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Marin-Recinos MF, Pucker B. Genetic factors explaining anthocyanin pigmentation differences. BMC PLANT BIOLOGY 2024; 24:627. [PMID: 38961369 PMCID: PMC11221117 DOI: 10.1186/s12870-024-05316-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/20/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Anthocyanins are important contributors to coloration across a wide phylogenetic range of plants. Biological functions of anthocyanins span from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins. RESULTS A systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties was performed within numerous plant species covering the taxonomic diversity of flowering plants. The literature was screened for cases in which genetic factors causing anthocyanin loss were reported. Additionally, transcriptomic data sets from four previous studies were reanalyzed to determine the genes possibly responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the intraspecific pigmentation differences was quantified. Differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are significantly more prone to account for pigmentation differences compared to bHLH or WD40 genes. Among the structural genes, DFR genes are most often associated with anthocyanin loss. CONCLUSIONS These findings support previous assumptions about the susceptibility of transcriptional regulation to evolutionary changes and its importance for the evolution of novel coloration phenotypes. Our findings underline the particular significance of MYBs and their apparent prevalent role in the specificity of the MBW complex.
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Affiliation(s)
- Maria F Marin-Recinos
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology and BRICS, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology and BRICS, TU Braunschweig, Braunschweig, Germany.
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2
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Lv W, Zhu L, Tan L, Gu L, Wang H, Du X, Zhu B, Zeng T, Wang C. Genome-Wide Identification Analysis of GST Gene Family in Wild Blueberry Vaccinium duclouxii and Their Impact on Anthocyanin Accumulation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1497. [PMID: 38891305 PMCID: PMC11174658 DOI: 10.3390/plants13111497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
Vaccinium duclouxii, a wild blueberry species native to the mountainous regions of southwestern China, is notable for its exceptionally high anthocyanin content, surpassing that of many cultivated varieties and offering significant research potential. Glutathione S-transferases (GSTs) are versatile enzymes crucial for anthocyanin transport in plants. Yet, the GST gene family had not been previously identified in V. duclouxii. This study utilized a genome-wide approach to identify and characterize the GST gene family in V. duclouxii, revealing 88 GST genes grouped into seven distinct subfamilies. This number is significantly higher than that found in closely related species, with these genes distributed across 12 chromosomes and exhibiting gene clustering. A total of 46 members are classified as tandem duplicates. The gene structure of VdGST is relatively conserved among related species, showing closer phylogenetic relations to V. bracteatum and evidence of purifying selection. Transcriptomic analysis and qRT-PCR indicated that VdGSTU22 and VdGSTU38 were highly expressed in flowers, VdGSTU29 in leaves, and VdGSTF11 showed significant expression in ripe and fully mature fruits, paralleling trends seen with anthocyanin accumulation. Subcellular localization identified VdGSTF11 primarily in the plasma membrane, suggesting a potential role in anthocyanin accumulation in V. duclouxii fruits. This study provides a foundational basis for further molecular-level functional analysis of the transport and accumulation of anthocyanins in V. duclouxii, enhancing our understanding of the molecular mechanisms underlying anthocyanin metabolism in this valuable species.
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Affiliation(s)
- Wei Lv
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (W.L.); (L.T.); (L.G.); (H.W.); (X.D.); (B.Z.)
| | - Liyong Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China;
| | - Lifa Tan
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (W.L.); (L.T.); (L.G.); (H.W.); (X.D.); (B.Z.)
| | - Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (W.L.); (L.T.); (L.G.); (H.W.); (X.D.); (B.Z.)
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (W.L.); (L.T.); (L.G.); (H.W.); (X.D.); (B.Z.)
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (W.L.); (L.T.); (L.G.); (H.W.); (X.D.); (B.Z.)
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (W.L.); (L.T.); (L.G.); (H.W.); (X.D.); (B.Z.)
| | - Tuo Zeng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (W.L.); (L.T.); (L.G.); (H.W.); (X.D.); (B.Z.)
| | - Caiyun Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China;
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Wang X, Dong J, Hu Y, Huang Q, Lu X, Huang Y, Sheng M, Cao L, Xu B, Li Y, Zong Y, Guo W. Identification and Characterization of the Glutathione S-Transferase Gene Family in Blueberry ( Vaccinium corymbosum) and Their Potential Roles in Anthocyanin Intracellular Transportation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1316. [PMID: 38794388 PMCID: PMC11125127 DOI: 10.3390/plants13101316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
The glutathione S-transferases (GSTs, EC 2.5.1.18) constitute a versatile enzyme family with pivotal roles in plant stress responses and detoxification processes. Recent discoveries attributed the additional function of facilitating anthocyanin intracellular transportation in plants to GSTs. Our study identified 178 VcGST genes from 12 distinct subfamilies in the blueberry genome. An uneven distribution was observed among these genes across blueberry's chromosomes. Members within the same subfamily displayed homogeneity in gene structure and conserved protein motifs, whereas marked divergence was noted among subfamilies. Functional annotations revealed that VcGSTs were significantly enriched in several gene ontology and KEGG pathway categories. Promoter regions of VcGST genes predominantly contain light-responsive, MYB-binding, and stress-responsive elements. The majority of VcGST genes are subject to purifying selection, with whole-genome duplication or segmental duplication serving as key processes that drive the expansion of the VcGST gene family. Notably, during the ripening of the blueberry fruit, 100 VcGST genes were highly expressed, and the expression patterns of 24 of these genes demonstrated a strong correlation with the dynamic content of fruit anthocyanins. Further analysis identified VcGSTF8, VcGSTF20, and VcGSTF22 as prime candidates of VcGST genes involved in the anthocyanin intracellular transport. This study provides a reference for the exploration of anthocyanin intracellular transport mechanisms and paves the way for investigating the spectrum of GST functions in blueberries.
