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Denoyes B, Prohaska A, Petit J, Rothan C. Deciphering the genetic architecture of fruit color in strawberry. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6306-6320. [PMID: 37386925 PMCID: PMC10627153 DOI: 10.1093/jxb/erad245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/28/2023] [Indexed: 07/01/2023]
Abstract
Fruits of Fragaria species usually have an appealing bright red color due to the accumulation of anthocyanins, water-soluble flavonoid pigments. Octoploid cultivated strawberry (Fragaria × ananassa) is a major horticultural crop for which fruit color and associated nutritional value are main breeding targets. Great diversity in fruit color intensity and pattern is observed not only in cultivated strawberry but also in wild relatives such as its octoploid progenitor F. chiloensis or the diploid woodland strawberry F. vesca, a model for fruit species in the Rosaceae. This review examines our understanding of fruit color formation in strawberry and how ongoing developments will advance it. Natural variations of fruit color as well as color changes during fruit development or in response to several cues have been used to explore the anthocyanin biosynthetic pathway and its regulation. So far, the successful identification of causal genetic variants has been largely driven by the availability of high-throughput genotyping tools and high-quality reference genomes of F. vesca and F. × ananassa. The current completion of haplotype-resolved genomes of F. × ananassa combined with QTL mapping will accelerate the exploitation of the untapped genetic diversity of fruit color and help translate the findings into strawberry improvement.
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Affiliation(s)
- Béatrice Denoyes
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Alexandre Prohaska
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
- INVENIO, MIN de Brienne, Bordeaux, France
| | - Johann Petit
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Christophe Rothan
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
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Liu Z, Ma Y, Lv X, Li N, Li X, Xing J, Li C, Hu B. Abiotic factors and endophytes co-regulate flavone and terpenoid glycoside metabolism in Glycyrrhiza uralensis. Appl Microbiol Biotechnol 2023; 107:2671-2688. [PMID: 36864204 PMCID: PMC10033487 DOI: 10.1007/s00253-023-12441-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023]
Abstract
Recently, endorhizospheric microbiota is realized to be able to promote the secondary metabolism in medicinal plants, but the detailed metabolic regulation metabolisms and whether the promotion is influenced by environmental factors are unclear yet. Here, the major flavonoids and endophytic bacterial communities in various Glycyrrhiza uralensis Fisch. roots collected from seven distinct places in northwest China, as well as the edaphic conditions, were characterized and analyzed. It was found that the soil moisture and temperature might modulate the secondary metabolism in G. uralensis roots partially through some endophytes. One rationally isolated endophyte Rhizobium rhizolycopersici GUH21 was proved to promote the accumulation of isoliquiritin and glycyrrhizic acid significantly in roots of the potted G. uralensis under the relatively high-level watering and low temperature. Furthermore, we did the comparative transcriptome analysis of G. uralensis seedling roots in different treatments to investigate the detailed mechanisms of the environment-endophyte-plant interactions and found that the low temperature went hand in hand with the high-level watering to activate the aglycone biosynthesis in G. uralensis, while GUH21 and the high-level watering cooperatively promoted the in planta glucosyl unit production. Our study is of significance for the development of methods to rationally promote the medicinal plant quality. KEY POINTS: • Soil temperature and moisture related to isoliquiritin contents in Glycyrrhiza uralensis Fisch. • Soil temperature and moisture related to the hosts' endophytic bacterial community structures. • The causal relation among abiotic factors-endophytes-host was proved through the pot experiment.
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Affiliation(s)
- Zidi Liu
- Institute of Biochemical Engineering, College of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102401, People's Republic of China
| | - Yunyang Ma
- Institute of Biochemical Engineering, College of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102401, People's Republic of China
| | - Xuelian Lv
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, People's Republic of China
| | - Nannan Li
- Institute of Biochemical Engineering, College of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102401, People's Republic of China
| | - Xiaohan Li
- Institute of Biochemical Engineering, College of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102401, People's Republic of China
| | - Jianmin Xing
- CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
| | - Chun Li
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China.
| | - Bing Hu
- Institute of Biochemical Engineering, College of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102401, People's Republic of China.
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology of China, Beijing, 102401, People's Republic of China.
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Yuan H, Cai W, Chen X, Pang F, Wang J, Zhao M. Heterozygous frameshift mutation in FaMYB10 is responsible for the natural formation of red and white-fleshed strawberry ( Fragaria x ananassa Duch). FRONTIERS IN PLANT SCIENCE 2022; 13:1027567. [PMID: 36388497 PMCID: PMC9644031 DOI: 10.3389/fpls.2022.1027567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
During natural evolution and artificial selection, the fruit color of many species has been repeatedly gained or lost and is generally associated with mutations in genes encoding R2R3-MYB transcription factors, especially MYB10. In this study, we show that a heterozygous frameshift mutation (FaMYB10AG-insert/FaMYB10wild ) is responsible for the loss of anthocyanins in the flesh of cultivated strawberry. Comparative transcriptomic and metabolomic analyses of red- and white-fleshed strawberry indicated that the low expression level of FaUFGT (flavonol-O-glucosyltransferases) was responsible for the loss of anthocyanins and accumulation of proanthocyanidin in the white-fleshed strawberry and was the crucial gene that encodes enzymes of the anthocyanin biosynthesis pathway. Accordingly, overexpression and silencing of FaUFGT altered anthocyanin content and changed the flesh color of strawberry fruits. Furthermore, whole-genome resequencing analyses identified an AG insertion in the FaMYB10 coding region (FaMYB10AG-insert ) of white-fleshed strawberry. Y1H and EMSA assays showed that FaMYB10wild was able to bind to the promoter of the FaUFGT gene, while the FaMYB10AG-insert could not. The skin and flesh color were tightly linked to the number of fully functional FaMYB10 copies in the selfing progeny of white-fleshed strawberry. Our results suggested that heterozygous frameshift mutation of FaMYB10 resulted in the loss of the ability to activate the expression of the FaUFGT gene, was responsible for the natural formation of red and white-fleshed strawberry.
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Cheng Z, Li R, Jiang Z, Tang Y, Li W, Shao Y. Combined effect of Bacillus siamensis and chlorogenic acid on maintenance of quality, control of disease in stored wax apple fruit. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Objectives
The purpose of this study was to evaluate the effect of combined postharvest use of Bacillus siamensis strain and chlorogenic acid on quality mainteance and disease control in wax apple fruit.
Materials and Methods
Wax apple fruit were treated with Bacillus siamensis strain (N1), chlorogenic acid (CHA) and N1+CHA and preserved at 25℃for 12 days. The appearance and quality parameters were evaluated, along with the disease index (DI), content of total soluble solids (TSS), total acid (TA), vitamin C (Vc), total phenolic, and flavonoids during cold storage. Meanwhile, the activities of β-1,3-glucanase (GLU) , phenylalanine ammonialyase (PAL), polyphenol oxidase (PPO), and peroxidase (POD) were determined. Furthermore, the transcriptome and the expression level of key defense enzyme genes were analyzed by RNA-seq and real-time quantitative reverse transcription PCR (qRT-PCR).
Results
N1+CHA treatment significantly lowered DI and delayed fruit quality deterioration by slowing TSS and TA loss and enhancing antioxidant capacity, including Vc, total phenolic, and flavonoids content. Meanwhile, the activities of GLU, PAL, PPO and POD were dramatically increased by N1+CHA treatment. Additionally, N1+CHA treatment modulated several metabolic pathways, including those involved in plant-hormone signal transduction and plant-pathogen interaction. The expression level of key defense enzyme genes were significantly up-regulated in stored wax apple fruit by the N1+CHA treatment, which were well coincided with the transcriptome data.
Conclusion
The combined use of N1+CHA significantly prevent disease and maintain fruit quality of wax apple during storage. These findings indicate that it could serve as a promising biological technique for preserving wax apple fruit.
