of 8 candidate core anthocyanin biosynthesis genes in the red-flowered accession was uncovered. This was further complemented by an upregulation of candidate MYB75 (PAP1) and bHLH42 (TT8) transcription factors. A candidate carotenoid cleavage dioxygenase (CCD4a) gene cluster also manifested a marked upregulation in white flowers. The study unveils the molecular groundwork of lantana's flower color variation, offering insights for future research and potential applications in breeding ornamental plants with desired color traits.
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Affiliation(s)
- Stephen Brooks Parrish
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
| | - Dev Paudel
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
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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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Yin C, Tang D, Liu X, Li Z, Xiang Y, Gao K, Li H, Yuan L, Huang B, Li J. Transcriptome analysis reveals important regulatory genes and pathways for tuber color variation in Pinellia ternata (Thunb.) Breit. PROTOPLASMA 2023; 260:1313-1325. [PMID: 36918417 DOI: 10.1007/s00709-023-01845-7] [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: 07/28/2022] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
During the growth of Pinellia ternata (Thunb.) Breit. (P. ternata), the violet-red skin was occasionally produced spontaneously under natural cultivation. However, the specific mechanism leading to the color change is still unclear. This study performed transcriptomes in violet-red and pale-yellow skin and their peeled tubers of P. ternata, and the total flavonoids and anthocyanin contents were also determined. The results showed that the majority of genes involved in anthocyanin production were considerably increased in the violet-red skin of P. ternata tuber compared to the pale-yellow skin. Especially, phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) showed a remarkable increase in gene expression levels. Notably, shikimate O-hydroxycinnamoyltransferase (HCT), naringenin 3-dioxygenase (F3H), flavanone 4-reductase (DFR), and anthocyanidin synthase (ANS) were explicitly expressed in violet-red skin of P. ternata tuber, while undetectable in pale-yellow skin. The upregulation of these genes may explain the accumulation of anthocyanins, which forms the violet-red skin of P. ternata tuber. The transcription factors, including C2H2, bZIP, ERF, GATA, bHLH, C3H, NAC, MYB-related, and MYB families, might trigger the skin color change in P. ternata. The entire anthocyanin content in the violet-red skin of P. ternata tuber was 71.10 μg/g, and pale-yellow skin was 7.74 μg/g. According to phenotypic and transcriptome results, the elevated expression levels of genes linked to the synthesis of anthocyanins considerably contributed to the violet-red skin alterations in P. ternata tuber. This study provides a new understanding of the formation of the violet-red skin, lays a theoretical foundation for the cultivation of unique varieties of P. ternata, and provides transcriptome data for further study of the differences between different colors of P. ternata.
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Affiliation(s)
- Cong Yin
- Hubei Province Key Laboratory of Traditional Chinese Medicine Resource and Chemistry, College of Pharmacy, Hubei University of Chinese Medicine, Huang-Jia-Hu West Road 16#, Hongshan District, Wuhan, Hubei, 430065, China
| | - Ding Tang
- Hubei Province Key Laboratory of Traditional Chinese Medicine Resource and Chemistry, College of Pharmacy, Hubei University of Chinese Medicine, Huang-Jia-Hu West Road 16#, Hongshan District, Wuhan, Hubei, 430065, China
| | - Xiaoyu Liu
- Hubei Province Key Laboratory of Traditional Chinese Medicine Resource and Chemistry, College of Pharmacy, Hubei University of Chinese Medicine, Huang-Jia-Hu West Road 16#, Hongshan District, Wuhan, Hubei, 430065, China
| | - Zihan Li
- Hubei Province Key Laboratory of Traditional Chinese Medicine Resource and Chemistry, College of Pharmacy, Hubei University of Chinese Medicine, Huang-Jia-Hu West Road 16#, Hongshan District, Wuhan, Hubei, 430065, China
| | - Yulin Xiang
- Hubei Province Key Laboratory of Traditional Chinese Medicine Resource and Chemistry, College of Pharmacy, Hubei University of Chinese Medicine, Huang-Jia-Hu West Road 16#, Hongshan District, Wuhan, Hubei, 430065, China
| | - Kaiming Gao
- Hubei Province Key Laboratory of Traditional Chinese Medicine Resource and Chemistry, College of Pharmacy, Hubei University of Chinese Medicine, Huang-Jia-Hu West Road 16#, Hongshan District, Wuhan, Hubei, 430065, China
| | - Heyu Li
- Hubei Province Key Laboratory of Traditional Chinese Medicine Resource and Chemistry, College of Pharmacy, Hubei University of Chinese Medicine, Huang-Jia-Hu West Road 16#, Hongshan District, Wuhan, Hubei, 430065, China
- Tianjin Ubasio Technology Group Co., Ltd., Tianjin, 300457, China
| | - Lin Yuan
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Diseases, Hubei Minzu University, Enshi, Hubei, 445000, China
| | - Bisheng Huang
- Hubei Province Key Laboratory of Traditional Chinese Medicine Resource and Chemistry, College of Pharmacy, Hubei University of Chinese Medicine, Huang-Jia-Hu West Road 16#, Hongshan District, Wuhan, Hubei, 430065, China
| | - Juan Li
- Hubei Province Key Laboratory of Traditional Chinese Medicine Resource and Chemistry, College of Pharmacy, Hubei University of Chinese Medicine, Huang-Jia-Hu West Road 16#, Hongshan District, Wuhan, Hubei, 430065, China.