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Affiliation(s)
- Xuxiang Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Jiajia Dong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Yiting Hu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Qiaoyu Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Xiaoying Lu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Yilin Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Mingyang Sheng
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Lijun Cao
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Buhuai Xu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Yongqiang Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Yu Zong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Weidong Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
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4
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Pei Z, Huang Y, Ni J, Liu Y, Yang Q. For a Colorful Life: Recent Advances in Anthocyanin Biosynthesis during Leaf Senescence. BIOLOGY 2024; 13:329. [PMID: 38785811 PMCID: PMC11117936 DOI: 10.3390/biology13050329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Leaf senescence is the last stage of leaf development, and it is accompanied by a leaf color change. In some species, anthocyanins are accumulated during leaf senescence, which are vital indicators for both ornamental and commercial value. Therefore, it is essential to understand the molecular mechanism of anthocyanin accumulation during leaf senescence, which would provide new insight into autumn coloration and molecular breeding for more colorful plants. Anthocyanin accumulation is a surprisingly complex process, and significant advances have been made in the past decades. In this review, we focused on leaf coloration during senescence. We emphatically discussed several networks linked to genetic, hormonal, environmental, and nutritional factors in regulating anthocyanin accumulation during leaf senescence. This paper aims to provide a regulatory model for leaf coloration and to put forward some prospects for future development.
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Affiliation(s)
- Ziqi Pei
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; (Z.P.); (Y.H.); (Y.L.)
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing 100083, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Yifei Huang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; (Z.P.); (Y.H.); (Y.L.)
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing 100083, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Junbei Ni
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Yong Liu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; (Z.P.); (Y.H.); (Y.L.)
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing 100083, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Qinsong Yang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; (Z.P.); (Y.H.); (Y.L.)
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing 100083, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing 100083, China
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5
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Zhang Z, Yuan L, Dang J, Zhang Y, Wen Y, Du Y, Liang Y, Wang Y, Liu T, Li T, Hu X. 5-Aminolevulinic acid improves cold resistance through regulation of SlMYB4/SlMYB88-SlGSTU43 module to scavenge reactive oxygen species in tomato. HORTICULTURE RESEARCH 2024; 11:uhae026. [PMID: 38495031 PMCID: PMC10940124 DOI: 10.1093/hr/uhae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/14/2024] [Indexed: 03/19/2024]
Abstract
Cold stress severely affects the growth and quality of tomato. 5-Aminolevulinic acid (ALA) can effectively improve tomato's cold stress tolerance. In this study, a tomato glutathione S-transferase gene, SlGSTU43, was identified. Results showed that ALA strongly induced the expression of SlGSTU43 under cold stress. SlGSTU43-overexpressing lines showed increased resistance to cold stress through an enhanced ability to scavenge reactive oxygen species. On the contrary, slgstu43 mutant lines were sensitive to cold stress, and ALA did not improve their cold stress tolerance. Thus, SlGSTU43 is a key gene in the process of ALA improving tomato cold tolerance. Through yeast library screening, SlMYB4 and SlMYB88 were preliminarily identified as transcription factors that bind to the SlGSTU43 promoter. Electrophoretic mobility shift, yeast one-hybrid, dual luciferase, and chromatin immunoprecipitation assays experiments verified that SlMYB4 and SlMYB88 can bind to the SlGSTU43 promoter. Further experiments showed that SlMYB4 and SlMYB88 are involved in the process of ALA-improving tomato's cold stress tolerance and they positively regulate the expression of SlGSTU43. The findings provide new insights into the mechanism by which ALA improves cold stress tolerance. SlGSTU43, as a valuable gene, could be added to the cold-responsive gene repository. Subsequently, it could be used in genetic engineering to enhance the cold tolerance of tomato.
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Affiliation(s)
- Zhengda Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Protected Horticulture Engineering in Northwest, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Luqiao Yuan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Protected Horticulture Engineering in Northwest, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Jiao Dang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Protected Horticulture Engineering in Northwest, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Yuhui Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Protected Horticulture Engineering in Northwest, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Yongshuai Wen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Protected Horticulture Engineering in Northwest, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Yu Du
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yufei Liang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ya Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tao Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaohui Hu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Protected Horticulture Engineering in Northwest, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
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Duan AQ, Deng YJ, Tan SS, Liu SS, Liu H, Xu ZS, Shu S, Xiong AS. DcGST1, encoding a glutathione S-transferase activated by DcMYB7, is the main contributor to anthocyanin pigmentation in purple carrot. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1069-1083. [PMID: 37947285 DOI: 10.1111/tpj.16539] [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: 06/21/2023] [Revised: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023]
Abstract
The color of purple carrot taproots mainly depends on the anthocyanins sequestered in the vacuoles. Glutathione S-transferases (GSTs) are key enzymes involved in anthocyanin transport. However, the precise mechanism of anthocyanin transport from the cytosolic surface of the endoplasmic reticulum (ER) to the vacuoles in carrots remains unclear. In this study, we conducted a comprehensive analysis of the carrot genome, leading to the identification of a total of 41 DcGST genes. Among these, DcGST1 emerged as a prominent candidate, displaying a strong positive correlation with anthocyanin pigmentation in carrot taproots. It was highly expressed in the purple taproot tissues of purple carrot cultivars, while it was virtually inactive in the non-purple taproot tissues of purple and non-purple carrot cultivars. DcGST1, a homolog of Arabidopsis thaliana TRANSPARENT TESTA 19 (TT19), belongs to the GSTF clade and plays a crucial role in anthocyanin transport. Using the CRISPR/Cas9 system, we successfully knocked out DcGST1 in the solid purple carrot cultivar 'Deep Purple' ('DPP'), resulting in carrots with orange taproots. Additionally, DcMYB7, an anthocyanin activator, binds to the DcGST1 promoter, activating its expression. Compared with the expression DcMYB7 alone, co-expression of DcGST1 and DcMYB7 significantly increased anthocyanin accumulation in carrot calli. However, overexpression of DcGST1 in the two purple carrot cultivars did not change the anthocyanin accumulation pattern or significantly increase the anthocyanin content. These findings improve our understanding of anthocyanin transport mechanisms in plants, providing a molecular foundation for improving and enhancing carrot germplasm.
