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Marin-Recinos MF, Pucker B. Genetic factors explaining anthocyanin pigmentation differences. BMC PLANT BIOLOGY 2024; 24:627. [PMID: 38961369 PMCID: PMC11221117 DOI: 10.1186/s12870-024-05316-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/20/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Anthocyanins are important contributors to coloration across a wide phylogenetic range of plants. Biological functions of anthocyanins span from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins. RESULTS A systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties was performed within numerous plant species covering the taxonomic diversity of flowering plants. The literature was screened for cases in which genetic factors causing anthocyanin loss were reported. Additionally, transcriptomic data sets from four previous studies were reanalyzed to determine the genes possibly responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the intraspecific pigmentation differences was quantified. Differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are significantly more prone to account for pigmentation differences compared to bHLH or WD40 genes. Among the structural genes, DFR genes are most often associated with anthocyanin loss. CONCLUSIONS These findings support previous assumptions about the susceptibility of transcriptional regulation to evolutionary changes and its importance for the evolution of novel coloration phenotypes. Our findings underline the particular significance of MYBs and their apparent prevalent role in the specificity of the MBW complex.
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Affiliation(s)
- Maria F Marin-Recinos
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology and BRICS, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology and BRICS, TU Braunschweig, Braunschweig, Germany.
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Zhang M, Li Y, Wang J, Shang S, Wang H, Yang X, Lu C, Wang M, Sun X, Liu X, Wang X, Wei B, Lv W, Mu G. Integrated transcriptomic and metabolomic analyses reveals anthocyanin biosynthesis in leaf coloration of quinoa (Chenopodium quinoa Willd.). BMC PLANT BIOLOGY 2024; 24:203. [PMID: 38509491 PMCID: PMC10953167 DOI: 10.1186/s12870-024-04821-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/14/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Quinoa leaves demonstrate a diverse array of colors, offering a potential enhancement to landscape aesthetics and the development of leisure-oriented sightseeing agriculture in semi-arid regions. This study utilized integrated transcriptomic and metabolomic analyses to investigate the mechanisms underlying anthocyanin synthesis in both emerald green and pink quinoa leaves. RESULTS Integrated transcriptomic and metabolomic analyses indicated that both flavonoid biosynthesis pathway (ko00941) and anthocyanin biosynthesis pathway (ko00942) were significantly associated with anthocyanin biosynthesis. Differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were analyzed between the two germplasms during different developmental periods. Ten DEGs were verified using qRT-PCR, and the results were consistent with those of the transcriptomic sequencing. The elevated expression of phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), 4-coumarate CoA ligase (4CL) and Hydroxycinnamoyltransferase (HCT), as well as the reduced expression of flavanone 3-hydroxylase (F3H) and Flavonol synthase (FLS), likely cause pink leaf formation. In addition, bHLH14, WRKY46, and TGA indirectly affected the activities of CHS and 4CL, collectively regulating the levels of cyanidin 3-O-(3'', 6''-O-dimalonyl) glucoside and naringenin. The diminished expression of PAL, 4CL, and HCT decreased the formation of cyanidin-3-O-(6"-O-malonyl-2"-O-glucuronyl) glucoside, leading to the emergence of emerald green leaves. Moreover, the lowered expression of TGA and WRKY46 indirectly regulated 4CL activity, serving as another important factor in maintaining the emerald green hue in leaves N1, N2, and N3. CONCLUSION These findings establish a foundation for elucidating the molecular regulatory mechanisms governing anthocyanin biosynthesis in quinoa leaves, and also provide some theoretical basis for the development of leisure and sightseeing agriculture.
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Affiliation(s)
- Min Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China
| | - Yueyou Li
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, Hebei Province, 050000, P. R. China
| | - Junling Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China
| | - Shaopu Shang
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, Hebei Province, 050000, P. R. China
| | - Hongxia Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China
| | - Xinlei Yang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China
| | - Chuan Lu
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, Hebei Province, 050000, P. R. China
| | - Mei Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China
| | - Xinbo Sun
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China
| | - Xiaoqing Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China
| | - Xiaoxia Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China
| | - Boxiang Wei
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China
| | - Wei Lv
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, Hebei Province, 050000, P. R. China.
| | - Guojun Mu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, The Key Laboratory of Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, 071000, P. R. China.
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhangjiakou, Hebei Province, 075000, P. R. China.
- The Quinoa S&T Academy Park of Rural Special Technology Association of China, Zhangjiakou, Hebei Province, 075000, P. R. China.