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Mackon E, Jeazet Dongho Epse Mackon GC, Yao Y, Guo Y, Ma Y, Dai X, Jandan TH, Liu P. Integrative HPLC profiling and transcriptome analysis revealed insights into anthocyanin accumulation and key genes at three developmental stages of black rice ( Oryza sativa. L) caryopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1211326. [PMID: 37727854 PMCID: PMC10505814 DOI: 10.3389/fpls.2023.1211326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/11/2023] [Indexed: 09/21/2023]
Abstract
Introduction Anthocyanins are plants' secondary metabolites belonging to the flavonoid class with potential health-promoting properties. They are greatly employed in the food industry as natural alternative food colorants for dairy and ready-to-eat desserts and pH indicators. These tremendous advantages make them economically important with increasing market trends. Black rice is a rich source of anthocyanin that can be used to ensure food and nutritional security around the world. However, research on anthocyanin accumulation and gene expression during rice caryopsis development is lacking. Methods In this study, we combined high-performance liquid chromatography (HPLC) and transcriptome analysis to profile the changes in anthocyanin content and gene expression dynamics at three developmental stages (milky, doughy, and mature). Results Our results showed that anthocyanin accumulation started to be visible seven days after flowering (DAF), increased rapidly from milky (11 DAF) to dough stage, then started decreasing after the peak was attained at 18 DAF. RNA-seq showed that 519 out of 14889, 477 out of 17914, and 1614 out of 18810 genes were uniquely expressed in the milky, doughy, and mature stages, respectively. We performed three pairwise comparisons: milky vs. dough, milky vs. mature, and dough vs. mature, and identified 6753, 9540, and 2531 DEGs, respectively. The DEGs' abundance was higher in milky vs. mature, with 5527 up-regulated genes and 4013 down-regulated genes, while it was smaller in dough vs. mature, with 1419 up-regulated genes and 1112 down-regulated DEGs. This result was consistent with the changes in anthocyanin profiling, and the expression of structural, regulatory, and transporter genes involved in anthocyanin biosynthesis showed their highest expression at the dough stage. Through the gene expression profile and protein interaction network, we deciphered six main contributors of the anthocyanin peak observed at dough stage, including OsANS, OsDFR, OsGSTU34, OsMYB3, OsbHLH015, and OsWD40-50. Discussion This study is the first to report the investigation of anthocyanin and gene expression at three developmental stages of black rice caryopsis. The findings of this study could aid in predicting the best harvesting time to achieve maximum anthocyanin content and the best time to collect samples for various gene expression analysis, laying the groundwork for future research into the molecular mechanisms underlying rice caryopsis coloration.