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Affiliation(s)
- Ao-Qi Duan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan-Jie Deng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shan-Shan Tan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shan-Shan Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sheng Shu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Facility Horticulture Research Institute of Suqian, Suqian Research Institute of Nanjing Agricultural University, Suqian, Jiangsu, 223800, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Facility Horticulture Research Institute of Suqian, Suqian Research Institute of Nanjing Agricultural University, Suqian, Jiangsu, 223800, China
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7
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de los Cobos FP, García-Gómez BE, Orduña-Rubio L, Batlle I, Arús P, Matus JT, Eduardo I. Exploring large-scale gene coexpression networks in peach ( Prunus persica L.): a new tool for predicting gene function. HORTICULTURE RESEARCH 2024; 11:uhad294. [PMID: 38487296 PMCID: PMC10939413 DOI: 10.1093/hr/uhad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/17/2023] [Indexed: 03/17/2024]
Abstract
Peach is a model for Prunus genetics and genomics, however, identifying and validating genes associated to peach breeding traits is a complex task. A gene coexpression network (GCN) capable of capturing stable gene-gene relationships would help researchers overcome the intrinsic limitations of peach genetics and genomics approaches and outline future research opportunities. In this study, we created four GCNs from 604 Illumina RNA-Seq libraries. We evaluated the performance of every GCN in predicting functional annotations using an algorithm based on the 'guilty-by-association' principle. The GCN with the best performance was COO300, encompassing 21 956 genes. To validate its performance predicting gene function, we performed two case studies. In case study 1, we used two genes involved in fruit flesh softening: the endopolygalacturonases PpPG21 and PpPG22. Genes coexpressing with both genes were extracted and referred to as melting flesh (MF) network. Finally, we performed an enrichment analysis of MF network and compared the results with the current knowledge regarding peach fruit softening. The MF network mostly included genes involved in cell wall expansion and remodeling, and with expressions triggered by ripening-related phytohormones, such as ethylene, auxin, and methyl jasmonate. In case study 2, we explored potential targets of the anthocyanin regulator PpMYB10.1 by comparing its gene-centered coexpression network with that of its grapevine orthologues, identifying a common regulatory network. These results validated COO300 as a powerful tool for peach and Prunus research. This network, renamed as PeachGCN v1.0, and the scripts required to perform a function prediction analysis are available at https://github.com/felipecobos/PeachGCN.
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Affiliation(s)
- Felipe Pérez de los Cobos
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA) , Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Beatriz E García-Gómez
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Luis Orduña-Rubio
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, 46908, Valencia, Spain
| | - Ignasi Batlle
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA) , Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
| | - Pere Arús
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, 46908, Valencia, Spain
| | - Iban Eduardo
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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8
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Zhou P, Lei S, Zhang X, Wang Y, Guo R, Yan S, Jin G, Zhang X. Genome sequencing revealed the red-flower trait candidate gene of a peach landrace. HORTICULTURE RESEARCH 2023; 10:uhad210. [PMID: 38023475 PMCID: PMC10681006 DOI: 10.1093/hr/uhad210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Peach (Prunus persica) is an economically important fruit crop globally and an excellent material for genomic studies. While considerable progress has been made in unveiling trait-associated genes within cultivars and wild relatives, certain novel genes controlling valuable traits in peach landraces, such as the red-flowering gene, remained unclear. In this study, we sequenced and assembled the diploid genome of the red-flower landrace 'Yingzui' (abbreviated as 'RedY'). Multi-omics profiling of red petals of 'RedY' revealed the intensified red coloration associated with anthocyanins accumulation and concurrent decline in flavonols. This phenomenon is likely attributed to a natural variant of Flavonol Synthase (FLS) harboring a 9-bp exonic insertion. Intriguingly, the homozygous allelic configurations of this FLS variant were only observed in red-flowered peaches. Furthermore, the 9-bp sequence variation tightly associated with pink/red petal color in genome-wide association studies (GWAS) of collected peach germplasm resources. Functional analyses of the FLS variant, purified from procaryotic expression system, demonstrated its diminished enzymatic activity in flavonols biosynthesis, impeccably aligning with the cardinal trait of red flowers. Therefore, the natural FLS variant was proposed as the best candidate gene for red-flowering trait in peach. The pioneering unveiling of the red-flowered peach genome, coupled with the identification of the candidate gene, expanded the knowledge boundaries of the genetic basis of peach traits and provided valuable insights for future peach breeding efforts.