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Huang X, Liu L, Qiang X, Meng Y, Li Z, Huang F. Integrated Metabolomic and Transcriptomic Profiles Provide Insights into the Mechanisms of Anthocyanin and Carotenoid Biosynthesis in Petals of Medicago sativa ssp. sativa and Medicago sativa ssp. falcata. PLANTS (BASEL, SWITZERLAND) 2024; 13:700. [PMID: 38475545 DOI: 10.3390/plants13050700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/16/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
The petals of Medicago sativa ssp. sativa and M. sativa ssp. falcata are purple and yellow, respectively. Free hybridization between M. sativa ssp. sativa and M. sativa ssp. falcata has created hybrids with various flower colors in nature. Moreover, the flower colors of alfalfa are closely correlated with yield, nutritional quality, stress tolerance and other agronomic characteristics. To elucidate the underlying mechanisms of flower color formation in M. sativa ssp. sativa and M. sativa ssp. falcata, we conducted an integrative analysis of the transcriptome and metabolome of alfalfa with three different petal colors (purple, yellow and cream). The metabolic profiles suggested that anthocyanins and carotenoids are the crucial pigments in purple and yellow flowers, respectively. A quantitative exploration of the anthocyanin and carotenoid components indicated that the accumulations of cyanidin, delphinidin, peonidin, malvidin, pelargonidin and petunidin derivatives are significantly higher in purple flowers than in cream flowers. In addition, the content of carotenes (phytoene, α-carotene and β-carotene) and xanthophylls (α-cryptoxanthin, lutein, β-cryptoxanthin, zeaxanthin, antheraxanthin and violaxanthin derivatives) was markedly higher in yellow flowers than in cream flowers. Furthermore, we found that delphinidin-3,5-O-diglucoside and lutein were the predominant pigments accumulated in purple and yellow flowers, respectively. The transcriptomic results revealed that twenty-five upregulated structural genes (one C4H, three 4CL, twelve CHS, two CHI, one F3H, one F3'H, one F3'5'H and four DFR) are involved in the accumulation of anthocyanins in purple flowers, and nine structural genes (two PSY, one ZDS, two CRTISO, two BCH, one ZEP and one ECH) exert an effect on the carotenoid biosynthesis pathway in yellow flowers. The findings of this study reveal the underlying mechanisms of anthocyanin and carotenoid biosynthesis in alfalfa with three classic flower colors.
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Affiliation(s)
- Xiuzheng Huang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 100081, China
| | - Lei Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 100081, China
| | - Xiaojing Qiang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 100081, China
| | - Yuanfa Meng
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 100081, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 100081, China
| | - Fan Huang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 100081, China
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Liu M, Li C, Jiang T, Wang R, Wang Y, Zhang W, Pan X. Chromosome-scale genome assembly provides insights into flower coloration mechanisms of Canna indica. Int J Biol Macromol 2023; 251:126148. [PMID: 37591424 DOI: 10.1016/j.ijbiomac.2023.126148] [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: 05/17/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Canna indica, which produce conspicuous and colorful flowers, are widely appreciated as ornamental plants. We used Pacific Biosciences sequencing (PacBio) and chromosome conformation capture (Hi-C) genome scaffolding to build a high-quality chromosome-scale genome assembly of C. indica and the genome assembly was 821Mb with a contig N50 of 48Mb assembled into nine chromosomes. The genome of C. indica was predicted to contain 31,130 genes and 30,816 genes were functionally annotated. Genome annotation identified 522 Mb (63.59 %) as repetitive sequences. Genome evolution analysis showed that whole-genome duplication occurred 53.4 million years ago. Transcriptome analysis revealed that petal coloration was linked with the expression of genes encoding enzymes involved in anthocyanin biosynthesis, carotenoid biosynthesis, and the methylerythritol phosphate (MEP) pathway. Furthermore, modules of co-expressed genes and hub genes were identified via weighted gene co-expression network analysis. These results suggested that, in Canna indica, deep red petal coloration was regulated by CHS2 and yellow petal coloration was associated with expression of ARF6 and NAC14. Considered together, the current study revealed a high-quality reference genome which may provide new insights into the molecular basis of flower coloration in Canna indica and help enhance the conservation and breeding of ornamental plants in general.
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Affiliation(s)
- Mengmeng Liu
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Cheng Li
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Tang Jiang
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Ruipu Wang
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Yong Wang
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Wen'e Zhang
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Xuejun Pan
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
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Comparative Transcriptome Analysis Unveils the Molecular Mechanism Underlying Sepal Colour Changes under Acidic pH Substratum in Hydrangea macrophylla. Int J Mol Sci 2022; 23:ijms232315428. [PMID: 36499756 PMCID: PMC9739076 DOI: 10.3390/ijms232315428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The hydrangea (Hydrangea macrophylla (Thunb). Ser.), an ornamental plant, has good marketing potential and is known for its capacity to change the colour of its inflorescence depending on the pH of the cultivation media. The molecular mechanisms causing these changes are still uncertain. In the present study, transcriptome and targeted metabolic profiling were used to identify molecular changes in the RNAome of hydrangea plants cultured at two different pH levels. De novo assembly yielded 186,477 unigenes. Transcriptomic datasets provided a comprehensive and systemic overview of the dynamic networks of the gene expression underlying flower colour formation in hydrangeas. Weighted analyses of gene co-expression network identified candidate genes and hub genes from the modules linked closely to the hyper accumulation of Al3+ during different stages of flower development. F3'5'H, ANS, FLS, CHS, UA3GT, CHI, DFR, and F3H were enhanced significantly in the modules. In addition, MYB, bHLH, PAL6, PAL9, and WD40 were identified as hub genes. Thus, a hypothesis elucidating the colour change in the flowers of Al3+-treated plants was established. This study identified many potential key regulators of flower pigmentation, providing novel insights into the molecular networks in hydrangea flowers.
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Zhang X, Yang H, Li M, Bai Y, Chen C, Guo D, Guo C, Shu Y. A Pan-Transcriptome Analysis Indicates Efficient Downregulation of the FIB Genes Plays a Critical Role in the Response of Alfalfa to Cold Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:3148. [PMID: 36432878 PMCID: PMC9692835 DOI: 10.3390/plants11223148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/25/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Alfalfa (Medicago sativa L.) is a perennial forage legume that is widely distributed throughout the world, and cold stress is an important environmental factor limiting the growth and production of alfalfa in cold regions. However, little is known of the molecular mechanisms regarding cold tolerance in alfalfa. Here, we conducted physiological metabolism assays and pan-transcriptome sequencing on eight cultivars of alfalfa under cold stress conditions. The results of the RNA-seq analysis showed that the genes are "oxidoreductase activity" and "transcription regulator activity", suggesting that genes with such functions are more likely to play important roles in the response to cold stress by alfalfa. In addition, to identify specific gene modules and hub genes in response to alfalfa cold stress, we applied weighted gene co-expression network (WGCNA) analyses to the RNA-seq data. Our results indicate that the modules of genes that focus on the ATPase complex, ribosome biogenesis, are more likely to be involved in the alfalfa response to cold stress. It is important to note that we identified two fibronectin (FIB) genes as hub genes in alfalfa in response to cold stress and that they negatively regulate alfalfa response to chilling stress, and it is possible that dormant alfalfa is more effective at down-regulating FIB expression and therefore more resistant to cold stress.