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Affiliation(s)
- Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | | | - Yuhang Yao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yongqiang Guo
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yafei Ma
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xianggui Dai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Tahir Hussain Jandan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Piqing Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
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Zhang D, Zhao XW, Li YY, Ke SJ, Yin WL, Lan S, Liu ZJ. Advances and prospects of orchid research and industrialization. HORTICULTURE RESEARCH 2022; 9:uhac220. [PMID: 36479582 PMCID: PMC9720451 DOI: 10.1093/hr/uhac220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xue-Wei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shi-Jie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei-Lun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Lim AH, Low ZJ, Shingate PN, Hong JH, Chong SC, Ng CCY, Liu W, Vaser R, Šikić M, Sung WKK, Nagarajan N, Tan P, Teh BT. Genome assembly and chemogenomic profiling of National Flower of Singapore Papilionanthe Miss Joaquim 'Agnes' reveals metabolic pathways regulating floral traits. Commun Biol 2022; 5:967. [PMID: 36109650 PMCID: PMC9477820 DOI: 10.1038/s42003-022-03940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/02/2022] [Indexed: 11/22/2022] Open
Abstract
Singapore's National Flower, Papilionanthe (Ple.) Miss Joaquim 'Agnes' (PMJ) is highly prized as a horticultural flower from the Orchidaceae family. A combination of short-read sequencing, single-molecule long-read sequencing and chromatin contact mapping was used to assemble the PMJ genome, spanning 2.5 Gb and 19 pseudo-chromosomal scaffolds. Genomic resources and chemical profiling provided insights towards identifying, understanding and elucidating various classes of secondary metabolite compounds synthesized by the flower. For example, presence of the anthocyanin pigments detected by chemical profiling coincides with the expression of ANTHOCYANIN SYNTHASE (ANS), an enzyme responsible for the synthesis of the former. Similarly, the presence of vandaterosides (a unique class of glycosylated organic acids with the potential to slow skin aging) discovered using chemical profiling revealed the involvement of glycosyltransferase family enzymes candidates in vandateroside biosynthesis. Interestingly, despite the unnoticeable scent of the flower, genes involved in the biosynthesis of volatile compounds and chemical profiling revealed the combination of oxygenated hydrocarbons, including traces of linalool, beta-ionone and vanillin, forming the scent profile of PMJ. In summary, by combining genomics and biochemistry, the findings expands the known biodiversity repertoire of the Orchidaceae family and insights into the genome and secondary metabolite processes of PMJ.
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Affiliation(s)
- Abner Herbert Lim
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
| | - Zhen Jie Low
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
| | | | - Jing Han Hong
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Shu Chen Chong
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
| | | | - Wei Liu
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore
| | - Robert Vaser
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Mile Šikić
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Wing-Kin Ken Sung
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Duke-NUS Medical School, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, Singapore, Singapore.
| | - Bin Tean Teh
- SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore, Singapore.
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Duke-NUS Medical School, Singapore, Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Singapore, Singapore.
- National Cancer Center Singapore, Singapore, Singapore.
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Hu F, Bi X, Liu H, Fu X, Li Y, Yang Y, Zhang X, Wu R, Li G, Lv Y, Huang J, Luo X, Shi R. Transcriptome and carotenoid profiling of different varieties of Coffea arabica provides insights into fruit color formation. PLANT DIVERSITY 2022; 44:322-334. [PMID: 35769592 PMCID: PMC9209900 DOI: 10.1016/j.pld.2021.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/04/2021] [Accepted: 11/16/2021] [Indexed: 06/15/2023]
Abstract
The processability and ultimate quality of coffee (C offea arabica) are determined by the composition of the matured fruits. The basis of genetic variation in coffee fruit quality could be explained by studying color formation during fruit maturation. Transcriptome profiling was conducted on matured fruits of four C. arabica varieties (orange colored fruits (ORF); purple colored fruits (PF); red colored fruits (RF) and yellow colored fruits (YF)) to identify key color-regulating genes, biosynthesis pathways and transcription factors implicated in fruit color formation. A total of 39,938 genes were identified in the transcriptomes of the four C. arabica varieties. In all, 2745, 781 and 1224 differentially expressed genes (DEGs) were detected in YF_vs_PF, YF_vs_RF and YF_vs_ORF, respectively, with 1732 DEGs conserved among the three pairwise groups. Functional annotation of the DEGs led to the detection of 28 and 82 key genes involved in the biosynthesis of carotenoids and anthocyanins, respectively. Key transcription factors bHLH, MYB, NAC, MADS, and WRKY implicated in fruit color regulation were detected. The high expression levels of gene-LOC113688784 (PSY), gene-LOC113730013 (β-CHY), gene-LOC113728842 (CCD7), gene-LOC113689681 (NCED) and gene-LOC113729473 (ABA2) in YF may have accounted for the yellow coloration. The differential expression of several anthocyanin and carotenoid-specific genes in the fruits substantially account for the purple (PF), red (RF), and orange (ORF) colorations. This study provides important insights into fruit color formation and variations in C. arabica and will help to develop coffee varieties with specific color and quality traits.