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Affiliation(s)
- Ping Zhou
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Research Centre for Engineering Technology of Fujian Deciduous Fruits, Fuzhou 350013, China
| | - Siru Lei
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaodan Zhang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yinghao Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Rui Guo
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Research Centre for Engineering Technology of Fujian Deciduous Fruits, Fuzhou 350013, China
| | - Shaobin Yan
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Research Centre for Engineering Technology of Fujian Deciduous Fruits, Fuzhou 350013, China
| | - Guang Jin
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Research Centre for Engineering Technology of Fujian Deciduous Fruits, Fuzhou 350013, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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9
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Yang Y, Zhao T, Wang F, Liu L, Liu B, Zhang K, Qin J, Yang C, Qiao Y. Identification of candidate genes for soybean seed coat-related traits using QTL mapping and GWAS. FRONTIERS IN PLANT SCIENCE 2023; 14:1190503. [PMID: 37384360 PMCID: PMC10293793 DOI: 10.3389/fpls.2023.1190503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/17/2023] [Indexed: 06/30/2023]
Abstract
Seed coat color is a typical morphological trait that can be used to reveal the evolution of soybean. The study of seed coat color-related traits in soybeans is of great significance for both evolutionary theory and breeding practices. In this study, 180 F10 recombinant inbred lines (RILs) derived from the cross between the yellow-seed coat cultivar Jidou12 (ZDD23040, JD12) and the wild black-seed coat accession Y9 (ZYD02739) were used as materials. Three methods, single-marker analysis (SMA), interval mapping (IM), and inclusive composite interval mapping (ICIM), were used to identify quantitative trait loci (QTLs) controlling seed coat color and seed hilum color. Simultaneously, two genome-wide association study (GWAS) models, the generalized linear model (GLM) and mixed linear model (MLM), were used to jointly identify seed coat color and seed hilum color QTLs in 250 natural populations. By integrating the results from QTL mapping and GWAS analysis, we identified two stable QTLs (qSCC02 and qSCC08) associated with seed coat color and one stable QTL (qSHC08) related to seed hilum color. By combining the results of linkage analysis and association analysis, two stable QTLs (qSCC02, qSCC08) for seed coat color and one stable QTL (qSHC08) for seed hilum color were identified. Upon further investigation using Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we validated the previous findings that two candidate genes (CHS3C and CHS4A) reside within the qSCC08 region and identified a new QTL, qSCC02. There were a total of 28 candidate genes in the interval, among which Glyma.02G024600, Glyma.02G024700, and Glyma.02G024800 were mapped to the glutathione metabolic pathway, which is related to the transport or accumulation of anthocyanin. We considered the three genes as potential candidate genes for soybean seed coat-related traits. The QTLs and candidate genes detected in this study provide a foundation for further understanding the genetic mechanisms underlying soybean seed coat color and seed hilum color and are of significant value in marker-assisted breeding.
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Affiliation(s)
- Yue Yang
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Tiantian Zhao
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Fengmin Wang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Luping Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Bingqiang Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jun Qin
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Yake Qiao
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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Sun P, Yang C, Zhu W, Wu J, Lin X, Wang Y, Zhu J, Chen C, Zhou K, Qian M, Shen J. Metabolome, Plant Hormone, and Transcriptome Analyses Reveal the Mechanism of Spatial Accumulation Pattern of Anthocyanins in Peach Flesh. Foods 2023; 12:2297. [PMID: 37372513 DOI: 10.3390/foods12122297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Anthocyanins are important secondary metabolites in fruits, and anthocyanin accumulation in the flesh of peach exhibits a spatial pattern, but the relevant mechanism is still unknown. In this study, the yellow-fleshed peach, cv. 'Jinxiu', with anthocyanin accumulation in the mesocarp around the stone was used as the experimental material. Red flesh (RF) and yellow flesh (YF) were sampled separately for flavonoid metabolite (mainly anthocyanins), plant hormone, and transcriptome analyses. The results showed that the red coloration in the mesocarp was due to the accumulation of cyanidin-3-O-glucoside, with an up-regulation of anthocyanin biosynthetic genes (F3H, F3'H, DFR, and ANS), transportation gene GST, and regulatory genes (MYB10.1 and bHLH3). Eleven ERFs, nine WRKYs, and eight NACs were also defined as the candidate regulators of anthocyanin biosynthesis in peach via RNA-seq. Auxin, cytokinin, abscisic acid (ABA), salicylic acid (SA), and 1-aminocyclopropane-1-carboxylic acid (ACC, ethylene precursor) were enriched in the peach flesh, with auxin, cytokinin, ACC, and SA being highly accumulated in the RF, but ABA was mainly distributed in the YF. The activators and repressors in the auxin and cytokinin signaling transduction pathways were mostly up-regulated and down-regulated, respectively. Our results provide new insights into the regulation of spatial accumulation pattern of anthocyanins in peach flesh.
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Affiliation(s)
- Ping Sun
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua 321000, China
| | - Chengkun Yang
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory of Quality Regulation of Tropical Horticultural Crop in Hainan Province, Department of Horticulture, School of Horticulture, Haidian Campus, Hainan University, Haikou 570228, China
| | - Wencan Zhu
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory of Quality Regulation of Tropical Horticultural Crop in Hainan Province, Department of Horticulture, School of Horticulture, Haidian Campus, Hainan University, Haikou 570228, China
| | - Jiaqi Wu
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua 321000, China
| | - Xianrui Lin
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua 321000, China
| | - Yi Wang
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua 321000, China
| | - Jianxi Zhu
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua 321000, China
| | - Chenfei Chen
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua 321000, China
| | - Kaibing Zhou
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory of Quality Regulation of Tropical Horticultural Crop in Hainan Province, Department of Horticulture, School of Horticulture, Haidian Campus, Hainan University, Haikou 570228, China
| | - Minjie Qian
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory of Quality Regulation of Tropical Horticultural Crop in Hainan Province, Department of Horticulture, School of Horticulture, Haidian Campus, Hainan University, Haikou 570228, China
| | - Jiansheng Shen
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua 321000, China
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11
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Zhao L, Zhang Y, Sun J, Yang Q, Cai Y, Zhao C, Wang F, He H, Han Y. PpHY5 is involved in anthocyanin coloration in the peach flesh surrounding the stone. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:951-964. [PMID: 36919360 DOI: 10.1111/tpj.16189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 05/27/2023]
Abstract
Red coloration around the stone (Cs) is an important trait of canned peaches (Prunus persica). In this study, an elongated hypocotyl 5 gene in peach termed PpHY5 was identified to participate in the regulation of the Cs trait. The E3 ubiquitin ligase PpCOP1 was expressed in the flesh around the stone and could interact with PpHY5. Although HY5 is known to be degraded by COP1 in darkness, the PpHY5 gene was activated in the flesh tissue surrounding the stone at the ripening stages and its expression was consistent with anthocyanin accumulation. PpHY5 was able to promote the transcription of PpMYB10.1 through interacting with its partner PpBBX10. Silencing of PpHY5 in the flesh around the stone caused a reduction in anthocyanin pigmentation, while transient overexpression of PpHY5 and PpBBX10 resulted in anthocyanin accumulation in peach fruits. Moreover, transgenic Arabidopsis seedlings overexpressing PpHY5 showed increased anthocyanin accumulation in leaves. Our results improve our understanding of the mechanisms of anthocyanin coloration in plants.