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PpMYB39 Activates PpDFR to Modulate Anthocyanin Biosynthesis during Peach Fruit Maturation. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Anthocyanins are a class of water-soluble flavonoids widely present in fruits and vegetablesresponsible for the red flesh formation of peach fruit. Previously, several genes of the MYB family have been reported as transcriptional regulators of the anthocyanin biosynthetic pathway of structural genes in plants. In this study, through comparative transcriptome analysis of the white and red flesh peach cultivars of Harrow Blood and Asama Hakuto, a predicted transcription factor of the R2R3MYB family, PpMYB39, was identified to be associated with anthocyanin biosynthesis in peach fruit. In red-fleshed peach cultivars, the maximum amount of anthocyanin accumulated 95 days after full bloom (DAFB), at full maturity near ripening. Our results showed that, at this stage, PpMYB39 had the highest expression level among the 13 differentially expressed genes (DEGs) found in both red- and white-fleshed fruits, as well as a high correlation with total anthocyanin content throughout fruit development. Moreover, the expression analysis of the structural genes of the anthocyanin biosynthetic pathway in peach fruit revealed that Prunus persica Dihydroflavonol-4-reductase (PpDFR) was co-expressed and up-regulated with PpMYB39 at 95 DAFB, suggesting its possible role as a transcriptional activator of MYB39. This was further confirmed by a yeast one-hybrid assay and a dual luciferase reporter assay. Our results will be helpful in the breeding of peach cultivars and the identification and significance of color in peaches and related fruit species, in addition to providing an understanding of color formation in peach fruit for future research.
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High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids. Sci Rep 2022; 12:3346. [PMID: 35228611 PMCID: PMC8885740 DOI: 10.1038/s41598-022-07318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/11/2022] [Indexed: 11/26/2022] Open
Abstract
Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.
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Gao X, Wang L, Zhang H, Zhu B, Lv G, Xiao J. Transcriptome analysis and identification of genes associated with floral transition and fruit development in rabbiteye blueberry (Vaccinium ashei). PLoS One 2021; 16:e0259119. [PMID: 34710165 PMCID: PMC8553168 DOI: 10.1371/journal.pone.0259119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Flowering and fruit set are important traits affecting fruit quality and yield in rabbiteye blueberry (Vaccinium ashei). Intense efforts have been made to elucidate the influence of vernalization and phytohormones on flowering, but the molecular mechanisms of flowering and fruit set remain unclear. To unravel these mechanisms, we performed transcriptome analysis to explore blueberry transcripts from flowering to early fruit stage. We divided flowering and fruit set into flower bud (S2), initial flower (S3), bloom flower (S4), pad fruit (S5), and cup fruit (S6) based on phenotype and identified 1,344, 69, 658, and 189 unique differentially expressed genes (DEGs) in comparisons of S3/S2, S4/S3, S5/S4, and S6/S5, respectively. There were obviously more DEGs in S3/S2 and S5/S4 than in S4/S3, and S6/S5, suggesting that S3/S2 and S5/S4 represent major transitions from buds to fruit in blueberry. GO and KEGG enrichment analysis indicated these DEGs were mostly enriched in phytohormone biosynthesis and signaling, transporter proteins, photosynthesis, anthocyanins biosynthesis, disease resistance protein and transcription factor categories, in addition, transcript levels of phytohormones and transporters changed greatly throughout the flowering and fruit set process. Gibberellic acid and jasmonic acid mainly acted on the early stage of flowering development like expression of the florigen gene FT, while the expression of auxin response factor genes increased almost throughout the process from bud to fruit development. Transporter proteins were mainly associated with minerals during the early flowering development stage and sugars during the early fruit stage. At the early fruit stage, anthocyanins started to accumulate, and the fruit was susceptible to diseases such as fungal infection. Expression of the transcription factor MYB86 was up-regulated during initial fruit development, which may promote anthocyanin accumulation. These results will aid future studies exploring the molecular mechanism underlying flowering and fruit set of rabbiteye blueberry.
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Affiliation(s)
- Xuan Gao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Lida Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Hong Zhang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
- Anhui Microanaly Gene Limited Liability Company, Hefei, Anhui, China
| | - Bo Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Guosheng Lv
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Jiaxin Xiao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
- * E-mail:
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Chen Z, Jiang J, Shu L, Li X, Huang J, Qian B, Wang X, Li X, Chen J, Xu H. Combined transcriptomic and metabolic analyses reveal potential mechanism for fruit development and quality control of Chinese raspberry (Rubus chingii Hu). PLANT CELL REPORTS 2021; 40:1923-1946. [PMID: 34333679 DOI: 10.1007/s00299-021-02758-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/15/2021] [Indexed: 05/09/2023]
Abstract
Combined transcriptomic and metabolic analyses reveal that fruit of Rubus chingii Hu launches biosynthesis of phenolic acids and flavonols at beginning of fruit set and then coordinately accumulated or converted to their derivatives. Rubus chingii Hu (Chinese raspberry) is an important dual functional food with nutraceutical and pharmaceutical values. Comprehensively understanding the mechanisms of fruit development and bioactive components synthesis and regulation could accelerate genetic analysis and molecular breeding for the unique species. Combined transcriptomic and metabolic analyses of R. chingii fruits from different developmental stages, including big green, green-to-yellow, yellow-to-orange, and red stages, were conducted. A total of 89,188 unigenes were generated and 57,545 unigenes (64.52%) were annotated. Differential expression genes (DEGs) and differentially accumulated metabolites (DAMs) were mainly involved in the biosynthesis of secondary metabolites. The fruit launched the biosynthesis of phenolic acids and flavonols at the very beginning of fruit set and then coordinately accumulated or converted to their derivatives. This was tightly regulated by expressions of the related genes and MYB and bHLH transcription factors. The core genes products participated in the biosynthesis of ellagic acid (EA) and kaempferol-3-O-rutinoside (K-3-R), such as DAHPS, DQD/SDH, PAL, 4CL, CHS, CHI, F3H, F3'H, FLS, and UGT78D2, and their corresponding metabolites were elaborately characterized. Our research reveals the molecular and chemical mechanisms of the fruit development of R. chingii. The results provide a solid foundation for the genetic analysis, functional genes isolation, fruit quality improvement and modifiable breeding of R. chingii.
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Affiliation(s)
- Zhen Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China.
| | - Jingyong Jiang
- Institute of Horticulture, Taizhou Academy of Agricultural Sciences, Linhai, 317000, People's Republic of China
| | - Liangzuo Shu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Xiaobai Li
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Jing Huang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Baoying Qian
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Xiaoyan Wang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Xin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Jiangxia Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Haidan Xu
- School of Pharmaceutical, Chemical and Materials Engineering, Taizhou University, Taizhou, 318000, People's Republic of China
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Ye JH, Lv YQ, Liu SR, Jin J, Wang YF, Wei CL, Zhao SQ. Effects of Light Intensity and Spectral Composition on the Transcriptome Profiles of Leaves in Shade Grown Tea Plants ( Camellia sinensis L.) and Regulatory Network of Flavonoid Biosynthesis. Molecules 2021; 26:molecules26195836. [PMID: 34641378 PMCID: PMC8510202 DOI: 10.3390/molecules26195836] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 01/18/2023] Open
Abstract
Black net shade treatment attenuates flavonoid biosynthesis in tea plants, while the effect of light quality is still unclear. We investigated the flavonoid and transcriptome profiles of tea leaves under different light conditions, using black nets with different shade percentages, blue, yellow and red nets to alter the light intensity and light spectral composition in the fields. Flavonol glycosides are more sensitive to light intensity than catechins, with a reduction percentage of total flavonol glycosides up to 79.6% compared with 38.7% of total catechins under shade treatment. A total of 29,292 unigenes were identified, and the KEGG result indicated that flavonoid biosynthesis was regulated by both light intensity and light spectral composition while phytohormone signal transduction was modulated under blue net shade treatment. PAL, CHS, and F3H were transcriptionally downregulated with light intensity. Co-expression analysis showed the expressions of key transcription factors MYB12, MYB86, C1, MYB4, KTN80.4, and light signal perception and signaling genes (UVR8, HY5) had correlations with the contents of certain flavonoids (p < 0.05). The level of abscisic acid in tea leaves was elevated under shade treatment, with a negative correlation with TFG content (p < 0.05). This work provides a potential route of changing light intensity and spectral composition in the field to alter the compositions of flavor substances in tea leaves and regulate plant growth, which is instructive to the production of summer/autumn tea and matcha.
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Affiliation(s)
- Jian-Hui Ye
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China; (J.-H.Y.); (Y.-Q.L.); (Y.-F.W.)
| | - Yi-Qing Lv
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China; (J.-H.Y.); (Y.-Q.L.); (Y.-F.W.)
| | - Sheng-Rui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, China;
| | - Jing Jin
- Zhejiang Agricultural Technical Extension Center, 29 Fengqidong Road, Hangzhou 310000, China;
| | - Yue-Fei Wang
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China; (J.-H.Y.); (Y.-Q.L.); (Y.-F.W.)