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Affiliation(s)
- Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Xiaofei Bi
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Hongming Liu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Xingfei Fu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Yang Yang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Xiaofang Zhang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Ruirui Wu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Guiping Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Yulan Lv
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Jiaxiong Huang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Xinping Luo
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, China
| | - Rui Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, China
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Fan W, Li B, Tian H, Li X, Ren H, Zhou Q. Metabolome and transcriptome analysis predicts metabolism of violet-red color change in Lilium bulbs. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:2903-2915. [PMID: 34761381 DOI: 10.1002/jsfa.11631] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/28/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND During the storage and processing of Lilium bulbs, the phenomenon of violet-red colour change in Lilium bulbs which is different from enzymatic browning often exists, but the specific mechanism is not clear. RESULTS In this study, we chose six-year-old Lilium davidii var. unicolor to study. Bulb scales which were sealed in polyethylene film plastic bags were exposed to room temperature (20 ± 2 °C) treatment for 5 days (12 h of sunshine and 12 h of sun shading). Metabolomics and transcript omics were conducted to elucidate the mechanism of violet-red color change in Lilium bulbs. The results showed that the color of Lilium bulb scales was obvious violet-red in 5 days; chromaticity value measuring showed the a values had the most significant upward trend. Metabolomics analysis showed many metabolites produced from the flavonoid biosynthesis pathway showed an upward trend. Transcriptome revealed that flavonoid biosynthesis pathway was significantly enriched, of which 20 synthesis genes were highly regulated expression. Metabolome and transcriptome co-analysis that up-regulated expression of flavonoids synthesis genes including ten chalcone synthase, two anthocyanidin reductase, and chalcone isomerase, 3'-hydroxylase, 3-hydroxylase, dihydroflavonol 4-reductase, anthocyanin synthase, anthocyanidin 3-O-glucosyltransferase and flavonol synthase were highly positive correlated with epicatechin, rutin and cyanidin 3-rutinoside. CONCLUSION Phenotypic, metabolomic and transcriptomic analysis indicated that the up-related expression levels of genes and accumulated flavonoids related to flavonoid metabolism contributed greatly to the violet-red colour change in Lilium bulbs. The results of this study will deepen our understanding of the color formation of violet-red Lilium bulbs and provide the basis for future storage and preservation of Lilium bulbs. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Wenguang Fan
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, P. R. China
| | - Baoyu Li
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, P. R. China
| | - Hui Tian
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, P. R. China
| | - Xin Li
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, P. R. China
| | - Haiwei Ren
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, P. R. China
| | - Qifen Zhou
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, P. R. China
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10
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Ghai D, Kaur A, Kahlon PS, Pawar SV, Sembi JK. A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach. FRONTIERS IN PLANT SCIENCE 2022; 13:837563. [PMID: 35574139 PMCID: PMC9100589 DOI: 10.3389/fpls.2022.837563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Orchids have a huge reservoir of secondary metabolites making these plants of immense therapeutic importance. Their potential as curatives has been realized since times immemorial and are extensively studied for their medicinal properties. Secondary metabolism is under stringent genetic control in plants and several molecular factors are involved in regulating the production of the metabolites. However, due to the complex molecular networks, a complete understanding of the specific molecular cues is lacking. High-throughput omics technologies have the potential to fill up this lacuna. The present study deals with comparative analysis of high-throughput transcript data involving gene identification, functional annotation, and differential expression in more than 30 orchid transcriptome data sets, with a focus to elucidate the role of various factors in alkaloid and flavonoid biosynthesis. Comprehensive analysis of the mevalonate (MVA) pathway, methyl-d-erythritol 4-phosphate (MEP) pathway, and phenylpropanoid pathway provide specific insights to the potential gene targets for drug discovery. It is envisaged that a positive stimulation of these pathways through regulation of pivotal genes and alteration of specific gene expression, could facilitate the production of secondary metabolites and enable efficient tapping of the therapeutic potential of orchids. This further would lay the foundation for developing strategies for genetic and epigenetic improvement of these plants for development of therapeutic products.