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Affiliation(s)
| | | | | | | | | | | | - Changhong Guo
- Correspondence: (C.G.); (Y.S.); Tel.: +86-451-8806-0576 (Y.S. & C.G.)
| | - Yongjun Shu
- Correspondence: (C.G.); (Y.S.); Tel.: +86-451-8806-0576 (Y.S. & C.G.)
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7
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Zhang S, Chen J, Jiang T, Cai X, Wang H, Liu C, Tang L, Li X, Zhang X, Zhang J. Genetic mapping, transcriptomic sequencing and metabolic profiling indicated a glutathione S-transferase is responsible for the red-spot-petals in Gossypium arboreum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3443-3454. [PMID: 35986130 DOI: 10.1007/s00122-022-04191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
A GST for red-spot-petals in Gossypium arboreum was identified as the candidate under the scope of multi-omics approaches. Colored petal spots are correlated with insect pollination efficiency in Gossypium species. However, molecular mechanisms concerning the formation of red spots on Gossypium arboreum flowers remain elusive. In the current study, the Shixiya1-R (SxyR, with red spots) × Shixiya1-W (SxyW, without red spots) segregating population was utilized to determine that the red-spot-petal phenotype was levered by a single dominant locus. This phenotype was expectedly related to the anthocyanin metabolites, wherein the cyanidin and delphinidin derivatives constituted the major partition. Subsequently, this dominant locus was narrowed to a 3.27 Mb range on chromosome 7 by genomic resequencing from the two parents and the two segregated progeny bulks that have spotted petals or not. Furthermore, differential expressed genes generated from the two bulks at either of three sequential flower developmental stages that spanning the spot formation were intersected with the annotated ones that allocated to the 3.27 Mb interval, which returned eight genes. A glutathione S-transferase-coding gene (Gar07G08900) out of the eight was the only one that exhibited simultaneously differential expression among all three developmental stages, and it was therefore considered to be the probable candidate. Finally, functional validation upon this candidate was achieved by the appearance of scattered petal spots with inhibited expression of Gar07G08900. In conclusion, the current report identified a key gene for the red spotted petal in G. arboreum under the scope of multi-omics approaches, such efforts and embedded molecular resources would benefit future applications underlying the flower color trait in cotton.
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Affiliation(s)
- Sujun Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Jie Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Tao Jiang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Xiao Cai
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Haitao Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Cunjing Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Liyuan Tang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Xinghe Li
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Xiangyun Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China.
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China.
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Targeted Metabolomics Provide Chemotaxonomic Insights of Medicago ruthenica, with Coupled Transcriptomics Elucidating the Mechanism Underlying Floral Coloration. PLANTS 2022; 11:plants11182408. [PMID: 36145809 PMCID: PMC9505912 DOI: 10.3390/plants11182408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022]
Abstract
Medicago ruthenica, a wild legume forage widely distributed in the Eurasian steppe, demonstrates high genetic and phenotypic variation. M. ruthenica with a purely yellow flower (YFM), differing from the general phenotype of M. ruthenica with a purple flower (PFM), was recently discovered. The similar characteristics of YFM with Medicago falcata have led to conflicting opinions on its taxonomy using traditional morphological methods. The lack of chemotaxonomy information about M. ruthenica species and the unclear flower coloration mechanisms have hampered their study. Here, we investigated M. ruthenica using targeted metabolomics based on the chemotaxonomy method and elaborated the floral coloration mechanisms using transcriptomics. The identified flavonoids were the same types, but there were different contents in YFM and PFM, especially the contents of cyanidin-3-O-glucoside (C3G), an anthocyanin that causes the purple-reddish color of flowers. The over-accumulation of C3G in PFM was 1,770 times more than YFM. Nineteen anthocyanin-related genes were downregulated in YFM compared with their expression in PFM. Thus, YFM could be defined as a variety of M. ruthenica rather than a different species. The loss of purple flower coloration in YFM was attributed to the downregulation of these genes, resulting in reduced C3G accumulation. The taxonomic characteristics and molecular and physiological characteristics of this species will contribute to further research on other species with similar external morphologies.
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Wang L, Du M, Wang B, Duan H, Zhang B, Wang D, Li Y, Wang J. Transcriptome analysis of halophyte Nitraria tangutorum reveals multiple mechanisms to enhance salt resistance. Sci Rep 2022; 12:14031. [PMID: 35982183 PMCID: PMC9388663 DOI: 10.1038/s41598-022-17839-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 08/01/2022] [Indexed: 12/05/2022] Open
Abstract
As a typical halophyte, Nitraria tangutorum Bobr. has attracted the interest of many researchers with the excellent salt tolerance. Elucidation of the mechanism of N. tangutorum salinity tolerance will facilitate the genetic improvement of productive plants faced with salinity. To reveal the molecular response to gradually accumulated salt stress in N. tangutorum, RNA-sequencing and analysis of gradually accumulated NaCl treated samples and control samples were performed, and a total of 1419 differentially expressed genes were identified, including 949 down-regulated genes and 470 up-regulated genes. Detailed analysis uncovered that the catabolism of organic compounds mainly based on oxidative phosphorylation genes was up-regulated. Additionally, various antioxidant genes, especially anthocyanin-related genes, were found to help N. tangutorum remove reactive oxygen species. Moreover, the Mitogen activated protein kinase signaling pathway and other signaling pathways co-regulated various salt tolerance activities. Additionally, intracellular ion homeostasis was maintained via regulation of osmotic regulator-related genes, cutin-related genes, and cell elongation-related genes to retain cellular water and reduce ion concentration. In particularly, simultaneous up-regulation in cytoskeleton-related genes, cell wall-related genes, and auxin-related genes, provided evidence of important role of cell expansion in plant salt tolerance. In conclusion, complex regulatory mechanisms modulated by multiple genes might contribute to the salt tolerance by N. tangutorum.