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, China;
- Correspondence: (C.-L.W.); (S.-Q.Z.)
| | - Shi-Qi Zhao
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China; (J.-H.Y.); (Y.-Q.L.); (Y.-F.W.)
- Correspondence: (C.-L.W.); (S.-Q.Z.)
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Developmental transcriptome profiling uncovered carbon signaling genes associated with almond fruit drop. Sci Rep 2021; 11:3401. [PMID: 33564060 PMCID: PMC7873282 DOI: 10.1038/s41598-020-69395-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/29/2020] [Indexed: 01/30/2023] Open
Abstract
Almond is one of the most featured nut crops owing to its high nutritional value. However, due to three different waves of flower and fruitlet drop, fruit drop is a major concern for growers. In this study, we carried out a time-course transcriptome analysis to investigate gene expression differences between normal and abnormal fruitlet development. By de novo assembly analysis, we identified 33,577 unigenes and provided their functional annotations. In total, we identified 7,469 differentially expressed genes and observed the most apparent difference between normal and abnormal fruits at 12 and 17 days after flowering. Their biological functions were enriched in carbon metabolism, carbon fixation in photosynthetic organisms and plant hormone signal transduction. RT-qPCR validated the expression pattern of 14 representative genes, including glycosyltransferase like family 2, MYB39, IAA13, gibberellin-regulated protein 11-like and POD44, which confirmed the reliability of our transcriptome data. This study provides an insight into the association between abnormal fruit development and carbohydrate signaling from the early developmental stages and could be served as useful information for understanding the regulatory mechanisms related to almond fruit drop.
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Zhao F, Song P, Zhang X, Li G, Hu P, Aslam A, Zhao X, Zhou H. Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis. PeerJ 2021; 9:e10739. [PMID: 33604178 PMCID: PMC7863778 DOI: 10.7717/peerj.10739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022] Open
Abstract
Strawberries are one of the most economically important berry fruits worldwide and exhibit colours ranging from white to dark red, providing a rich genetic resource for strawberry quality improvement. In the present study, we conducted transcriptome analyses of three strawberry cultivars, namely, 'Benihoppe', 'Xiaobai', and 'Snow White', and compared their gene expression profiles. Among the high-quality sequences, 5,049 and 53,200 differentially expressed genes (DEGs) were obtained when comparing the diploid and octoploid strawberry genomes and analysed to identify anthocyanin-related candidate genes. Sixty-five DEGs in the diploid genome (transcriptome data compared to the diploid strawberry genome) and 317 DEGs in the octoploid genome (transcriptome data compared to the octoploid strawberry genome) were identified among the three cultivars. Among these DEGs, 19 and 70 anthocyanin pathway genes, six and 42 sugar pathway genes, 23 and 101 hormone pathway genes, and 17 and 104 transcription factors in the diploid and octoploid genomes, respectively, correlated positively or negatively with the anthocyanin accumulation observed among the three cultivars. Real-time qPCR analysis of nine candidate genes showed a good correlation with the transcriptome data. For example, the expression of PAL was higher in 'Benihoppe' and 'Xiaobai' than in 'Snow White', consistent with the RNA-seq data. Thus, the RNA-seq data and candidate DEGs identified in the present study provide a sound basis for further studies of strawberry fruit colour formation.
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Affiliation(s)
- Fengli Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Pan Song
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiangfen Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Gang Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Panpan Hu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xia Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Houcheng Zhou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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12
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Castillejo C, Waurich V, Wagner H, Ramos R, Oiza N, Muñoz P, Triviño JC, Caruana J, Liu Z, Cobo N, Hardigan MA, Knapp SJ, Vallarino JG, Osorio S, Martín-Pizarro C, Posé D, Toivainen T, Hytönen T, Oh Y, Barbey CR, Whitaker VM, Lee S, Olbricht K, Sánchez-Sevilla JF, Amaya I. Allelic Variation of MYB10 Is the Major Force Controlling Natural Variation in Skin and Flesh Color in Strawberry ( Fragaria spp.) Fruit. THE PLANT CELL 2020; 32:3723-3749. [PMID: 33004617 PMCID: PMC7721342 DOI: 10.1105/tpc.20.00474] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/13/2020] [Accepted: 09/25/2020] [Indexed: 05/02/2023]
Abstract
The fruits of diploid and octoploid strawberry (Fragaria spp) show substantial natural variation in color due to distinct anthocyanin accumulation and distribution patterns. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 is the main activator in strawberry fruit. Here, we show that mutations in MYB10 cause most of the variation in anthocyanin accumulation and distribution observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F ×ananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function mutations in MYB10 were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses of octoploid Fragaria spp revealed that FaMYB10-2, one of three MYB10 homoeologs identified, regulates anthocyanin biosynthesis in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression. Our findings suggest that cis-regulatory elements in FaEnSpm-2 are responsible for enhanced MYB10-2 expression and anthocyanin biosynthesis in strawberry fruit flesh.
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Affiliation(s)
- Cristina Castillejo
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Veronika Waurich
- Hansabred GmbH & Co. KG, 01108 Dresden, Germany
- Institut für Botanik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Henning Wagner
- Hansabred GmbH & Co. KG, 01108 Dresden, Germany
- Institut für Botanik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Rubén Ramos
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Nicolás Oiza
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Pilar Muñoz
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | | | - Julie Caruana
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Nicolás Cobo
- Department of Plant Sciences, University of California, Davis, California 95616
- Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco 01145, Chile
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, California 95616
| | - José G Vallarino
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - Sonia Osorio
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - Carmen Martín-Pizarro
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - David Posé
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - Tuomas Toivainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00790, Finland
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00790, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00790, Finland
- National Institute of Agricultural Botany East Malling Research (NIAB EMR), Kent ME19 6BJ, United Kingdom
| | - Youngjae Oh
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Christopher R Barbey
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Vance M Whitaker
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Seonghee Lee
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | | | - José F Sánchez-Sevilla
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Iraida Amaya
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
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Jiang C, Fan Z, Li Z, Niu D, Li Y, Zheng M, Wang Q, Jin H, Guo J. Bacillus cereus AR156 triggers induced systemic resistance against Pseudomonas syringae pv. tomato DC3000 by suppressing miR472 and activating CNLs-mediated basal immunity in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2020; 21:854-870. [PMID: 32227587 PMCID: PMC7214473 DOI: 10.1111/mpp.12935] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/28/2020] [Accepted: 02/28/2020] [Indexed: 05/18/2023]
Abstract
Small RNAs play an important role in plant innate immunity. However, their regulatory function in induced systemic resistance (ISR) triggered by plant growth-promoting rhizobacteria remains unclear. Here, using Arabidopsis as a model system, one plant endogenous small RNA, miR472, was identified as an important regulator involved in the process of Bacillus cereus AR156 ISR against Pseudomonas syringae pv. tomato (Pst) DC3000. The results revealed that miR472 was down-regulated with B. cereus AR156 treatment by comparing small RNA profiles and northern blot analysis of Arabidopsis with or without B. cereus AR156 treatment. Plants overexpressing miR472 showed higher susceptibility to Pst DC3000; by contrast, plant lines with miR472 knocked down/out showed the opposite. The transcriptome sequencing revealed thousands of differentially expressed genes in the transgenic plants. Target prediction showed that miR472 targets lots of coiled coil nucleotide-binding site (NBS) and leucine-rich repeat (LRR) type resistance genes and the expression of these targets was negatively correlated with the expression of miR472. In addition, transgenic plants with knocked-out target genes exhibited decreased resistance to Pst DC3000 invasion. Quantitative reverse transcription PCR results indicated that target genes of miR472 were expressed during the process of B. cereus AR156-triggered ISR. Taken together, our results demonstrate that the miR472-mediated silencing pathway is an important regulatory checkpoint occurring via post-transcriptional control of NBS-LRR genes during B. cereus AR156-triggered ISR in Arabidopsis.