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Affiliation(s)
- Lei Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, Botanical Garden, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yuanqiang Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, Botanical Garden, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Juanli Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, Botanical Garden, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Qiurui Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, Botanical Garden, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Yaming Cai
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, Botanical Garden, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Caiping Zhao
- College of horticulture, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Furong Wang
- Institute of Fruit Tree and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430209, China
| | - Huaping He
- Institute of Fruit Tree and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430209, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, Botanical Garden, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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12
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Li F, Xu S, Xiao Z, Wang J, Mei Y, Hu H, Li J, Liu J, Hou Z, Zhao J, Yang S, Wang J. Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa. HORTICULTURE RESEARCH 2023; 10:uhad005. [PMID: 36938565 PMCID: PMC10022486 DOI: 10.1093/hr/uhad005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/08/2021] [Indexed: 06/18/2023]
Abstract
Rhodomyrtus tomentosa is an important fleshy-fruited tree and a well-known medicinal plant of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world. However, studies on the evolution and genomic breeding of R. tomentosa were hindered by the lack of a reference genome. Here, we presented a chromosome-level gap-free T2T genome assembly of R. tomentosa using PacBio and ONT long read sequencing. We assembled the genome with size of 470.35 Mb and contig N50 of ~43.80 Mb with 11 pseudochromosomes. A total of 33 382 genes and 239.31 Mb of repetitive sequences were annotated in this genome. Phylogenetic analysis elucidated the independent evolution of R. tomentosa starting from 14.37MYA and shared a recent WGD event with other Myrtaceae species. We identified four major compounds of anthocyanins and their synthetic pathways in R. tomentosa. Comparative genomic and gene expression analysis suggested the coloring and high anthocyanin accumulation in R. tomentosa tends to be determined by the activation of anthocyanin synthesis pathway. The positive selection and up-regulation of MYB transcription factors were the implicit factors in this process. The copy number increase of downstream anthocyanin transport-related OMT and GST gene were also detected in R. tomentosa. Expression analysis and pathway identification enriched the importance of starch degradation, response to stimuli, effect of hormones, and cell wall metabolism during the fleshy fruit development in Myrtaceae. Our genome assembly provided a foundation for investigating the origins and differentiation of Myrtaceae species and accelerated the genetic improvement of R. tomentosa.
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Affiliation(s)
| | | | | | - Jingming Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Yu Mei
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China
| | - Haifei Hu
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jingyu Li
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China
| | - Jieying Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Zhuangwei Hou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Junliang Zhao
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shaohai Yang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China
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13
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Differentially expression analyses in fruit of cultivated and wild species of grape and peach. Sci Rep 2023; 13:1997. [PMID: 36737657 PMCID: PMC9898514 DOI: 10.1038/s41598-023-29025-w] [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: 06/07/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Through agronomic traits and sequencing data, the cultivated and wild varieties of grapes and peaches were analyzed and compared in terms of fruit size, fruit flavor, fruit resistance, and fruit color. Cultivated grapes and peaches have advantages in fruit size, soluble sugar content, sugar and acid ratio, etc. Wild grapes and peaches have utility value in resistance. The results showed that there were 878 and 301 differentially expressed genes in cultivated and wild grapes and peaches in the three growth stages, respectively based on the next-generation sequencing study. Ten and twelve genes related to the differences between cultivated and wild grapes and peaches were found respectively. Among them, three genes, namely chalcone synthase (CHS), glutathione S-transferase (GST) and malate dehydrogenase (MDH1) were present in both cultivated and wild grapes and peaches.
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14
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Zhu L, Wang Y, Zhang Z, Hu D, Wang Z, Hu J, Ma C, Yang L, Sun S, Li Y. Chromosomal fragment deletion in APRR2-repeated locus modulates the dark stem color in Cucurbita pepo. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4277-4288. [PMID: 36098750 DOI: 10.1007/s00122-022-04217-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Cp4.1LG15g03420 (CpDsc-1), which encodes a two-component response regulator-like protein (APRR2) in the nucleus, influences dark green stem formation in Cucurbita pepo by regulating the chlorophyll content. Stem color is an important agronomic trait in zucchini (Cucurbita pepo) for robust seeding and high yield. However, the gene controlling the stem color has not been characterized. In this study, we identified a single locus accounting for the dark green stem color of C. pepo (CpDsc-1). Genetic analysis of this trait in segregated populations derived from two parental lines (line 296 with dark green stems and line 274 with light green stems) revealed that stem color was controlled by a single dominant gene (dark green vs. light green). In bulked segregant analysis, CpDsc-1 was mapped to a 2.09-Mb interval on chromosome 15. This region was further narrowed to 65.2 kb using linkage analysis of the F2 population. Sequencing analysis revealed a 14 kb deletion between Cp4.1LG15g03420 and Cp4.1LG15g03360; these two genes both encoded a two-component response regulator-like protein (APRR2). The incomplete structures of the two APRR2 genes and abnormal chloroplasts in line 274 might be the main cause of the light green phenotype. Gene expression pattern analysis showed that only Cp4.1LG15g03420 was upregulated in line 296. Subcellular localization analysis indicated that Cp4.1LG15g03420 was a nuclear gene. Furthermore, a co-dominant marker, G4563 (93% accuracy rate), and a co-segregation marker, Fra3, were established in 111 diverse germplasms; both of these markers were tightly linked with the color trait. This study provided insights into chlorophyll regulation mechanisms and revealed the markers valuable for marker-assisted selection in future zucchini breeding.