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Affiliation(s)
- Devina Ghai
- Department of Botany, Panjab University, Chandigarh, India
| | - Arshpreet Kaur
- Department of Botany, Panjab University, Chandigarh, India
| | - Parvinderdeep S. Kahlon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Sandip V. Pawar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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11
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Zhang L, Cai Y, Zhang M, Du G, Wang J. Selection and Evaluation of Candidate Reference Genes for Quantitative Real-Time PCR in Aboveground Tissues and Drought Conditions in Rhododendron Delavayi. Front Genet 2022; 13:876482. [PMID: 35495151 PMCID: PMC9046656 DOI: 10.3389/fgene.2022.876482] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/17/2022] [Indexed: 11/18/2022] Open
Abstract
There has been no systematic identification and screening of candidate reference genes for normalization of quantitative real-time PCR (qRT-PCR) results in Rhododendron delavayi to date. Therefore, the present study used GAPDH, Act, EF1, Tub-, Tub-5, UEC1, TATA, TATA-2, UEP, TIP41, and Ubiquitin to predict their stabilities on different aboveground tissues (matured leaves (ML), stem tips (STM), and flower buds (FB)) at different developmental stages (young and adult plants) using five statistical algorithms: Delta Ct method, BestKeeper, geNorm, Normfinder, and RefFinder. The findings were confirmed using ML obtained from plants that had been stressed by drought. By using RefFinder with ML samples collected under drought conditions, it was determined that the top five most stable reference genes were GAPDH > UEC1 > Actin > Tubulin- > Tubulin—5, whereas the least stable reference gene was Ubiquitin. In addition, under control conditions, UEC1, UEC2, Actin, and GAPDH were selected as the highest stable potential reference genes at the juvenile stage of R. delavayi with ML and STM. When ML and STM were combined with drought-stressed samples, TIP41, GAPDH, or their combination proved to be the most effective qRT-PCR primers. The findings will aid in the improvement of the precision and reliability of qRT-PCR data and laying the groundwork for future gene functional studies in R. delavayi.
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Affiliation(s)
- Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, China
| | - Yanfei Cai
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, China
| | - Mingchao Zhang
- School of Agriculture, Yunnan University, Kunming, China
| | - Guanghui Du
- School of Agriculture, Yunnan University, Kunming, China
- *Correspondence: Guanghui Du, ; Jihua Wang,
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, China
- *Correspondence: Guanghui Du, ; Jihua Wang,
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Wang N, Shu X, Zhang F, Zhuang W, Wang T, Wang Z. Comparative Transcriptome Analysis Identifies Key Regulatory Genes Involved in Anthocyanin Metabolism During Flower Development in Lycoris radiata. FRONTIERS IN PLANT SCIENCE 2021; 12:761862. [PMID: 34975946 PMCID: PMC8715008 DOI: 10.3389/fpls.2021.761862] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Lycoris is used as a garden flower due to the colorful and its special flowers. Floral coloration of Lycoris is a vital trait that is mainly regulated via the anthocyanin biosynthetic pathway. In this study, we performed a comparative transcriptome analysis of Lycoris radiata petals at four different flower development stages. A total of 38,798 differentially expressed genes (DEGs) were identified by RNA sequencing, and the correlation between the expression level of the DEGs and the anthocyanin content was explored. The identified DEGs are significantly categorized into 'flavonoid biosynthesis,' 'phenylpropanoid biosynthesis,' 'Tropane, piperidine and pyridine alkaloid biosynthesis,' 'terpenoid backbone biosynthesis' and 'plant hormone signal transduction' by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The candidate genes involved in anthocyanin accumulation in L. radiata petals during flower development stages were also identified, which included 56 structural genes (especially LrDFR1 and LrFLS) as well as 27 key transcription factor DEGs (such as C3H, GATA, MYB, and NAC). In addition, a key structural gene namely LrDFR1 of anthocyanin biosynthesis pathway was identified as a hub gene in anthocyanin metabolism network. During flower development stages, the expression level of LrDFR1 was positively correlated with the anthocyanin content. Subcellular localization revealed that LrDFR1 is majorly localized in the nucleus, cytoplasm and cell membrane. Overexpression of LrDFR1 increased the anthocyanin accumulation in tobacco leaves and Lycoris petals, suggesting that LrDFR1 acts as a positively regulator of anthocyanin biosynthesis. Our results provide new insights for elucidating the function of anthocyanins in L. radiata petal coloring during flower development.