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Affiliation(s)
- Chunhao Jiang
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Zhihang Fan
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Zijie Li
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Dongdong Niu
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
| | - Yan Li
- Department of Plant PathologyCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Mingzi Zheng
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Qi Wang
- Department of Plant PathologyCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Hailing Jin
- Department of Plant Pathology and MicrobiologyUniversity of CaliforniaRiversideCAUSA
| | - Jianhua Guo
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
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14
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Li Y, Xu P, Chen G, Wu J, Liu Z, Lian H. FvbHLH9 Functions as a Positive Regulator of Anthocyanin Biosynthesis by Forming a HY5-bHLH9 Transcription Complex in Strawberry Fruits. PLANT & CELL PHYSIOLOGY 2020; 61:826-837. [PMID: 32016380 DOI: 10.1093/pcp/pcaa010] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/24/2020] [Indexed: 05/18/2023]
Abstract
Anthocyanin accumulation is transcriptionally regulated by the MYB-bHLH-WD40 complex. Light is indispensable for anthocyanin accumulation, and light-inducible MYB and HY5 were considered to promote anthocyanin accumulation in many fruits. Whether and how light-inducible bHLH transcription factor and HY5 regulate anthocyanin synthesis in strawberry is unknown. In this study, we identified a bHLH transcription factor, FvbHLH9, which was induced by light as well as FvHY5, and found that, similar to FvHY5, the transient overexpression and interference FvbHLH9 in strawberry fruits can promote and decrease anthocyanin accumulation, respectively, indicating FvbHLH9 functions as a positive regulator of anthocyanin biosynthesis. Furthermore, we confirmed that both FvHY5 and FvbHLH9 specifically bind to the promoter region of some key enzyme genes, including FvDFR, and the expression of FvDFR was activated through the heterodimer formation between FvHY5 and FvbHLH9. Finally, we confirmed that FvbHLH9-promoted anthocyanin accumulation is dependent on HY5-bHLH heterodimerisation in Arabidopsis. Our findings provide insights into a mechanism involving the synergistic regulation of light-dependent coloration and anthocyanin biosynthesis via a HY5-bHLH heterodimer formed by the interaction of FvHY5 and FvbHLH9 in strawberry fruits.
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Affiliation(s)
- Yang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pengbo Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guanqun Chen
- School of Design, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jun Wu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Hongli Lian
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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15
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Zhao J, Li H, Yin Y, An W, Qin X, Wang Y, Li Y, Fan Y, Cao Y. Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening. Sci Rep 2020; 10:4354. [PMID: 32152358 PMCID: PMC7062791 DOI: 10.1038/s41598-020-61064-5] [Citation(s) in RCA: 16] [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: 12/18/2018] [Accepted: 11/15/2019] [Indexed: 12/31/2022] Open
Abstract
Red wolfberry (or goji berry, Lycium barbarum; LB) is an important agricultural product with a high content of pharmacologically important secondary metabolites such as phenylpropanoids. A close relative, black wolfberry (L. ruthenicum; LR), endemic to the salinized deserts of northwestern China, is used only locally. The two fruits exhibit many morphological and phytochemical differences, but genetic mechanisms underlying them remain poorly explored. In order to identify the genes of interest for further studies, we studied transcriptomic (Illumina HiSeq) and metabolomic (LC-MS) profiles of the two fruits during five developmental stages (young to ripe). As expected, we identified much higher numbers of significantly differentially regulated genes (DEGs) than metabolites. The highest numbers were identified in pairwise comparisons including the first stage for both species, but total numbers were consistently somewhat lower for the LR. The number of differentially regulated metabolites in pairwise comparisons of developmental stages varied from 66 (stages 3 vs 4) to 133 (stages 2 vs 5) in both species. We identified a number of genes (e.g. AAT1, metE, pip) and metabolites (e.g. rutin, raffinose, galactinol, trehalose, citrulline and DL-arginine) that may be of interest to future functional studies of stress adaptation in plants. As LB is also highly suitable for combating soil desertification and alleviating soil salinity/alkalinity/pollution, its potential for human use may be much wider than its current, highly localized, relevance.
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Affiliation(s)
- Jianhua Zhao
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Haoxia Li
- Desertification Control Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 750002, China
| | - Yue Yin
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Wei An
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Xiaoya Qin
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Yajun Wang
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Yanlong Li
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Yunfang Fan
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Youlong Cao
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China.
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16
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Thole V, Bassard JE, Ramírez-González R, Trick M, Ghasemi Afshar B, Breitel D, Hill L, Foito A, Shepherd L, Freitag S, Nunes dos Santos C, Menezes R, Bañados P, Naesby M, Wang L, Sorokin A, Tikhonova O, Shelenga T, Stewart D, Vain P, Martin C. RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics. BMC Genomics 2019; 20:995. [PMID: 31856735 PMCID: PMC6924045 DOI: 10.1186/s12864-019-6183-2] [Citation(s) in RCA: 20] [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: 05/02/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are often limited, despite their value in underpinning the in-depth study of metabolic pathways, fruit ripening as well as in the identification of genotypes rich in bioactive compounds. RESULTS To access the genetic diversity of wild and cultivated berry fruit species that accumulate high levels of phenolic compounds in their fleshy berry(-like) fruits, we selected 13 species from Europe, South America and Asia representing eight genera, seven families and seven orders within three clades of the kingdom Plantae. RNA from either ripe fruits (ten species) or three ripening stages (two species) as well as leaf RNA (one species) were used to construct, assemble and analyse de novo transcriptomes. The transcriptome sequences are deposited in the BacHBerryGEN database (http://jicbio.nbi.ac.uk/berries) and were used, as a proof of concept, via its BLAST portal (http://jicbio.nbi.ac.uk/berries/blast.html) to identify candidate genes involved in the biosynthesis of phenylpropanoid compounds. Genes encoding regulatory proteins of the anthocyanin biosynthetic pathway (MYB and basic helix-loop-helix (bHLH) transcription factors and WD40 repeat proteins) were isolated using the transcriptomic resources of wild blackberry (Rubus genevieri) and cultivated red raspberry (Rubus idaeus cv. Prestige) and were shown to activate anthocyanin synthesis in Nicotiana benthamiana. Expression patterns of candidate flavonoid gene transcripts were also studied across three fruit developmental stages via the BacHBerryEXP gene expression browser (http://www.bachberryexp.com) in R. genevieri and R. idaeus cv. Prestige. CONCLUSIONS We report a transcriptome resource that includes data for a wide range of berry(-like) fruit species that has been developed for gene identification and functional analysis to assist in berry fruit improvement. These resources will enable investigations of metabolic processes in berries beyond the phenylpropanoid biosynthetic pathway analysed in this study. The RNA-seq data will be useful for studies of berry fruit development and to select wild plant species useful for plant breeding purposes.
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Affiliation(s)
- Vera Thole
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jean-Etienne Bassard
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg, Denmark
- Present address: Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 Rue General Zimmer, 67084 Strasbourg, France
| | | | - Martin Trick
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Bijan Ghasemi Afshar
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Dario Breitel
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present address: Tropic Biosciences UK LTD, Norwich Research Park, Norwich, NR4 7UG UK
| | - Lionel Hill
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | | | - Sabine Freitag
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - Cláudia Nunes dos Santos
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Rua Câmara Pestana 6, 1150-082 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Regina Menezes
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Rua Câmara Pestana 6, 1150-082 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Pilar Bañados
- Facultad De Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna Ote, 4860 Macul, Chile
| | | | - Liangsheng Wang
- Institute of Botany, The Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
| | - Artem Sorokin
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Olga Tikhonova
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Tatiana Shelenga
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Derek Stewart
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | - Philippe Vain
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Cathie Martin
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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17
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Zhang L, Wang L, Zeng X, Chen R, Yang S, Pan S. Comparative transcriptome analysis reveals fruit discoloration mechanisms in postharvest strawberries in response to high ambient temperature. FOOD CHEMISTRY-X 2019; 2:100025. [PMID: 31432012 PMCID: PMC6694852 DOI: 10.1016/j.fochx.2019.100025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023]
Abstract
The aim of this study was to examine both physiological and molecular evidences related to fruit discoloration in postharvest strawberries under high ambient temperature. The results showed the total anthocyanin and their main components in the strawberries under 35 °C were greatly increased due to the significant up-regulations of anthocyanin biosynthetic genes and transportation genes. High ambient temperature greatly improved the activities of peroxidase (POD) and enhanced gene expressions of POD3, POD6 and POD63. At the same time, high storage temperature activated laccase genes expression including laccase-9 and laccase-14, which was closely related to anthocyanin degradation. Levels of reactive oxygen species (ROS) metabolism were also increased under high ambient temperature at transcript levels. Therefore, we concluded that high ambient temperature could enhance anthocyanin accumulation and degradation at the same time, which maybe the main reasons for the fruits discoloration of postharvest strawberries under high ambient temperature.
