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Goeckeritz CZ, Grabb C, Grumet R, Iezzoni AF, Hollender CA. Genetic factors acting prior to dormancy in sour cherry influence bloom time the following spring. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4428-4452. [PMID: 38602443 PMCID: PMC11263489 DOI: 10.1093/jxb/erae157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/10/2024] [Indexed: 04/12/2024]
Abstract
Understanding the process of Prunus species floral development is crucial for developing strategies to manipulate bloom time and prevent crop loss due to climate change. Here, we present a detailed examination of flower development from initiation until bloom for early- and late-blooming sour cherries (Prunus cerasus) from a population segregating for a major bloom time QTL on chromosome 4. Using a new staging system, we show floral buds from early-blooming trees were persistently more advanced than those from late-blooming siblings. A genomic DNA coverage analysis revealed the late-blooming haplotype of this QTL, k, is located on a subgenome originating from the late-blooming P. fruticosa progenitor. Transcriptome analyses identified many genes within this QTL as differentially expressed between early- and late-blooming trees during the vegetative-to-floral transition. From these, we identified candidate genes for the late bloom phenotype, including multiple transcription factors homologous to Reproductive Meristem B3 domain-containing proteins. Additionally, we determined that the basis of k in sour cherry is likely separate from candidate genes found in sweet cherry-suggesting several major regulators of bloom time are located on Prunus chromosome 4.
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Affiliation(s)
- Charity Z Goeckeritz
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
| | - Chloe Grabb
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
| | - Amy F Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
| | - Courtney A Hollender
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
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2
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Yuan Y, Zeng L, Kong D, Mao Y, Xu Y, Wang M, Zhao Y, Jiang CZ, Zhang Y, Sun D. Abscisic acid-induced transcription factor PsMYB306 negatively regulates tree peony bud dormancy release. PLANT PHYSIOLOGY 2024; 194:2449-2471. [PMID: 38206196 PMCID: PMC10980420 DOI: 10.1093/plphys/kiae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/08/2023] [Accepted: 12/02/2023] [Indexed: 01/12/2024]
Abstract
Bud dormancy is a crucial strategy for perennial plants to withstand adverse winter conditions. However, the regulatory mechanism of bud dormancy in tree peony (Paeonia suffruticosa) remains largely unknown. Here, we observed dramatically reduced and increased accumulation of abscisic acid (ABA) and bioactive gibberellins (GAs) GA1 and GA3, respectively, during bud endodormancy release of tree peony under prolonged chilling treatment. An Illumina RNA sequencing study was performed to identify potential genes involved in the bud endodormancy regulation in tree peony. Correlation matrix, principal component, and interaction network analyses identified a downregulated MYB transcription factor gene, PsMYB306, the expression of which positively correlated with 9-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (PsNCED3) expression. Protein modeling analysis revealed 4 residues within the R2R3 domain of PsMYB306 to possess DNA binding capability. Transcription of PsMYB306 was increased by ABA treatment. Overexpression of PsMYB306 in petunia (Petunia hybrida) inhibited seed germination and plant growth, concomitant with elevated ABA and decreased GA contents. Silencing of PsMYB306 accelerated cold-triggered tree peony bud burst and influenced the production of ABA and GAs and the expression of their biosynthetic genes. ABA application reduced bud dormancy release and transcription of ENT-KAURENOIC ACID OXIDASE 1 (PsKAO1), GA20-OXIDASE 1 (PsGA20ox1), and GA3-OXIDASE 1 (PsGA3ox1) associated with GA biosynthesis in PsMYB306-silenced buds. In vivo and in vitro binding assays confirmed that PsMYB306 specifically transactivated the promoter of PsNCED3. Silencing of PsNCED3 also promoted bud break and growth. Altogether, our findings suggest that PsMYB306 negatively modulates cold-induced bud endodormancy release by regulating ABA production.