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Affiliation(s)
- Ning Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiaochun Shu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Weibing Zhuang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Tao Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Zhong Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Combined transcriptome and metabolome integrated analysis of Acer mandshuricum to reveal candidate genes involved in anthocyanin accumulation. Sci Rep 2021; 11:23148. [PMID: 34848790 PMCID: PMC8633053 DOI: 10.1038/s41598-021-02607-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/18/2021] [Indexed: 12/28/2022] Open
Abstract
The red color formation of Acer mandshuricum leaves is caused by the accumulation of anthocyanins primarily, but the molecular mechanism researches which underlie anthocyanin biosynthesis in A. mandshuricum were still lacking. Therefore, we combined the transcriptome and metabolome and analyzed the regulatory mechanism and accumulation pattern of anthocyanins in three different leaf color states. In our results, 26 anthocyanins were identified. Notably, the metabolite cyanidin 3-O-glucoside was found that significantly correlated with the color formation, was the predominant metabolite in anthocyanin biosynthesis of A. mandshuricum. By the way, two key structural genes ANS (Cluster-20561.86285) and BZ1 (Cluster-20561.99238) in anthocyanidin biosynthesis pathway were significantly up-regulated in RL, suggesting that they might enhance accumulation of cyanidin 3-O-glucoside which is their downstream metabolite, and contributed the red formation of A. mandshuricum leaves. Additionally, most TFs (e.g., MYBs, bZIPs and bHLHs) were detected differentially expressed in three leaf color stages that could participate in anthocyanin accumulation. This study sheds light on the anthocyanin molecular regulation of anthocyanidin biosynthesis and accumulation underlying the different leaf color change periods in A. mandshuricum, and it could provide basic theory and new insight for the leaf color related genetic improvement of A. mandshuricum.
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14
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Research Advances in Plant Genomics. Life (Basel) 2021; 11:life11121313. [PMID: 34947844 PMCID: PMC8703979 DOI: 10.3390/life11121313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
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15
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Li X, Fan J, Luo S, Yin L, Liao H, Cui X, He J, Zeng Y, Qu J, Bu Z. Comparative transcriptome analysis identified important genes and regulatory pathways for flower color variation in Paphiopedilum hirsutissimum. BMC PLANT BIOLOGY 2021; 21:495. [PMID: 34706650 PMCID: PMC8549352 DOI: 10.1186/s12870-021-03256-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/08/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Paphiopedilum hirsutissimum is a member of Orchidaceae family that is famous for its ornamental value around the globe, it is vulnerable due to over-exploitation and was listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents its trade across borders. Variation in flower color that gives rise to different flower patterns is a major trait contributing to its high ornamental value. However, the molecular mechanism underlying color formation in P. hirsutissimum still remains unexplored. In the present study, we exploited natural variation in petal and labellum color of Paphiopedilum plants and used comparative transcriptome analysis as well as pigment measurements to explore the important genes, metabolites and regulatory pathways linked to flower color variation in P. hirsutissimum. RESULT We observed that reduced anthocyanin and flavonoid contents along with slightly higher carotenoids are responsible for albino flower phenotype. Comparative transcriptome analysis identified 3287 differentially expressed genes (DEGs) among normal and albino labellum, and 3634 DEGs between normal and albino petals. Two genes encoding for flavanone 3-hydroxylase (F3H) and one gene encoding for chalcone synthase (CHS) were strongly downregulated in albino labellum and petals compared to normal flowers. As both F3H and CHS catalyze essentially important steps in anthocyanin biosynthesis pathway, downregulation of these genes is probably leading to albino flower phenotype via down-accumulation of anthocyanins. However, we observed the downregulation of major carotenoid biosynthesis genes including VDE, NCED and ABA2 which was inconsistent with the increased carotenoid accumulation in albino flowers, suggesting that carotenoid accumulation was probably controlled at post-transcriptional or translational level. In addition, we identified several key transcription factors (MYB73, MYB61, bHLH14, bHLH106, MADS-SOC1, AP2/ERF1, ERF26 and ERF87) that may regulate structural genes involved in flower color formation in P. hirsutissimum. Importantly, over-expression of some of these candidate TFs increased anthocyanin accumulation in tobacco leaves which provided important evidence for the role of these TFs in flower color formation probably via regulating key structural genes of the anthocyanin pathway. CONCLUSION The genes identified here could be potential targets for breeding P. hirsutissimum with different flower color patterns by manipulating the anthocyanin and carotenoid biosynthesis pathways.
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Affiliation(s)
- Xiuling Li
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Jizheng Fan
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Shuming Luo
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Ling Yin
- Guangxi Key Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Hongying Liao
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Xueqiang Cui
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Jingzhou He
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Yanhua Zeng
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Junjie Qu
- Guangxi Key Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
| | - Zhaoyang Bu
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
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