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Affiliation(s)
- Lirong Wang
- Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Qinghai Minzu University, Xining, 810007, China.,Institute of Ecology and Environment of Qinghai-Tibet Plateau, Qinghai Minzu University, Xining, 810007, China
| | - Meng Du
- Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Qinghai Minzu University, Xining, 810007, China
| | - Bo Wang
- College of Forestry, Gansu Agricultural University, Lanzhou, 730000, China
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Benyin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Dong Wang
- Lanzhou Agriculture and Rural Affairs Bureau in Gansu Province, Lanzhou, 730030, China
| | - Yi Li
- College of Forestry, Gansu Agricultural University, Lanzhou, 730000, China.
| | - Jiuli Wang
- Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Qinghai Minzu University, Xining, 810007, China. .,Institute of Ecology and Environment of Qinghai-Tibet Plateau, Qinghai Minzu University, Xining, 810007, China.
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10
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Wang D, Wang J, Wang Y, Yao D, Niu Y. Metabolomic and Transcriptomic Profiling Uncover the Underlying Mechanism of Color Differentiation in Scutellaria baicalensis Georgi. Flowers. FRONTIERS IN PLANT SCIENCE 2022; 13:884957. [PMID: 35755689 PMCID: PMC9218823 DOI: 10.3389/fpls.2022.884957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Scutellaria baicalensis Georgi. (Chinese skullcap or Huang-qin) is an extremely crucial medicinal plant in the Labiate family, and the color of its flowers naturally appears purple. However, during the long-term cultivation of S. baicalensis, very few plants of S. baicalensis also present white and purple-red flower colors under the same ecological conditions. However, the complex metabolic and transcriptional networks underlying color formation in white, purple-red, and purple flowers of S. baicalensis remain largely unclarified. To gain an insight into this issue, we conducted transcriptome and metabolomic profiling to elucidate the anthocyanin synthesis metabolic pathway in the flowers of S. baicalensis, and to identify the differentially expressed candidate genes potentially involved in the biosynthesis of anthocyanins. The results showed that 15 anthocyanins were identified, among which cyanidin 3-rutinoside and delphin chloride were the primary anthocyanins, and accumulation was significantly related to the flower color changes of S. baicalensis. Furthermore, the down-regulation of SbDFR (Sb02g31040) reduced the anthocyanin levels in the flowers of S. baicalensis. The differential expression of the Sb3GT (Sb07g04780 and Sb01g72290) gene in purple and purple-red flowers affected anthocyanin accumulation, suggesting that anthocyanin levels were closely associated with the expression of SbDFR and Sb3GT, which play important roles in regulating the anthocyanin biosynthesis process of S. baicalensis flowers. Transcriptomic analysis revealed that transcription factors WRKY, bHLH, and NAC were also highly correlated with anthocyanin accumulation, especially for NAC35, which positively regulated SbDFR (Sb02g31040) gene expression and modulated anthocyanin biosynthesis in flower color variation of S. baicalensis. Overall, this study presents the first experimental evidence for the metabolomic and transcriptomic profiles of S. baicalensis in response to flower coloration, which provides a foundation for dynamic metabolic engineering and plant breeding, and to understand floral evolution in S. baicalensis plants.
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Affiliation(s)
| | | | | | | | - Yanbing Niu
- College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
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11
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Cheng H, Kong W, Tang T, Ren K, Zhang K, Wei H, Lin T. Identification of Key Gene Networks Controlling Soluble Sugar and Organic Acid Metabolism During Oriental Melon Fruit Development by Integrated Analysis of Metabolic and Transcriptomic Analyses. FRONTIERS IN PLANT SCIENCE 2022; 13:830517. [PMID: 35646021 PMCID: PMC9135470 DOI: 10.3389/fpls.2022.830517] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Oriental melon (Cucumis melo var. acidulus) is one of the most economically important fruit crops worldwide. To elucidate the molecular basis related to soluble sugar and organic acid metabolism in the fruits of two oriental melon cultivars with different sweetness, we performed integrated metabolomic and transcriptomic analyses of the fruits of 'Tianbao' (A) with high sweetness and 'Xiaocuigua' (B) with low sweetness at different ripening stages. The high accumulation of sucrose, D-glucose, D-(+)-raffinose, and the relatively lower citric acid and malic acid might contribute to the sweet taste of A. By screening the differentially expressed genes (DEGs) and correlation analysis of the DEGs and differentially accumulated metabolites, we deduced that the B cultivar might promote the conversion of glucose and fructose into intermediate compounds for downstream processes such as glycolysis. The tricarboxylic acid (TCA) cycle might also be enhanced compared to A, thus resulting in the differential accumulation of soluble sugars and organic acids, ultimately causing the taste difference between the two oriental melon cultivars. Our finding provides important information for further exploring the metabolic mechanisms of soluble sugars and organic acids in oriental melon.