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Affiliation(s)
- Lei Zhu
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Yong Wang
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China
| | - Zhenli Zhang
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Deju Hu
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Zanlin Wang
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Jianbin Hu
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Changsheng Ma
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Luming Yang
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Shouru Sun
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China.
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China.
| | - Yanman Li
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China.
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15
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Qiu K, Pan H, Sheng Y, Wang Y, Shi P, Xie Q, Zhang J, Zhou H. The Peach ( Prunus persica) CBL and CIPK Family Genes: Protein Interaction Profiling and Expression Analysis in Response to Various Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:3001. [PMID: 36365452 PMCID: PMC9653928 DOI: 10.3390/plants11213001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/01/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The plant calcineurin B-like protein-CBL interacting protein kinase (CBL-CIPK) signaling pathway is a Ca2+-related signaling pathway that responds strongly to both biological and abiotic environmental stimuli. This study identified eight CBL and eighteen CIPK genes from peach for the first time. Their basic properties and gene structure were analyzed, and the CBL and CIPK members from Arabidopsis and apple were combined to study their evolutionary relationships. Using RT-qPCR and RNA-seq data, we detected the expression patterns of PprCBLs and PprCIPKs in different tissues and fruit development stages of peach. Among them, the expression levels of PprCBL1 and PprCIPK18 were stable in various tissues and stages. The expression patterns of other members showed specificity between cultivars and developmental stages. By treating shoots with drought and salt stress simulated using PEG6000 and NaCl, it was found that PprCIPK3, PprCIPK6, PprCIPK15 and PprCIPK16 were strongly responsive to salt stress, and PprCIPK3, PprCIPK4, PprCIPK10, PprCIPK14, PprCIPK15, PprCIPK16 and PprCIPK18 were sensitive to drought stress. Three genes, PprCIPK3, PprCIPK15 and PprCIPK16, were sensitive to both salt and drought stress. We cloned four PprCBL and several PprCIPK genes and detected their interaction by yeast two-hybrid assay (Y2H). The results of Y2H show not only the evolutionary conservation of the interaction network of CBL-CIPK but also the specificity among different species. In conclusion, CBL and CIPK genes are important in peach and play an important role in the response to various abiotic stresses.
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Affiliation(s)
- Keli Qiu
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Haifa Pan
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Yu Sheng
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Yunyun Wang
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Pei Shi
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Qingmei Xie
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Jinyun Zhang
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Hui Zhou
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
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Prudencio AS, Devin SR, Mahdavi SME, Martínez-García PJ, Salazar JA, Martínez-Gómez P. Spontaneous, Artificial, and Genome Editing-Mediated Mutations in Prunus. Int J Mol Sci 2022; 23:ijms232113273. [PMID: 36362061 PMCID: PMC9653787 DOI: 10.3390/ijms232113273] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Mutation is a source of genetic diversity widely used in breeding programs for the acquisition of agronomically interesting characters in commercial varieties of the Prunus species, as well as in the rest of crop species. Mutation can occur in nature at a very low frequency or can be induced artificially. Spontaneous or bud sport mutations in somatic cells can be vegetatively propagated to get an individual with the mutant phenotype. Unlike animals, plants have unlimited growth and totipotent cells that let somatic mutations to be transmitted to the progeny. On the other hand, in vitro tissue culture makes it possible to induce mutation in plant material and perform large screenings for mutant’s selection and cleaning of chimeras. Finally, targeted mutagenesis has been boosted by the application of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 and Transcription activator-like effector nuclease (TALEN) editing technologies. Over the last few decades, environmental stressors such as global warming have been threatening the supply of global demand for food based on population growth in the near future. For this purpose, the release of new varieties adapted to such changes is a requisite, and selected or generated Prunus mutants by properly regulated mechanisms could be helpful to this task. In this work, we reviewed the most relevant mutations for breeding traits in Prunus species such as flowering time, self-compatibility, fruit quality, and disease tolerance, including new molecular perspectives in the present postgenomic era including CRISPR/Cas9 and TALEN editing technologies.
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Affiliation(s)
- Angel S. Prudencio
- Department of Plant Breeding, Centro de Edafología y Biología Apliacada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Espinardo, Spain
| | - Sama Rahimi Devin
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran
| | | | - Pedro J. Martínez-García
- Department of Plant Breeding, Centro de Edafología y Biología Apliacada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Espinardo, Spain
| | - Juan A. Salazar
- Department of Plant Breeding, Centro de Edafología y Biología Apliacada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Espinardo, Spain
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, Centro de Edafología y Biología Apliacada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Espinardo, Spain
- Correspondence: ; Tel.: +34-968-396-200
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Anthocyanin Biosynthesis Associated with Natural Variation in Autumn Leaf Coloration in Quercus aliena Accessions. Int J Mol Sci 2022; 23:ijms232012179. [DOI: 10.3390/ijms232012179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/29/2022] [Accepted: 10/09/2022] [Indexed: 11/17/2022] Open
Abstract
Quercus aliena is an economically important tree species and one of the dominant native oak species in China. Although its leaves typically turn yellow in autumn, we observed natural variants with red leaves. It is important to understand the mechanisms involved in leaf color variation in this species. Therefore, we compared a Q. aliena tree with yellow leaves and three variants with red leaves at different stages of senescence in order to determine the causes of natural variation. We found that the accumulation of anthocyanins such as cyanidin 3-O-glucoside and cyanidin 3-O-sambubiglycoside had a significant effect on leaf coloration. Gene expression analysis showed upregulation of almost all genes encoding enzymes involved in anthocyanin synthesis in the red-leaved variants during the early and main discoloration stages of senescence. These findings are consistent with the accumulation of anthocyanin in red variants. Furthermore, the variants showed significantly higher expression of transcription factors associated with anthocyanin synthesis, such as those encoded by genes QaMYB1 and QaMYB3. Our findings provide new insights into the physiological and molecular mechanisms involved in autumn leaf coloration in Q. aliena, as well as provide genetic resources for further development and cultivation of valuable ornamental variants of this species.