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Affiliation(s)
- Liping Zhang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lu Wang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiangguo Zeng
- Economic Crop Research Institute, Hubei Academy of Agricultural Sciences, PR China
| | - Ruixu Chen
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shuzhen Yang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Siyi Pan
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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18
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Jiang CH, Yao XF, Mi DD, Li ZJ, Yang BY, Zheng Y, Qi YJ, Guo JH. Comparative Transcriptome Analysis Reveals the Biocontrol Mechanism of Bacillus velezensis F21 Against Fusarium Wilt on Watermelon. Front Microbiol 2019; 10:652. [PMID: 31001229 PMCID: PMC6456681 DOI: 10.3389/fmicb.2019.00652] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022] Open
Abstract
The watermelon (Citrullus lanatus) is one of the most important horticultural crops for fruit production worldwide. However, the production of watermelon is seriously restricted by one kind of soilborne disease, Fusarium wilt, which is caused by Fusarium oxysporum f. sp. niveum (Fon). In this study, we identified an efficient PGPR strain B. velezensis F21, which could be used in watermelon production for Fon control. The results of biocontrol mechanisms showed that B. velezensis F21 could suppress the growth and spore germination of Fon in vitro. Moreover, B. velezensis F21 could also enhance plant basal immunity to Fon by increasing the expression of plant defense related genes and activities of some defense enzymes, such as CAT, POD, and SOD. To elucidate the detailed mechanisms regulating B. velezensis F21 biocontrol of Fusarium wilt in watermelon, a comparative transcriptome analysis using watermelon plant roots treated with B. velezensis F21 or sterile water alone and in combination with Fon inoculation was conducted. The transcriptome sequencing results revealed almost one thousand ripening-related differentially expressed genes (DEGs) in the process of B. velezensis F21 triggering ISR (induced systemic resistance) to Fon. In addition, the Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that numerous of transcription factors (TFs) and plant disease resistance genes were activated and validated by using quantitative real-time PCR (qRT-PCR), which showed significant differences in expression levels in the roots of watermelon with different treatments. In addition, genes involved in the MAPK signaling pathway and phytohormone signaling pathway were analyzed, and the results indicated that B. velezensis F21 could enhance plant disease resistance to Fon through the above related genes and phytohormone signal factors. Taken together, this study substantially expands transcriptome data resources and suggests a molecular framework for B. velezensis F21 inducing systemic resistance to Fon in watermelon. In addition, it also provides an effective strategy for the control of Fusarium wilt in watermelon.
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Affiliation(s)
- Chun-Hao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xie-Feng Yao
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Dan-Dan Mi
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
| | - Zi-Jie Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
| | - Bing-Ye Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
| | - Ying Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
| | - Yi-Jun Qi
- Tsinghua Peking Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jian-Hua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
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Li D, Mou W, Xia R, Li L, Zawora C, Ying T, Mao L, Liu Z, Luo Z. Integrated analysis of high-throughput sequencing data shows abscisic acid-responsive genes and miRNAs in strawberry receptacle fruit ripening. HORTICULTURE RESEARCH 2019; 6:26. [PMID: 30729016 DOI: 10.1038/s41438-018-0100-108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/25/2018] [Accepted: 09/02/2018] [Indexed: 05/25/2023]
Abstract
The perception and signal transduction of the plant hormone abscisic acid (ABA) are crucial for strawberry fruit ripening, but the underlying mechanism of how ABA regulates ripening-related genes has not been well understood. By employing high-throughput sequencing technology, we comprehensively analyzed transcriptomic and miRNA expression profiles simultaneously in ABA- and nordihydroguaiaretic acid (NDGA, an ABA biosynthesis blocker)-treated strawberry fruits with temporal resolution. The results revealed that ABA regulated many genes in different pathways, including hormone signal transduction and the biosynthesis of secondary metabolites. Transcription factor genes belonging to WRKY and heat shock factor (HSF) families might play key roles in regulating the expression of ABA inducible genes, whereas the KNOTTED1-like homeobox protein and Squamosa Promoter-Binding-like protein 18 might be responsible for ABA-downregulated genes. Additionally, 20 known and six novel differentially expressed miRNAs might be important regulators that assist ABA in regulating target genes that are involved in versatile physiological processes, such as hormone balance regulation, pigments formation and cell wall degradation. Furthermore, degradome analysis showed that one novel miRNA, Fa_novel6, could degrade its target gene HERCULES1, which likely contributed to fruit size determination during strawberry ripening. These results expanded our understanding of how ABA drives the strawberry fruit ripening process as well as the role of miRNAs in this process.
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Affiliation(s)
- Dongdong Li
- 1College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
- 2Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Wangshu Mou
- 1College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
| | - Rui Xia
- 3State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642 Guangzhou, P.R. China
| | - Li Li
- 1College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
| | - Christopher Zawora
- 2Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Tiejin Ying
- 1College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
| | - Linchun Mao
- 1College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
| | - Zhongchi Liu
- 2Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Zisheng Luo
- 1College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
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20
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Li D, Mou W, Xia R, Li L, Zawora C, Ying T, Mao L, Liu Z, Luo Z. Integrated analysis of high-throughput sequencing data shows abscisic acid-responsive genes and miRNAs in strawberry receptacle fruit ripening. HORTICULTURE RESEARCH 2019; 6:26. [PMID: 30729016 PMCID: PMC6355886 DOI: 10.1038/s41438-018-0100-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/25/2018] [Accepted: 09/02/2018] [Indexed: 05/04/2023]
Abstract
The perception and signal transduction of the plant hormone abscisic acid (ABA) are crucial for strawberry fruit ripening, but the underlying mechanism of how ABA regulates ripening-related genes has not been well understood. By employing high-throughput sequencing technology, we comprehensively analyzed transcriptomic and miRNA expression profiles simultaneously in ABA- and nordihydroguaiaretic acid (NDGA, an ABA biosynthesis blocker)-treated strawberry fruits with temporal resolution. The results revealed that ABA regulated many genes in different pathways, including hormone signal transduction and the biosynthesis of secondary metabolites. Transcription factor genes belonging to WRKY and heat shock factor (HSF) families might play key roles in regulating the expression of ABA inducible genes, whereas the KNOTTED1-like homeobox protein and Squamosa Promoter-Binding-like protein 18 might be responsible for ABA-downregulated genes. Additionally, 20 known and six novel differentially expressed miRNAs might be important regulators that assist ABA in regulating target genes that are involved in versatile physiological processes, such as hormone balance regulation, pigments formation and cell wall degradation. Furthermore, degradome analysis showed that one novel miRNA, Fa_novel6, could degrade its target gene HERCULES1, which likely contributed to fruit size determination during strawberry ripening. These results expanded our understanding of how ABA drives the strawberry fruit ripening process as well as the role of miRNAs in this process.
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Affiliation(s)
- Dongdong Li
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Wangshu Mou
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642 Guangzhou, P.R. China
| | - Li Li
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
| | - Christopher Zawora
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Tiejin Ying
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, 310058 Hangzhou, P.R. China
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21
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Bai L, Chen Q, Jiang L, Lin Y, Ye Y, Liu P, Wang X, Tang H. Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla. HORTICULTURE RESEARCH 2019; 6:42. [PMID: 30854215 PMCID: PMC6397888 DOI: 10.1038/s41438-019-0128-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/19/2019] [Accepted: 01/22/2019] [Indexed: 05/18/2023]
Abstract
To investigate the molecular mechanism underlying fruit development and color change, comparative transcriptome analysis was employed to generate transcriptome profiles of two typical wild varieties of Fragaria pentaphylla at three fruit developmental stages (green fruit stage, turning stage, and ripe fruit stage). We identified 25,699 long noncoding RNAs (lncRNAs) derived from 25,107 loci in the F. pentaphylla fruit transcriptome, which showed distinct stage- and genotype-specific expression patterns. Time course analysis detected a large number of differentially expressed protein-coding genes and lncRNAs associated with fruit development and ripening in both of the F. pentaphylla varieties. The target genes downregulated in the late stages were enriched in terms of photosynthesis and cell wall organization or biogenesis, suggesting that lncRNAs may act as negative regulators to suppress photosynthesis and cell wall organization or biogenesis during fruit development and ripening of F. pentaphylla. Pairwise comparisons of two varieties at three developmental stages identified 365 differentially expressed lncRNAs in total. Functional annotation of target genes suggested that lncRNAs in F. pentaphylla may play roles in fruit color formation by regulating the expression of structural genes or regulatory factors. Construction of the regulatory network further revealed that the low expression of Fra a and CHS may be the main cause of colorless fruit in F. pentaphylla.