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Affiliation(s)
- Hong Cheng
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Weiping Kong
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Taoxia Tang
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Kaili Ren
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Kaili Zhang
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Huxia Wei
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Tao Lin
- College of Horticulture, China Agricultural University, Beijing, China
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12
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Mo Z, Duan L, Pu Y, Tian Z, Ke Y, Luo W, Pi K, Huang Y, Nie Q, Liu R. Proteomics and Co-expression Network Analysis Reveal the Importance of Hub Proteins and Metabolic Pathways in Nicotine Synthesis and Accumulation in Tobacco ( Nicotiana tabacum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:860455. [PMID: 35574122 PMCID: PMC9096834 DOI: 10.3389/fpls.2022.860455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/24/2022] [Indexed: 05/31/2023]
Abstract
Nicotine is a unique alkaloid present in tobacco that is widely used in cigarettes and in the agricultural, chemical, and pharmaceutical industries. However, the research on nicotine is mostly limited to its synthesis pathways, and only a few studies have explored the effects of other metabolic pathways on nicotine precursors. Regulating the nicotine content in tobacco can greatly promoting the application of nicotine in other fields. In this study, we performed global data-independent acquisition proteomics analysis of four tobacco varieties. Of the four varieties, one had high nicotine content and three had a low nicotine content. A total of 31,259 distinct peptides and 6,018 proteins across two samples were identified. A total of 45 differentially expressed proteins (DEPs) co-existed in the three comparison groups and were mainly involved in the transport and metallic processes of the substances. Most DEPs were enriched in the biosynthesis of secondary metals, glutathione metabolism, carbon metabolism, and glycolysis/gluconeogenesis. In addition, the weighted gene co-expression network analysis identified an expression module closely related to the nicotine content (Brown, r = 0.74, P = 0.006). Gene Ontology annotation and Kyoto Encyclopaedia of Genes and Genomes enrichment analysis showed that the module proteins were mainly involved in the synthesis and metabolism of nicotine precursors such as arginine, ornithine aspartate, proline, and glutathione. The increased levels of these precursors lead to the synthesis and accumulation of nicotine in plants. More importantly, these proteins regulate nicotine synthesis by affecting the formation of putrescine, which is the core intermediate product in nicotine anabolism. Our results provide a reference for tobacco variety selection with a suitable nicotine content and regulation of the nicotine content. Additionally, the results highlight the importance of other precursor metabolism in nicotine synthesis.
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Affiliation(s)
- Zejun Mo
- College of Agriculture, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Lili Duan
- College of Agriculture, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Yuanyuan Pu
- College of Agriculture, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Zonglin Tian
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
- College of Tobacco, Guizhou University, Guiyang, China
| | - Yuzhou Ke
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
- College of Tobacco, Guizhou University, Guiyang, China
| | - Wen Luo
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
- College of Tobacco, Guizhou University, Guiyang, China
| | - Kai Pi
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
- College of Tobacco, Guizhou University, Guiyang, China
| | - Ying Huang
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
- College of Tobacco, Guizhou University, Guiyang, China
| | - Qiong Nie
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
- College of Tobacco, Guizhou University, Guiyang, China
| | - Renxiang Liu
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
- College of Tobacco, Guizhou University, Guiyang, China
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13
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Yu Y, Yang Z, Jiang Y, Wang L, Wu Y, Liao J, Yang R, Zhang L. Inheritance and QTL Mapping for Flower Color in Salvia miltiorrhiza Bunge. J Hered 2022; 113:248-256. [PMID: 35259262 DOI: 10.1093/jhered/esac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/04/2022] [Indexed: 11/12/2022] Open
Abstract
Salvia miltiorrhiza Bunge is an outcross-pollinated plant with diverse flower colors, ranging from white to purple. To clarify the genetic basis of S. miltiorrhiza flower color, we crossed white-flowered S. miltiorrhiza f. alba with dark violet-flowered S. miltiorrhiza, and selfed F1 to obtain an F2 population. The RGB color system was used to describe the flower color of the parents, F1 progeny, and F2 individuals. Afterward, we used genotyping-by-sequencing (GBS) technology to construct a high-density linkage map of S. miltiorrhiza based on the F2 population. Finally, the linkage map was used to locate the QTLs of the genes that control flower color in S. miltiorrhiza. Through measurement and cluster analysis of the R, G, and B values of flowers from the parents, F1, and F2 individuals, it was found that the purple flower color of S. miltiorrhiza is a quantitative trait controlled by two loci of major genes. The genetic map contained 605 SNPs with a total length of 738.3 cM in eight linkage groups (LGs), and the average distance between two markers was 1.22 cM. Based on the constructed genetic map and the flower R, G, B, and R+G+B values, two QTLs were detected for flower color, located on LG4 and LG5. The results of this study lay the foundation for cloning genes that control flower color and studying the molecular mechanism of flower color regulation in S. miltiorrhiza.