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Affiliation(s)
- Yanping Yuan
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lingling Zeng
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Derong Kong
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanxiang Mao
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yingru Xu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meiling Wang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yike Zhao
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- Crops Pathology and Genetics Research Unit, USDA-ARS, Davis, CA 95616, USA
| | - Yanlong Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Daoyang Sun
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
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Song GQ, Liu Z, Zhong GY. Regulatory frameworks involved in the floral induction, formation and developmental programming of woody horticultural plants: a case study on blueberries. FRONTIERS IN PLANT SCIENCE 2024; 15:1336892. [PMID: 38410737 PMCID: PMC10894941 DOI: 10.3389/fpls.2024.1336892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
Flowering represents a crucial stage in the life cycles of plants. Ensuring strong and consistent flowering is vital for maintaining crop production amidst the challenges presented by climate change. In this review, we summarized key recent efforts aimed at unraveling the complexities of plant flowering through genetic, genomic, physiological, and biochemical studies in woody species, with a special focus on the genetic control of floral initiation and activation in woody horticultural species. Key topics covered in the review include major flowering pathway genes in deciduous woody plants, regulation of the phase transition from juvenile to adult stage, the roles of CONSTANS (CO) and CO-like gene and FLOWERING LOCUS T genes in flower induction, the floral regulatory role of GA-DELLA pathway, and the multifunctional roles of MADS-box genes in flowering and dormancy release triggered by chilling. Based on our own research work in blueberries, we highlighted the central roles played by two key flowering pathway genes, FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1, which regulate floral initiation and activation (dormancy release), respectively. Collectively, our survey shows both the conserved and diverse aspects of the flowering pathway in annual and woody plants, providing insights into the potential molecular mechanisms governing woody plants. This paves the way for enhancing the resilience and productivity of fruit-bearing crops in the face of changing climatic conditions, all through the perspective of genetic interventions.
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Affiliation(s)
- Guo-Qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Zongrang Liu
- USDA Agricultural Research Services, Appalachian Fruit Research Station, Kearneysville, WV, United States
| | - Gan-Yuan Zhong
- USDA Agricultural Research Services, Grape Genetics Research Unit and Plant Genetic Resources Unit, Geneva, NY, United States
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Chu X, Wang M, Fan Z, Li J, Yin H. Molecular Mechanisms of Seasonal Gene Expression in Trees. Int J Mol Sci 2024; 25:1666. [PMID: 38338945 PMCID: PMC10855862 DOI: 10.3390/ijms25031666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
In trees, the annual cycling of active and dormant states in buds is closely regulated by environmental factors, which are of primary significance to their productivity and survival. It has been found that the parallel or convergent evolution of molecular pathways that respond to day length or temperature can lead to the establishment of conserved periodic gene expression patterns. In recent years, it has been shown in many woody plants that change in annual rhythmic patterns of gene expression may underpin the adaptive evolution in forest trees. In this review, we summarize the progress on the molecular mechanisms of seasonal regulation on the processes of shoot growth, bud dormancy, and bud break in response to day length and temperature factors. We focus on seasonal expression patterns of genes involved in dormancy and their associated epigenetic modifications; the seasonal changes in the extent of modifications, such as DNA methylation, histone acetylation, and histone methylation, at dormancy-associated loci have been revealed for their actions on gene regulation. In addition, we provide an outlook on the direction of research on the annual cycle of tree growth under climate change.
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Affiliation(s)
- Xian Chu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Minyan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| | - Zhengqi Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
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Liu P, Liu R, Xu Y, Zhang C, Niu Q, Lang Z. DNA cytosine methylation dynamics and functional roles in horticultural crops. HORTICULTURE RESEARCH 2023; 10:uhad170. [PMID: 38025976 PMCID: PMC10660380 DOI: 10.1093/hr/uhad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/20/2023] [Indexed: 12/01/2023]
Abstract
Methylation of cytosine is a conserved epigenetic modification that maintains the dynamic balance of methylation in plants under the regulation of methyltransferases and demethylases. In recent years, the study of DNA methylation in regulating the growth and development of plants and animals has become a key area of research. This review describes the regulatory mechanisms of DNA cytosine methylation in plants. It summarizes studies on epigenetic modifications of DNA methylation in fruit ripening, development, senescence, plant height, organ size, and under biotic and abiotic stresses in horticultural crops. The review provides a theoretical basis for understanding the mechanisms of DNA methylation and their relevance to breeding, genetic improvement, research, innovation, and exploitation of new cultivars of horticultural crops.