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Affiliation(s)
- Lijun Bai
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
- Chengdu Life Baseline Technology Co., LTD, Chengdu, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Leiyu Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yuntian Ye
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Peng Liu
- Chengdu Life Baseline Technology Co., LTD, Chengdu, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
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22
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Baldi P, Orsucci S, Moser M, Brilli M, Giongo L, Si-Ammour A. Gene expression and metabolite accumulation during strawberry (Fragaria × ananassa) fruit development and ripening. PLANTA 2018; 248:1143-1157. [PMID: 30066220 DOI: 10.1007/s00425-018-2962-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/25/2018] [Indexed: 05/20/2023]
Abstract
A coordinated regulation of different metabolic pathways was highlighted leading to the accumulation of important compounds that may contribute to the final quality of strawberry fruit. Strawberry fruit development and ripening involve complex physiological and biochemical changes, ranging from sugar accumulation to the production of important volatiles compounds that contribute to the final fruit flavor. To better understand the mechanisms controlling fruit growth and ripening in cultivated strawberry (Fragaria × ananassa), we applied a molecular approach combining suppression subtractive hybridization and next generation sequencing to identify genes regulating developmental stages going from fruit set to full ripening. The results clearly indicated coordinated regulation of several metabolic processes such as the biosynthesis of flavonoid, phenylpropanoid and branched-chain amino acids, together with glycerolipid metabolism and pentose and glucuronate interconversion. In particular, genes belonging to the flavonoid pathway were activated in two distinct phases, the first one at the very early stages of fruit development and the second during ripening. The combination of expression analysis with metabolomic data revealed that the functional meaning of these two inductions is different, as during the early stages gene activation of flavonoid pathway leads to the production of proanthocyanidins and ellagic acid-derived tannins, while during ripening anthocyanins are the main product of flavonoid pathway activation. Moreover, the subtractive approach allowed the identification of different members of the same gene family coding for the same or very similar enzymes that in some cases showed opposite regulation during strawberry fruit development. Such regulation is an important trait that can help to understand how plants specifically channel metabolic intermediates towards separate branches of a biosynthetic pathway or use different isoforms of the same enzyme in different organs or developmental stages.
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Affiliation(s)
- Paolo Baldi
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy.
| | - Saverio Orsucci
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Mirko Moser
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Matteo Brilli
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Lara Giongo
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Azeddine Si-Ammour
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
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Developmental Variation in Fruit Polyphenol Content and Related Gene Expression of a Red-Fruited versus a White-Fruited Fragaria vesca Genotype. HORTICULTURAE 2018. [DOI: 10.3390/horticulturae4040030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Two cultivars of F. vesca, red-fruited Baron Solemacher (BS) and white-fruited Pineapple Crush (PC), were studied to compare and contrast the quantitative accumulation of major polyphenols and related biosynthetic pathway gene expression patterns during fruit development and ripening. Developing PC fruit showed higher levels of hydroxycinnamic acids in green stages and a greater accumulation of ellagitannins in ripe fruit in comparison to BS. In addition to anthocyanin, red BS fruit had greater levels of flavan-3-ols when ripe than PC. Expression patterns of key structural genes and transcription factors of the phenylpropanoid/flavonoid biosynthetic pathway, an abscisic acid (ABA) biosynthetic gene, and a putative ABA receptor gene that may regulate the pathway, were also analyzed during fruit development and ripening to determine which genes exhibited differences in expression and when such differences were first evident. Expression of all pathway genes differed between the red BS and white PC at one or more times during development, most notably at ripening when phenylalanine ammonia lyase 1 (PAL1), chalcone synthase (CHS), flavanone-3′-hydroxylase (F3′H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), and UDP:flavonoid-O-glucosyltransferase 1 (UFGT1) were significantly upregulated in the red BS fruit. The transcription factors MYB1 and MYB10 did not differ substantially between red and white fruit except at ripening, when both the putative repressor MYB1 and promoter MYB10 were upregulated in red BS but not white PC fruit. The expression of ABA-related gene 9-cis-epoxycarotenoid dioxygenase 1 (NCED1) was higher in red BS fruit but only in the early green stages of development. Thus, a multigenic effect at several points in the phenylpropanoid/flavonoid biosynthetic pathway due to lack of MYB10 upregulation may have resulted in white PC fruit.
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24
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Wang G, Chen B, Du H, Zhang F, Zhang H, Wang Y, He H, Geng S, Zhang X. Genetic mapping of anthocyanin accumulation-related genes in pepper fruits using a combination of SLAF-seq and BSA. PLoS One 2018; 13:e0204690. [PMID: 30261055 PMCID: PMC6160195 DOI: 10.1371/journal.pone.0204690] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022] Open
Abstract
Anthocyanins have significant functions in stress tolerance in pepper (Capsicum annuum L.) and also benefit human health. Nevertheless, the key structural genes and regulatory genes involved in anthocyanin accumulation in pepper fruits are still not well understood and fine mapped. For the present study, 383 F2 plants from a cross between the green-fruited C. annuum line Z5 and the purple-fruited line Z6 was developed. Two separate bulked DNA pools were constructed with DNAs extracted from either 37 plants with high anthocyanin content or from 18 plants with no anthocyanin. A combination of specific-locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was used to identify candidates for regions associated with anthocyanin accumulation. We identified a total of 127,004 high-quality single nucleotide polymorphism (SNP) markers, and detected 1674 high-quality SNP markers associated with anthocyanin accumulation. Three candidate anthocyanin-associated regions including the intervals from 12.48 to 20.00 Mb, from 54.67 to 56.59 Mb, and from 192.17 to 196.82 Mb were identified within a 14.10-Mb interval on chromosome 10 containing 126 candidate genes. Based on their annotations, we identified 12 candidate genes that are predicted to be associated with anthocyanin expression. The present results provide an efficient strategy for genetic mapping of and valuable insights into the genetic mechanisms of anthocyanin accumulation in pepper fruit, and allow us to clone and functionally analyze the genes that influence anthocyanin accumulation in this species.
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Affiliation(s)
- Guoyun Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Fenglan Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Haiying Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Yaqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Hongju He
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (XZ)
| | - Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (XZ)
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25
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Lin Y, Jiang L, Chen Q, Li Y, Zhang Y, Luo Y, Zhang Y, Sun B, Wang X, Tang H. Comparative Transcriptome Profiling Analysis of Red- and White-Fleshed Strawberry (Fragaria�ananassa) Provides New Insight into the Regulation of the Anthocyanin Pathway. PLANT & CELL PHYSIOLOGY 2018; 59:1844-1859. [PMID: 29800352 DOI: 10.1093/pcp/pcy098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/14/2018] [Indexed: 05/07/2023]
Abstract
Anthocyanins are water-soluble pigments in plants. They confer both economic and healthy profits for humans. To gain a deeper insight into the regulation of anthocyanin biosynthesis in octoploid strawberry (Fragaria�ananassa; Fa), a widely consumed economically important fruit, we performed comparative transcriptomic analysis of red- and white-fleshed strawberry cultivars in two ripening stages. In total, 365,455 non-redundant transcripts were assembled from the RNA sequencing (RNAseq) data. Of this collection, 377 were annotated as putative anthocyanin-related transcripts. Differential expression analysis revealed that 57 anthocyanin biosynthesis transcripts were down-regulated, and 89 transcription factors (TFs) were either down- or up-regulated under anthocyanin deficiency. Additionally, amongst the 50,601 putative long non-coding RNAs (lncRNAs) identified here, 68 lncRNAs were differentially expressed and co-expressed with differentially expressed anthocyanin-related mRNAs; 2,070 co-expressing lncRNA-mRNA pairs were generated. Expression profile analysis revealed that it was the limited expression of FaF3'H (flavonoid 3'-hydroxylase) that blocked the cyanidin 3-glucoside accumulation in the two investigated strawberry cultivars. This was further supported by a transient overexpression experiment with FaMYB10. The down-regulated lncRNAs might participate in anthocyanin regulation by acting as targets for microRNAs (miRNAs). The level of competitive intensity in miRNA and lncRNA for the same mRNA targets was probably lower in the white-fleshed strawberries, which can release the repression effect of the mRNAs in red-fleshed strawberry as a result. This study for the first time presents lncRNAs related to anthocyanins in strawberries, provides new insights into the anthocyanin regulatory network and also lays the foundation for identifying new anthocyanin regulators in strawberry.