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Affiliation(s)
- Yan Yu
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Zaijun Yang
- College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Yuanyuan Jiang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Long Wang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Yichao Wu
- College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Jinqiu Liao
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Ruiwu Yang
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Li Zhang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
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14
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Li J, Ma Y, Hu M, Zhao Y, Liu B, Wang C, Zhang M, Zhang L, Yang X, Mu G. Multi-Omics and miRNA Interaction Joint Analysis Highlight New Insights Into Anthocyanin Biosynthesis in Peanuts ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2022; 13:818345. [PMID: 35251087 PMCID: PMC8888885 DOI: 10.3389/fpls.2022.818345] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/24/2022] [Indexed: 06/01/2023]
Abstract
Peanut (Arachis hypogaea L.) is one of the most important economic and oil crops in the world. At present, peanut varieties with rich anthocyanin in testa are rare in the market, but the selection and breeding of varieties with the related traits has always attracted the attention of breeders. In this study, two peanut varieties with the pink and purple testa, G110 (G) and Z18-40 (Z) were used to conduct interaction joint analysis of multi-omics and miRNA-target gene. The anthocyanin content of Z18-40 was 7.49-8.62-folds higher than G110 on 30 DAF (days after flowering) and 45 DAF via Ultraviolet-visible Spectrophotometer (UV-5800, Shanghai, China). And then, a total of 14 candidate genes related with the anthocyanin biosynthesis were identified for correlation in different comparison groups (R 2 ≥ 0.80), among of a novel gene Ah21440 related with hydroxycinnamoyl transferase (HCT) biosynthesis was identified. In addition, Cyanidin 3-O-glucoside (Kuromanin, pmb0550) was the only common differentially accumulated metabolite (DAM) identified using multi-omics joint analysis in G1_vs_G2, Z1_vs_Z2, G1_vs_Z1, and G2_vs_Z2, respectively. Correlation analysis of miRNA-target genes and DEGs in the transcriptome shows that, AhmiR2950, AhmiR398, AhmiR50, and AhmiR51 regulated to HCT and chalcone biosynthesis related candidate genes (Ah21440, AhCHS, AhCHI). Lastly, all of 14 candidate genes and 4 differentially expressed miRNAs were validated using quantitative real-time PCR (qRT-PCR), which trends were consistent with that of the former transcriptome data. The results provide important reference for in-depth research on the anthocyanin metabolism mechanism in peanut testa.
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15
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Li H, Du Y, Zhang J, Feng H, Liu J, Yang G, Zhu Y. Unraveling the Mechanism of Purple Leaf Formation in Brassica napus by Integrated Metabolome and Transcriptome Analyses. FRONTIERS IN PLANT SCIENCE 2022; 13:945553. [PMID: 35903234 PMCID: PMC9315442 DOI: 10.3389/fpls.2022.945553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/13/2022] [Indexed: 05/12/2023]
Abstract
Brassica napus as both oilseed and vegetable, is widely cultivated in China. The purple leaf of B. napus is rich in anthocyanins and can provide valuable nutrients. Although several high-anthocyanin cultivars have been reported, the molecular mechanism underlying anthocyanin biosynthesis in B. napus remains lesser-known. Therefore, in this study, we conducted integrative metabolome and transcriptome analyses in three B. napus cultivars with different leaf colors. Overall, 39 flavonoids were identified (including 35 anthocyanins), and 22 anthocyanins were differentially accumulated in the leaves, contributing to the different leaf colors. Cyanidin-3,5,3'-O-triglucoside was confirmed as the main contributor of the purple leaf phenotype. Meanwhile, other anthocyanins may play important roles in deepening the color of B. napus leaves. A total of 5,069 differentially expressed genes (DEGs) and 32 overlapping DEGs were identified by RNA-sequencing; hence, the correlation between anthocyanin content and DEG expression levels was explored. Two structural genes (DFR and ANS), three GSTs (homologous to TT19), and 68 differentially expressed transcription factors (TFs), especially MYB-related TFs and WRKY44, were identified in three B. napus varieties characterized by different leaf color, thereby indicating that these genes may contribute to anthocyanin biosynthesis, transport, or accumulation in B. napus leaves. The findings of study provide important insights that may contribute to gaining a better understanding of the transcriptional regulation of anthocyanin metabolism in B. napus.
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16
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Medina CA, Samac DA, Yu LX. Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.). Sci Rep 2021; 11:17203. [PMID: 34446782 PMCID: PMC8390513 DOI: 10.1038/s41598-021-96712-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023] Open
Abstract
Alfalfa is an important legume forage grown worldwide and its productivity is affected by environmental stresses such as drought and high salinity. In this work, three alfalfa germplasms with contrasting tolerances to drought and high salinity were used for unraveling the transcriptomic responses to drought and salt stresses. Twenty-one different RNA samples from different germplasm, stress conditions or tissue sources (leaf, stem and root) were extracted and sequenced using the PacBio (Iso-Seq) and the Illumina platforms to obtain full-length transcriptomic profiles. A total of 1,124,275 and 91,378 unique isoforms and genes were obtained, respectively. Comparative analysis of transcriptomes identified differentially expressed genes and isoforms as well as transcriptional and post-transcriptional modifications such as alternative splicing events, fusion genes and nonsense-mediated mRNA decay events and non-coding RNA such as circRNA and lncRNA. This is the first time to identify the diversity of circRNA and lncRNA in response to drought and high salinity in alfalfa. The analysis of weighted gene co-expression network allowed to identify master genes and isoforms that may play important roles on drought and salt stress tolerance in alfalfa. This work provides insight for understanding the mechanisms by which drought and salt stresses affect alfalfa growth at the whole genome level.
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Affiliation(s)
- Cesar Augusto Medina
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, 99350, USA
| | - Deborah A Samac
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, 1991 Upper Buford Circle, 495 Borlaug Hall St, Paul, MN, 55108, USA
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, 99350, USA.