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Affiliation(s)
- Peipei Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Ruie Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaping Xu
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Caixi Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingfeng Niu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhaobo Lang
- Institute of Advanced Biotechnology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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Karami O, Mueller-Roeber B, Rahimi A. The central role of stem cells in determining plant longevity variation. PLANT COMMUNICATIONS 2023; 4:100566. [PMID: 36840355 PMCID: PMC10504568 DOI: 10.1016/j.xplc.2023.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/10/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Vascular plants display a huge variety of longevity patterns, from a few weeks for several annual species up to thousands of years for some perennial species. Understanding how longevity variation is structured has long been considered a fundamental aspect of the life sciences in view of evolution, species distribution, and adaptation to diverse environments. Unlike animals, whose organs are typically formed during embryogenesis, vascular plants manage to extend their life by continuously producing new tissues and organs in apical and lateral directions via proliferation of stem cells located within specialized tissues called meristems. Stem cells are the main source of plant longevity. Variation in plant longevity is highly dependent on the activity and fate identity of stem cells. Multiple developmental factors determine how stem cells contribute to variation in plant longevity. In this review, we provide an overview of the genetic mechanisms, hormonal signaling, and environmental factors involved in controlling plant longevity through long-term maintenance of stem cell fate identity.
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Affiliation(s)
- Omid Karami
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam, Germany
| | - Arezoo Rahimi
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
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Sapkota S, Salem M, Jahed KR, Artlip TS, Sherif SM. From endodormancy to ecodormancy: the transcriptional landscape of apple floral buds. FRONTIERS IN PLANT SCIENCE 2023; 14:1194244. [PMID: 37521930 PMCID: PMC10375413 DOI: 10.3389/fpls.2023.1194244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
This study endeavors to explore the transcriptomic profiles of two apple cultivars, namely, 'Honeycrisp' and 'Cripps Pink,' which represent late and early-blooming cultivars, respectively. Using RNA-sequencing technology, we analyzed floral bud samples collected at five distinct time intervals during both endodormancy and ecodormancy. To evaluate the transcriptomic profiles of the 30 sequenced samples, we conducted principal component analysis (PCA). PC1 explained 43% of the variance, separating endodormancy and ecodormancy periods, while PC2 explained 16% of the variance, separating the two cultivars. The number of differentially expressed genes (DEGs) increased with endodormancy progression and remained elevated during ecodormancy. The majority of DEGs were unique to a particular time point, with only a few overlapping among or between the time points. This highlights the temporal specificity of gene expression during the dormancy transition and emphasizes the importance of sampling at multiple time points to capture the complete transcriptomic dynamics of this intricate process. We identified a total of 4204 upregulated and 7817 downregulated DEGs in the comparison of endodormancy and ecodormancy, regardless of cultivar, and 2135 upregulated and 2413 downregulated DEGs in the comparison of 'Honeycrisp' versus 'Cripps Pink,' regardless of dormancy stage. Furthermore, we conducted a co-expression network analysis to gain insight into the coordinated gene expression profiles across different time points, dormancy stages, and cultivars. This analysis revealed the most significant module (ME 14), correlated with 1000 GDH and consisting of 1162 genes. The expression of the genes within this module was lower in 'Honeycrisp' than in 'Cripps Pink.' The top 20 DEGs identified in ME 14 were primarily related to jasmonic acid biosynthesis and signaling, lipid metabolism, oxidation-reduction, and transmembrane transport activity. This suggests a plausible role for these pathways in governing bud dormancy and flowering time in apple.