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Affiliation(s)
- Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Leiyu Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yali Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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26
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Hu P, Li G, Zhao X, Zhao F, Li L, Zhou H. Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries ( Fragaria × ananassa). PeerJ 2018; 6:e4976. [PMID: 29967718 PMCID: PMC6026456 DOI: 10.7717/peerj.4976] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/24/2018] [Indexed: 11/21/2022] Open
Abstract
Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste, and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. A total of five ubiquitin-conjugating enzymes and 10 MADS-box transcription factors were differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics in Fragaria × ananassa.
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Affiliation(s)
- Panpan Hu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Gang Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Xia Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Fengli Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Liangjie Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Houcheng Zhou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
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Luo H, Dai C, Li Y, Feng J, Liu Z, Kang C. Reduced Anthocyanins in Petioles codes for a GST anthocyanin transporter that is essential for the foliage and fruit coloration in strawberry. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2595-2608. [PMID: 29538703 PMCID: PMC5920330 DOI: 10.1093/jxb/ery096] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 03/04/2018] [Indexed: 05/18/2023]
Abstract
The red color of the foliage and fruit in strawberry comes from anthocyanins stored in the vacuole; however, how this anthocyanin accumulation is regulated remains unclear. A reduced anthocyanin in petioles (rap) mutant was identified in an N-ethyl-N-nitrosourea (ENU) mutagenized population of YW5AF7, a white-fruited variety of the wild strawberry Fragaria vesca. The causative mutation was identified to be a premature stop codon in a glutathione S-transferase (GST) gene. In addition to the foliage coloration, RAP also mediates fruit pigmentation and acts downstream of the fruit-specific transcription factor FvMYB10. Among all eight GST genes in the same subfamily, RAP is most abundantly expressed in the ripening fruit. Expression analysis and transient expression assays demonstrated that RAP is the principal transporter of anthocyanins among the paralogs. Moreover, domain-swap experiments showed that both the N- and C-terminals of RAP are essential for the binding capability of anthocyanins. In addition, transient knock-down of RAP resulted in reduced fruit coloration in cultivated strawberry. Collectively, our results demonstrate that RAP encodes the principal GST transporter of anthocyanins in the strawberry foliage and fruit, and it could be modified to alter the fruit color in strawberry.
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Affiliation(s)
- Huifeng Luo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Cheng Dai
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongping Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Jia Feng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Zhongchi Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Chunying Kang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Correspondence:
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28
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Hossain MR, Kim HT, Shanmugam A, Nath UK, Goswami G, Song JY, Park JI, Nou IS. Expression Profiling of Regulatory and Biosynthetic Genes in Contrastingly Anthocyanin Rich Strawberry (Fragaria × ananassa) Cultivars Reveals Key Genetic Determinants of Fruit Color. Int J Mol Sci 2018; 19:ijms19030656. [PMID: 29495391 PMCID: PMC5877517 DOI: 10.3390/ijms19030656] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 02/16/2018] [Accepted: 02/22/2018] [Indexed: 11/22/2022] Open
Abstract
Anthocyanins are the resultant end-point metabolites of phenylapropanoid/flavonoid (F/P) pathway which is regulated at transcriptional level via a series of structural genes. Identifying the key genes and their potential interactions can provide us with the clue for novel points of intervention for improvement of the trait in strawberry. We profiled the expressions of putative regulatory and biosynthetic genes of cultivated strawberry in three developmental and characteristically colored stages of fruits of contrastingly anthocyanin rich cultivars: Tokun, Maehyang and Soelhyang. Besides FaMYB10, a well-characterized positive regulator, FaMYB5, FabHLH3 and FabHLH3-delta might also act as potential positive regulators, while FaMYB11, FaMYB9, FabHLH33 and FaWD44-1 as potential negative regulators of anthocyanin biosynthesis in these high-anthocyanin cultivars. Among the early BGs, Fa4CL7, FaF3H, FaCHI1, FaCHI3, and FaCHS, and among the late BGs, FaDFR4-3, FaLDOX, and FaUFGT2 showed significantly higher expression in ripe fruits of high anthocyanin cultivars Maehyang and Soelhyang. Multivariate analysis revealed the association of these genes with total anthocyanins. Increasingly higher expressions of the key genes along the pathway indicates the progressive intensification of pathway flux leading to final higher accumulation of anthocyanins. Identification of these key genetic determinants of anthocyanin regulation and biosynthesis in Korean cultivars will be helpful in designing crop improvement programs.
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Affiliation(s)
- Mohammad Rashed Hossain
- Department of Horticulture, Suncheon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
| | - Hoy-Taek Kim
- Department of Horticulture, Suncheon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
- University-Industry Cooperation Foundation, Suncheon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
| | - Ashokraj Shanmugam
- Department of Horticulture, Suncheon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
| | - Ujjal Kumar Nath
- Department of Horticulture, Suncheon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
| | - Gayatri Goswami
- Department of Horticulture, Suncheon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
| | - Jae-Young Song
- Department of Crop Science, Chungbuk National University, Chengju 28644, Korea.
| | - Jong-In Park
- Department of Horticulture, Suncheon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Suncheon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
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Zhao F, Li G, Hu P, Zhao X, Li L, Wei W, Feng J, Zhou H. Identification of basic/helix-loop-helix transcription factors reveals candidate genes involved in anthocyanin biosynthesis from the strawberry white-flesh mutant. Sci Rep 2018; 8:2721. [PMID: 29426907 PMCID: PMC5807450 DOI: 10.1038/s41598-018-21136-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/30/2018] [Indexed: 12/03/2022] Open
Abstract
As the second largest transcription factor family in plant, the basic helix-loop-helix (bHLH) transcription factor family, characterized by the conserved bHLH domain, plays a central regulatory role in many biological process. However, the bHLH transcription factor family of strawberry has not been systematically identified, especially for the anthocyanin biosynthesis. Here, we identified a total of 113 bHLH transcription factors and described their chromosomal distribution and bioinformatics for the diploid woodland strawberry Fragaria vesca. In addition, transcription profiles of 113 orthologous bHLH genes from various tissues were analyzed for the cultivar 'Benihoppe', its white-flesh mutant 'Xiaobai', and the 'Snow Princess' from their fruit development to the ripening, as well as those under either the ABA or Eth treatment. Both the RT-PCR and qRT-PCR results show that seven selected FabHLH genes (FabHLH17, FabHLH25, FabHLH27, FabHLH29, FabHLH40, FabHLH80, FabHLH98) are responsive to the fruit anthocyanin biosynthesis and hormone signaling according to transcript profiles where three color modes are observed for strawberry's fruit skin and flesh. Further, prediction for the protein interaction network reveals that four bHLHs (FabHLH25, FabHLH29, FabHLH80, FabHLH98) are involved in the fruit anthocyanin biosynthesis and hormone signaling transduction. These bioinformatics and expression profiles provide a good basis for a further investigation of strawberry bHLH genes.
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Affiliation(s)
- Fengli Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture of China, Zhengzhou, China
| | - Gang Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture of China, Zhengzhou, China
| | - Panpan Hu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture of China, Zhengzhou, China
| | - Xia Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture of China, Zhengzhou, China
| | - Liangjie Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture of China, Zhengzhou, China
| | - Wei Wei
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Jiayue Feng
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Houcheng Zhou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture of China, Zhengzhou, China.
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30
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Yin S, Jiang X, Jiang H, Gao Q, Wang F, Fan S, Khan T, Jabeen N, Khan M, Ali A, Xu P, Pandita TK, Fan HY, Zhang Y, Shi Q. Histone acetyltransferase KAT8 is essential for mouse oocyte development by regulating reactive oxygen species levels. Development 2017; 144:2165-2174. [PMID: 28506985 DOI: 10.1242/dev.149518] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/29/2017] [Indexed: 12/22/2022]
Abstract
Proper oocyte development is crucial for female fertility and requires timely and accurate control of gene expression. K (lysine) acetyltransferase 8 (KAT8), an important component of the X chromosome dosage compensation system in Drosophila, regulates gene activity by acetylating histone H4 preferentially at lysine 16. To explore the function of KAT8 during mouse oocyte development, we crossed Kat8flox/flox mice with Gdf9-Cre mice to specifically delete Kat8 in oocytes. Oocyte Kat8 deletion resulted in female infertility, with follicle development failure in the secondary and preantral follicle stages. RNA-seq analysis revealed that Kat8 deficiency in oocytes results in significant downregulation of antioxidant genes, with a consequent increase in reactive oxygen species. Intraperitoneal injection of the antioxidant N-acetylcysteine rescued defective follicle and oocyte development resulting from Kat8 deficiency. Chromatin immunoprecipitation assays indicated that KAT8 regulates antioxidant gene expression by direct binding to promoter regions. Taken together, our findings demonstrate that KAT8 is essential for female fertility by regulating antioxidant gene expression and identify KAT8 as the first histone acetyltransferase with an essential function in oogenesis.