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17
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Zheng Q, Chen W, Luo M, Xu L, Zhang Q, Luo Z. Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon. BMC PLANT BIOLOGY 2021; 21:356. [PMID: 34325657 PMCID: PMC8323215 DOI: 10.1186/s12870-021-03133-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/01/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Proanthocyanidins (PAs) are important plant secondary metabolites that confer flavor, nutritional value, and resistance to pathogens. Persimmon is one of the PA richest crops. Mature fruits can be inedible because of the astringency caused by high PA levels and need to go through a de-astringency treatment before consumption. The molecular basis for PA accumulation is poorly known, particularly transcriptional regulators. We characterised three genotypes ('Luotiantianshi' (LT), 'Mopanshi' (MP), and 'Youhou' (YH)) with different PA accumulation patterns using an approach that combined PacBio full-length sequencing and Illumina-based RNA sequencing to build high-quality full-length transcriptomes. Additionally, we analysed transcriptome dynamics of the three genotypes (LT, MP, and YH) at four key fruit developmental stages. RESULTS A total of 96,463 transcripts were obtained. We identified 80,075 protein-coding sequences (CDSs), 71,137 simple sequence repeats (SSRs), and 27,845 long noncoding RNAs (lncRNAs). Pearson correlation coefficient (PCC), principal component analysis (PCA), and differentially expressed transcripts (DETs) analyses indicated that the four different developmental stages within a genotype exhibited similar transcriptome activities. A total of 2,164 transcripts specific to each fruit developmental stage were detected. The transcripts specific to early stages were attributed to phenylpropanoid and flavonoid biosynthesis. Co-expression network analyses revealed MEbrown and MEblue modules were strongly associated to PA accumulation. From these two modules, 20 hub TFs are potential regulators for PA accumulation. Among them, Cluster_78388 (SBP protein), Cluster_63454 (bZIP protein), and Cluster_66595 (MYB protein) appear to involve in the PA biosynthesis in Chinese genotypes. CONCLUSIONS This is the first high-quality reference transcriptome for commercial persimmon. Our work provides insights into the molecular pathways underlying PA accumulation and enhances our global understanding of transcriptome dynamics throughout fruit development.
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Affiliation(s)
- Qingyou Zheng
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wenxing Chen
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Man Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Liqing Xu
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qinglin Zhang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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18
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Sánchez-Cabrera M, Jiménez-López FJ, Narbona E, Arista M, Ortiz PL, Romero-Campero FJ, Ramanauskas K, Igić B, Fuller AA, Whittall JB. Changes at a Critical Branchpoint in the Anthocyanin Biosynthetic Pathway Underlie the Blue to Orange Flower Color Transition in Lysimachia arvensis. FRONTIERS IN PLANT SCIENCE 2021; 12:633979. [PMID: 33692818 PMCID: PMC7937975 DOI: 10.3389/fpls.2021.633979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/01/2021] [Indexed: 05/27/2023]
Abstract
Anthocyanins are the primary pigments contributing to the variety of flower colors among angiosperms and are considered essential for survival and reproduction. Anthocyanins are members of the flavonoids, a broader class of secondary metabolites, of which there are numerous structural genes and regulators thereof. In western European populations of Lysimachia arvensis, there are blue- and orange-petaled individuals. The proportion of blue-flowered plants increases with temperature and daylength yet decreases with precipitation. Here, we performed a transcriptome analysis to characterize the coding sequences of a large group of flavonoid biosynthetic genes, examine their expression and compare our results to flavonoid biochemical analysis for blue and orange petals. Among a set of 140 structural and regulatory genes broadly representing the flavonoid biosynthetic pathway, we found 39 genes with significant differential expression including some that have previously been reported to be involved in similar flower color transitions. In particular, F3'5'H and DFR, two genes at a critical branchpoint in the ABP for determining flower color, showed differential expression. The expression results were complemented by careful examination of the SNPs that differentiate the two color types for these two critical genes. The decreased expression of F3'5'H in orange petals and differential expression of two distinct copies of DFR, which also exhibit amino acid changes in the color-determining substrate specificity region, strongly correlate with the blue to orange transition. Our biochemical analysis was consistent with the transcriptome data indicating that the shift from blue to orange petals is caused by a change from primarily malvidin to largely pelargonidin forms of anthocyanins. Overall, we have identified several flavonoid biosynthetic pathway loci likely involved in the shift in flower color in L. arvensis and even more loci that may represent the complex network of genetic and physiological consequences of this flower color polymorphism.
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Affiliation(s)
- Mercedes Sánchez-Cabrera
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | | | - Eduardo Narbona
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
| | - Montserrat Arista
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Pedro L. Ortiz
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Francisco J. Romero-Campero
- Institute for Plant Biochemistry and Photosynthesis, University of Seville – Centro Superior de Investigación Científica, Seville, Spain
- Department of Computer Science and Artificial Intelligence, University of Seville, Seville, Spain
| | - Karolis Ramanauskas
- Department of Biological Science, University of Illinois at Chicago, Chicago, IL, United States
| | - Boris Igić
- Department of Biological Science, University of Illinois at Chicago, Chicago, IL, United States
| | - Amelia A. Fuller
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Justen B. Whittall
- Department of Biology, College of Arts and Sciences, Santa Clara University, Santa Clara, CA, United States
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19
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Xia Y, Chen W, Xiang W, Wang D, Xue B, Liu X, Xing L, Wu D, Wang S, Guo Q, Liang G. Integrated metabolic profiling and transcriptome analysis of pigment accumulation in Lonicera japonica flower petals during colour-transition. BMC PLANT BIOLOGY 2021; 21:98. [PMID: 33596836 PMCID: PMC7890969 DOI: 10.1186/s12870-021-02877-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/04/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Plants have remarkable diversity in petal colour through the biosynthesis and accumulation of various pigments. To better understand the mechanisms regulating petal pigmentation in Lonicera japonica, we used multiple approaches to investigate the changes in carotenoids, anthocyanins, endogenous hormones and gene expression dynamics during petal colour transitions, i.e., green bud petals (GB_Pe), white flower petals (WF_Pe) and yellow flower petals (YF_Pe). RESULTS Metabolome analysis showed that YF_Pe contained a much higher content of carotenoids than GB_Pe and WF_Pe, with α-carotene, zeaxanthin, violaxanthin and γ-carotene identified as the major carotenoid compounds in YF_Pe. Comparative transcriptome analysis revealed that the key differentially expressed genes (DEGs) involved in carotenoid biosynthesis, such as phytoene synthase, phytoene desaturase and ζ-carotene desaturase, were significantly upregulated in YF_Pe. The results indicated that upregulated carotenoid concentrations and carotenoid biosynthesis-related genes predominantly promote colour transition. Meanwhile, two anthocyanins (pelargonidin and cyanidin) were significantly increased in YF_Pe, and the expression level of an anthocyanidin synthase gene was significantly upregulated, suggesting that anthocyanins may contribute to vivid yellow colour in YF_Pe. Furthermore, analyses of changes in indoleacetic acid, zeatin riboside, gibberellic acid, brassinosteroid (BR), methyl jasmonate and abscisic acid (ABA) levels indicated that colour transitions are regulated by endogenous hormones. The DEGs involved in the auxin, cytokinin, gibberellin, BR, jasmonic acid and ABA signalling pathways were enriched and associated with petal colour transitions. CONCLUSION Our results provide global insight into the pigment accumulation and the regulatory mechanisms underlying petal colour transitions during the flower development process in L. japonica.