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Zhao L, Sun J, Cai Y, Yang Q, Zhang Y, Ogutu CO, Liu J, Zhao Y, Wang F, He H, Zheng B, Han Y. PpHYH is responsible for light-induced anthocyanin accumulation in fruit peel of Prunus persica. TREE PHYSIOLOGY 2022; 42:1662-1677. [PMID: 35220436 PMCID: PMC9366866 DOI: 10.1093/treephys/tpac025] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/18/2022] [Indexed: 05/29/2023]
Abstract
Peach Prunus persica is an economically important fruit tree crop worldwide. Although the external color of fruit is an important aspect of fruit quality, the mechanisms underlying its formation remain elusive in peach. Here, we report an elongated hypocotyl 5-homolog gene PpHYH involved in the regulation of anthocyanin pigmentation in peach fruit peel. Anthocyanin accumulation in fruit peel is light-dependent in peach. PpHYH had no auto-activation activity and its transcription was induced by sunlight. PpHYH activated transcription of a cluster of three PpMYB10 genes in the present of a cofactor PpBBX4 encoding a B-BOX protein, leading to anthocyanin accumulation in the sun-exposed peel. However, the PpHYH activity was repressed by a negative regulator of PpCOP1 encoding constitutive photomorphogenesis protein 1 which accumulated in the nucleus under dark condition, resulting in failure of anthocyanin accumulation in the shaded peel. PpCOP1 was re-localized into the cytosol under light condition, in accordance with fruit peel pigmentation. Additionally, transport of anthocyanins from the cytoplasm to the vacuole was a rate-limiting step for anthocyanin accumulation in peach fruit peel. Our results reveal for the first time the HYH gene involved in the regulation of anthocyanin accumulation in fruits, and provide target genes for genetic manipulation of fruit coloration.
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Affiliation(s)
- Lei Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Juanli Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Yaming Cai
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Qiurui Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Yuanqiang Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Collins Otieno Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
| | - Jingjing Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Yun Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Furong Wang
- Institute of Fruit Tree and Tea, Academy of Agricultural Science, Wuhan, Hubei 430209, China
| | - Huaping He
- Institute of Fruit Tree and Tea, Academy of Agricultural Science, Wuhan, Hubei 430209, China
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Genome-Wide Identification of Glutathione S-Transferase and Expression Analysis in Response to Anthocyanin Transport in the Flesh of the New Teinturier Grape Germplasm ‘Zhongshan-HongYu’. Int J Mol Sci 2022; 23:ijms23147717. [PMID: 35887065 PMCID: PMC9317864 DOI: 10.3390/ijms23147717] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 11/17/2022] Open
Abstract
Anthocyanins are synthesized in the endoplasmic reticulum and then transported to the vacuole in plants. Glutathione S-transferases (GSTs) are thought to play a key role in anthocyanin transport. To clarify the mechanism of GST genes in the accumulation and transport of anthocyanin in the early fruit stage, we analyzed and characterized the GST family in the flesh of ‘Zhongshan-HongYu’ (ZS-HY) based on the transcriptome. In this study, the 92 GST genes identified through a comprehensive bioinformatics analysis were unevenly present in all chromosomes of grapes, except chromosomes 3, 9 and 10. Through the analysis of the chromosomal location, gene structure, conserved domains, phylogenetic relationships and cis-acting elements of GST family genes, the phylogenetic tree divided the GST genes into 9 subfamilies. Eighteen GST genes were screened and identified from grape berries via a transcriptome sequencing analysis, of which 4 belonged to the phi subfamily and 14 to the tau subfamily, and the expression levels of these GST genes were not tissue-specific. The phylogenetic analysis indicated that VvGST4 was closely related to PhAN9 and AtTT19. This study provides a foundation for the analysis of the GST gene family and insight into the roles of GSTs in grape anthocyanin transport.
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Wang R, Lu N, Liu C, Dixon RA, Wu Q, Mao Y, Yang Y, Zheng X, He L, Zhao B, Zhang F, Yang S, Chen H, Jun JH, Li Y, Liu C, Liu Y, Chen J. MtGSTF7, a TT19-like GST gene, is essential for accumulation of anthocyanins, but not proanthocyanins in Medicago truncatula. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4129-4146. [PMID: 35294003 PMCID: PMC9232208 DOI: 10.1093/jxb/erac112] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/12/2022] [Indexed: 05/20/2023]
Abstract
Anthocyanins and proanthocyanins (PAs) are two end products of the flavonoid biosynthesis pathway. They are believed to be synthesized in the endoplasmic reticulum and then sequestered into the vacuole. In Arabidopsis thaliana, TRANSPARENT TESTA 19 (TT19) is necessary for both anthocyanin and PA accumulation. Here, we found that MtGSTF7, a homolog of AtTT19, is essential for anthocyanin accumulation but not required for PA accumulation in Medicago truncatula. MtGSTF7 was induced by the anthocyanin regulator LEGUME ANTHOCYANIN PRODUCTION 1 (LAP1), and its tissue expression pattern correlated with anthocyanin deposition in M. truncatula. Tnt1-insertional mutants of MtGSTF7 lost anthocyanin accumulation in vegetative organs, and introducing a genomic fragment of MtGSTF7 could complement the mutant phenotypes. Additionally, the accumulation of anthocyanins induced by LAP1 was significantly reduced in mtgstf7 mutants. Yeast-one-hybridization and dual-luciferase reporter assays revealed that LAP1 could bind to the MtGSTF7 promoter to activate its expression. Ectopic expression of MtGSTF7 in tt19 mutants could rescue their anthocyanin deficiency, but not their PA defect. Furthermore, PA accumulation was not affected in the mtgstf7 mutants. Taken together, our results show that the mechanism of anthocyanin and PA accumulation in M. truncatula is different from that in A. thaliana, and provide a new target gene for engineering anthocyanins in plants.