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Affiliation(s)
- Shi Yin
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Xiaohua Jiang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Hanwei Jiang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Qian Gao
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Fang Wang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Suixing Fan
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Teka Khan
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Nazish Jabeen
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Manan Khan
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Asim Ali
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Peng Xu
- USTC-Shenyang Jinghua Hospital Joint Center of Human Reproduction and Genetics, Shenyang, Liaoning 110000, China
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 75390, USA
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuanwei Zhang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Qinghua Shi
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
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31
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Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes. Sci Rep 2017; 7:45113. [PMID: 28327625 PMCID: PMC5361166 DOI: 10.1038/srep45113] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/17/2017] [Indexed: 01/22/2023] Open
Abstract
Strawberry fruits (Fragaria vesca) are valued for their sweet fruity flavor, juicy texture, and characteristic red color caused by anthocyanin pigments. To gain a deeper insight into the regulation of anthocyanin biosynthesis, we performed comparative metabolite profiling and transcriptome analyses of one red-fruited and two natural white-fruited strawberry varieties in two tissues and three ripening stages. Developing fruit of the three genotypes showed a distinctive pattern of polyphenol accumulation already in green receptacle and achenes. Global analysis of the transcriptomes revealed that the ripening process in the white-fruited varieties is already affected at an early developmental stage. Key polyphenol genes showed considerably lower transcript levels in the receptacle and achenes of both white genotypes, compared to the red genotype. The expression of the anthocyanidin glucosyltransferase gene and a glutathione S-transferase, putatively involved in the vacuolar transport of the anthocyanins, seemed to be critical for anthocyanin formation. A bHLH transcription factor is among the differentially expressed genes as well. Furthermore, genes associated with flavor formation and fruit softening appear to be coordinately regulated and seem to interact with the polyphenol biosynthesis pathway. This study provides new information about polyphenol biosynthesis regulators in strawberry, and reveals genes unknown to affect anthocyanin formation.
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Li W, Zhang L, Ding Z, Wang G, Zhang Y, Gong H, Chang T, Zhang Y. De novo sequencing and comparative transcriptome analysis of the male and hermaphroditic flowers provide insights into the regulation of flower formation in andromonoecious taihangia rupestris. BMC PLANT BIOLOGY 2017; 17:54. [PMID: 28241786 PMCID: PMC5329940 DOI: 10.1186/s12870-017-0990-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/31/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Taihangia rupestris, an andromonoecious plant species, bears both male and hermaphroditic flowers within the same individual. However, the establishment and development of male and hermaphroditic flowers in andromonoecious Taihangia remain poorly understood, due to the limited genetic and sequence information. To investigate the potential molecular mechanism in the regulation of Taihangia flower formation, we used de novo RNA sequencing to compare the transcriptome profiles of male and hermaphroditic flowers at early and late developmental stages. RESULTS Four cDNA libraries, including male floral bud, hermaphroditic floral bud, male flower, and hermaphroditic flower, were constructed and sequenced by using the Illumina RNA-Seq method. Totally, 84,596,426 qualified Illumina reads were obtained and then assembled into 59,064 unigenes, of which 24,753 unigenes were annotated in the NCBI non-redundant protein database. In addition, 12,214, 7,153, and 8,115 unigenes were assigned into 53 Gene Ontology (GO) functional groups, 25 Clusters of Orthologous Group (COG) categories, and 126 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. By pairwise comparison of unigene abundance between the samples, we identified 1,668 differential expressed genes (DEGs), including 176 transcription factors (TFs) between the male and hermaphroditic flowers. At the early developmental stage, we found 263 up-regulated genes and 436 down-regulated genes expressed in hermaphroditic floral buds, while 844 up-regulated genes and 314 down-regulated genes were detected in hermaphroditic flowers at the late developmental stage. GO and KEGG enrichment analyses showed that a large number of DEGs were associated with a wide range of functions, including cell cycle, epigenetic processes, flower development, and biosynthesis of unsaturated fatty acid pathway. Finally, real-time quantitative PCR was conducted to validate the DEGs identified in the present study. CONCLUSION In this study, transcriptome data of this rare andromonoecious Taihangia were reported for the first time. Comparative transcriptome analysis revealed the significant differences in gene expression profiles between male and hermaphroditic flowers at early and late developmental stages. The transcriptome data of Taihangia would be helpful to improve the understanding of the underlying molecular mechanisms in regulation of flower formation and unisexual flower establishment in andromonoecious plants.
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Affiliation(s)
- Weiguo Li
- College of Life Science, Changchun Normal University, Changchun, 130032 Jilin China
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Lihui Zhang
- College of Life Science, Changchun Normal University, Changchun, 130032 Jilin China
| | - Zhan Ding
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Guodong Wang
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Yandi Zhang
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Hongmei Gong
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Tianjun Chang
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Yanwen Zhang
- College of Life Science, Changchun Normal University, Changchun, 130032 Jilin China
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Hawkins C, Caruana J, Li J, Zawora C, Darwish O, Wu J, Alkharouf N, Liu Z. An eFP browser for visualizing strawberry fruit and flower transcriptomes. HORTICULTURE RESEARCH 2017; 4:17029. [PMID: 28674614 PMCID: PMC5478792 DOI: 10.1038/hortres.2017.29] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 05/05/2023]
Abstract
Wild strawberry Fragaria vesca is emerging as an important model system for the cultivated strawberry due to its diploid genome and availability of extensive transcriptome data and a range of molecular genetic tools. Being able to better utilize these tools, especially the transcriptome data, will greatly facilitate research progress in strawberry and other Rosaceae fruit crops. The electronic fluorescent pictograph (eFP) software is a useful and popular tool to display transcriptome data visually, and is widely used in other model organisms including Arabidopsis and mouse. Here we applied eFP to display wild strawberry RNA sequencing (RNA-seq) data from 42 different tissues and stages, including various flower and fruit developmental stages. In addition, we generated eight additional RNA-seq data sets to represent tissues from ripening-stage receptacle fruit from yellow-colored and red-colored wild strawberry varieties. Differential gene expression analysis between these eight data sets provides additional information for understanding fruit-quality traits. Together, this work greatly facilitates the utility of the extensive transcriptome data for investigating strawberry flower and fruit development as well as fruit-quality traits.
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Affiliation(s)
- Charles Hawkins
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Julie Caruana
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Jiaming Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
- Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Chris Zawora
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Omar Darwish
- Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA
| | - Jun Wu
- Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Genome-scale DNA variant analysis and functional validation of a SNP underlying yellow fruit color in wild strawberry. Sci Rep 2016; 6:29017. [PMID: 27377763 PMCID: PMC4932534 DOI: 10.1038/srep29017] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 06/10/2016] [Indexed: 11/18/2022] Open
Abstract
Fragaria vesca is a species of diploid strawberry being developed as a model for the octoploid garden strawberry. This work sequenced and compared the genomes of three F. vesca accessions: ‘Hawaii 4′, ‘Rügen’, and ‘Yellow Wonder’. Genome-scale analyses of shared and distinct SNPs among these three accessions have revealed that ‘Rügen’ and ‘Yellow Wonder’ are more similar to each other than they are to ‘Hawaii 4’. Though all three accessions are inbred seven generations, each accession still possesses extensive heterozygosity, highlighting the inherent differences between individual plants even of the same accession. The identification of the impact of each SNP as well as the large number of Indel markers provides a foundation for locating candidate mutations underlying phenotypic variations among these F. vesca accessions and for mapping new mutations generated through forward genetics screens. Through systematic analysis of SNP variants affecting genes in anthocyanin biosynthesis and regulation, a candidate SNP in FveMYB10 was identified and then functionally confirmed to be responsible for the yellow color fruits made by many F. vesca accessions. As a whole, this study provides further resources for F. vesca and establishes a foundation for linking traits of economic importance to specific genes and variants.
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