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Affiliation(s)
- Yan Xia
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China
| | - Weiwei Chen
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
- Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Weibo Xiang
- Rare Plant Research Institute of the Yangtze River (Yichang); Institute of Science and Technology, China Three Gorges Corporation, Beijing, 100083, China
| | - Dan Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China
| | - Baogui Xue
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China
| | - Xinya Liu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China
| | - Lehua Xing
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China
| | - Shuming Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China.
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China.
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Qiao Y, Cheng Q, Zhang Y, Yan W, Yi F, Shi F. Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers. BMC PLANT BIOLOGY 2021; 21:61. [PMID: 33482728 PMCID: PMC7825240 DOI: 10.1186/s12870-021-02827-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/05/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Sainfoin (Onobrychis viciifolia Scop) is not only a high-quality legume forage, but also a nectar-producing plant. Therefore, the flower color of sainfoin is an important agronomic trait, but the factors affecting its flower phenotype are still unclear. To gain insights into the regulatory networks associated with metabolic pathways of coloration compounds (flavonoids or anthocyanins) and identify the key genes, we conducted a comprehensive analysis of the phenotype, metabolome and transcriptome of WF and AF of sainfoin. RESULTS Delphinidin, petunidin and malvidin derivatives were the main anthocyanin compounds in the AF of sainfoin. These substances were not detected in the WF of sainfoin. The transcriptomes of WF and AF in sainfoin at the S1 and S3 stages were obtained using the Illumina HiSeq4000 platform. Overall, 10,166 (4273 upregulated and 5893 downregulated) and 15,334 (8174 upregulated and 7160 downregulated) DEGs were identified in flowers at S1 and S3 stages, respectively (WF-VS-AF). KEGG pathway annotations showed that 6396 unigenes were annotated to 120 pathways and contained 866 DEGs at S1 stages, and 6396 unigenes were annotated to 131 pathways and included 1546 DEGs at the S3 stage. Nine DEGs belonging to the "flavonoid biosynthesis"and "phenylpropanoid biosynthesis" pathways involved in flower color formation were identified and verified by RT-qPCR analyses. Among these DEGs, 4CL3, FLS, ANS, CHS, DFR and CHI2 exhibited downregulated expression, and F3H exhibited upregulated expression in the WF compared to the AF, resulting in a decrease in anthocyanin synthesis and the formation of WF in sainfoin. CONCLUSIONS This study is the first to use transcriptome technology to study the mechanism of white flower formation in sainfoin. Our transcriptome data will be a great enrichment of the genetic information for sainfoin. In addition, the data presented herein will provide valuable molecular information for genetic breeding and provide insight into the future study of flower color polymorphisms in sainfoin.
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Affiliation(s)
- Yu Qiao
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Qiming Cheng
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Yutong Zhang
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Wei Yan
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Fengyan Yi
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Fengling Shi
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China.
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21
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Jiang T, Zhang M, Wen C, Xie X, Tian W, Wen S, Lu R, Liu L. Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers. BMC PLANT BIOLOGY 2020; 20:349. [PMID: 32703155 PMCID: PMC7379815 DOI: 10.1186/s12870-020-02553-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND The objectives of this study were to reveal the anthocyanin biosynthesis metabolic pathway in white and purple flowers of Salvia miltiorrhiza using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis. RESULTS We analyzed the metabolomics and transcriptomics data of S. miltiorrhiza flowers. A total of 1994 differentially expressed genes and 84 flavonoid metabolites were identified between the white and purple flowers of S. miltiorrhiza. Integrated analysis of transcriptomics and metabolomics showed that cyanidin 3,5-O-diglucoside, malvidin 3,5-diglucoside, and cyanidin 3-O-galactoside were mainly responsible for the purple flower color of S. miltiorrhiza. A total of 100 unigenes encoding 10 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in S. miltiorrhiza flowers. Low expression of the ANS gene decreased the anthocyanin content but enhanced the accumulation of flavonoids in S. miltiorrhiza flowers. CONCLUSIONS Our results provide valuable information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways in S. miltiorrhiza.
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Affiliation(s)
- Tao Jiang
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Meidi Zhang
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Chunxiu Wen
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Xiaoliang Xie
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Wei Tian
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Saiqun Wen
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Ruike Lu
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Lingdi Liu
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China.
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