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Affiliation(s)
| | | | - Chenggang Liu
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Qing Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yating Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaoling Zheng
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Baolin Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Fan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Shengchao Yang
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Haitao Chen
- Sanjie Institute of Forage, Yangling, Shaanxi 712100, China
| | - Ji Hyung Jun
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Ying Li
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yu Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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Wong DCJ, Perkins J, Peakall R. Anthocyanin and Flavonol Glycoside Metabolic Pathways Underpin Floral Color Mimicry and Contrast in a Sexually Deceptive Orchid. FRONTIERS IN PLANT SCIENCE 2022; 13:860997. [PMID: 35401591 PMCID: PMC8983864 DOI: 10.3389/fpls.2022.860997] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/17/2022] [Indexed: 06/10/2023]
Abstract
Sexually deceptive plants secure pollination by luring specific male insects as pollinators using a combination of olfactory, visual, and morphological mimicry. Flower color is a key component to this attraction, but its chemical and genetic basis remains poorly understood. Chiloglottis trapeziformis is a sexually deceptive orchid which has predominantly dull green-red flowers except for the central black callus projecting from the labellum lamina. The callus mimics the female of the pollinator and the stark color contrast between the black callus and dull green or red lamina is thought to enhance the visibility of the mimic. The goal of this study was to investigate the chemical composition and genetic regulation of temporal and spatial color patterns leading to visual mimicry, by integrating targeted metabolite profiling and transcriptomic analysis. Even at the very young bud stage, high levels of anthocyanins were detected in the dark callus, with peak accumulation by the mature bud stage. In contrast, anthocyanin levels in the lamina peaked as the buds opened and became reddish-green. Coordinated upregulation of multiple genes, including dihydroflavonol reductase and leucoanthocyanidin dioxygenase, and the downregulation of flavonol synthase genes (FLS) in the callus at the very young bud stage underpins the initial high anthocyanin levels. Conversely, within the lamina, upregulated FLS genes promote flavonol glycoside over anthocyanin production, with the downstream upregulation of flavonoid O-methyltransferase genes further contributing to the accumulation of methylated flavonol glycosides, whose levels peaked in the mature bud stage. Finally, the peak anthocyanin content of the reddish-green lamina of the open flower is underpinned by small increases in gene expression levels and/or differential upregulation in the lamina in select anthocyanin genes while FLS patterns showed little change. Differential expression of candidate genes involved in specific transport, vacuolar acidification, and photosynthetic pathways may also assist in maintaining the distinct callus and contrasting lamina color from the earliest bud stage through to the mature flower. Our findings highlight that flower color in this sexually deceptive orchid is achieved by complex tissue-specific coordinated regulation of genes and biochemical pathways across multiple developmental stages.
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22
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Sheng Y, Yu H, Pan H, Qiu K, Xie Q, Chen H, Fu S, Zhang J, Zhou H. Genome-Wide Analysis of the Gene Structure, Expression and Protein Interactions of the Peach ( Prunus persica) TIFY Gene Family. FRONTIERS IN PLANT SCIENCE 2022; 13:792802. [PMID: 35251076 PMCID: PMC8891376 DOI: 10.3389/fpls.2022.792802] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
The TIFY family is a plant-specific gene family involved in regulating many plant processes, such as development and growth, defense and stress responses, fertility and reproduction, and the biosynthesis of secondary metabolites. The v2.0 peach (Prunus persica) genome, which has an improved chromosome-scale assembly and contiguity, has recently been released, but a genome-wide investigation of the peach TIFY family is lacking. In this study, 16 TIFY family genes from the peach genome were identified according to the peach reference genome sequence information and further validated by cloning sequencing. The synteny, phylogenetics, location, structure, and conserved domains and motifs of these genes were analyzed, and finally, the peach TIFY family was characterized into 9 JAZ, 1 TIFY, 1 PPD and 5 ZML subfamily members. Expression profiles of peach JAZ, PPD, and ZML genes in various organs and fruit developmental stages were analyzed, and they showed limited effects with fruit ripening cues. Four TIFY members were significantly affected at the mRNA level by exogenous treatment with MeJA in the peach epicarp, and among them, PpJAZ1, PpJAZ4 and PpJAZ5 were significantly correlated with fruit epicarp pigmentation. In addition, the TIFY family member protein interaction networks established by the yeast two-hybrid (Y2H) assay not only showed similar JAZ-MYC2 and JAZ homo- and heterodimer patterns as those found in Arabidopsis but also extended the JAZ dimer network to ZML-ZML and JAZ-ZML interactions. The PpJAZ3-PpZML4 interaction found in this study suggests the potential formation of the ZML-JAZ-MYC complex in the JA-signaling pathway, which may extend our knowledge of this gene family's functions in diverse biological processes.
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Affiliation(s)
- Yu Sheng
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Hong Yu
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Haifa Pan
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Keli Qiu
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qingmei Xie
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Hongli Chen
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Songling Fu
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Jinyun Zhang
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Hui Zhou
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
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