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Affiliation(s)
- Sangeeta Sapkota
- Virginia Agricultural Research and Extension Center, Virginia Tech, Winchester, VA, United States
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Mohamed Salem
- Department of Statistics, Virginia Tech, Blacksburg, VA, United States
| | - Khalil R. Jahed
- Virginia Agricultural Research and Extension Center, Virginia Tech, Winchester, VA, United States
| | - Timothy S. Artlip
- Appalachian Fruit Research Station, United States Department of Agriculture – Agricultural Research Service, Kearneysville, WV, United States
| | - Sherif M. Sherif
- Virginia Agricultural Research and Extension Center, Virginia Tech, Winchester, VA, United States
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Small RNA and Degradome Sequencing in Floral Bud Reveal Roles of miRNAs in Dormancy Release of Chimonanthus praecox. Int J Mol Sci 2023; 24:ijms24044210. [PMID: 36835618 PMCID: PMC9964840 DOI: 10.3390/ijms24044210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Chimonanthus praecox (wintersweet) is highly valued ornamentally and economically. Floral bud dormancy is an important biological characteristic in the life cycle of wintersweet, and a certain period of chilling accumulation is necessary for breaking floral bud dormancy. Understanding the mechanism of floral bud dormancy release is essential for developing measures against the effects of global warming. miRNAs play important roles in low-temperature regulation of flower bud dormancy through mechanisms that are unclear. In this study, small RNA and degradome sequencing were performed for wintersweet floral buds in dormancy and break stages for the first time. Small RNA sequencing identified 862 known and 402 novel miRNAs; 23 differentially expressed miRNAs (10 known and 13 novel) were screened via comparative analysis of breaking and other dormant floral bud samples. Degradome sequencing identified 1707 target genes of 21 differentially expressed miRNAs. The annotations of the predicted target genes showed that these miRNAs were mainly involved in the regulation of phytohormone metabolism and signal transduction, epigenetic modification, transcription factors, amino acid metabolism, and stress response, etc., during the dormancy release of wintersweet floral buds. These data provide an important foundation for further research on the mechanism of floral bud dormancy in wintersweet.
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Zhao K, Zhou Y, Zheng Y, Zheng RY, Hu M, Tong Y, Luo X, Zhang Y, Shen ML. The collaborative mode by PmSVPs and PmDAMs reveals neofunctionalization in the switch of the flower bud development and dormancy for Prunus mume. FRONTIERS IN PLANT SCIENCE 2022; 13:1023628. [PMID: 36561463 PMCID: PMC9763448 DOI: 10.3389/fpls.2022.1023628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
Prunus mume (Rosaceae, Prunoideae) serves as an excellent ornamental woody plant with a large-temperature-range cultivation scope. Its flower buds require a certain low temperature to achieve flowering circulation. Thus, it is important to delve into the processes of flower bud differentiation and dormancy, which affected its continuous flowering. These processes are generally considered as regulation by the MADS-box homologs, SHORT VEGETATIVE PHASE (SVP), and DORMANCY-ASSOCIATED MADS-BOX (DAM). However, a precise model on their interdependence and specific function, when acting as a complex in the flower development of P. mume, is needed. Therefore, this study highlighted the integral roles of PmDAMs and PmSVPs in flower organ development and dormancy cycle. The segregation of PmDAMs and PmSVPs in a different cluster suggested distinct functions and neofunctionalization. The expression pattern and yeast two-hybrid assays jointly revealed that eight genes were involved in the floral organ development stages, with PmDAM1 and PmDAM5 specifically related to prolificated flower formation. PmSVP1-2 mingled in the protein complex in bud dormancy stages with PmDAMs. Finally, we proposed the hypothesis that PmSVP1 and PmSVP2 could combine with PmDAM1 to have an effect on flower organogenesis and interact with PmDAM5 and PmDAM6 to regulate flower bud dormancy. These findings could help expand the current molecular mechanism based on MADS-box genes during flower bud development and dormancy.
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Affiliation(s)
- Kai Zhao
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yuzhen Zhou
- College of Landscape Architecture, Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center at College of Landscape Architecture, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Zheng
- College of Landscape Architecture, Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center at College of Landscape Architecture, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rui-yue Zheng
- College of Landscape Architecture, Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center at College of Landscape Architecture, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meijuan Hu
- College of Landscape Architecture, Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center at College of Landscape Architecture, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Tong
- College of Landscape Architecture, Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center at College of Landscape Architecture, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xianmei Luo
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yangting Zhang
- College of Landscape Architecture, Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center at College of Landscape Architecture, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ming-li Shen
- College of Life Sciences, Fujian Normal University, Fuzhou, China
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Quesada-Traver C, Lloret A, Carretero-Paulet L, Badenes ML, Ríos G. Evolutionary origin and functional specialization of Dormancy-Associated MADS box (DAM) proteins in perennial crops. BMC PLANT BIOLOGY 2022; 22:473. [PMID: 36199018 PMCID: PMC9533583 DOI: 10.1186/s12870-022-03856-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Bud dormancy is a phenological adaptation of temperate perennials that ensures survival under winter temperature conditions by ceasing growth and increasing cold hardiness. SHORT VEGETATIVE PHASE (SVP)-like factors, and particularly a subset of them named DORMANCY-ASSOCIATED MADS-BOX (DAM), are master regulators of bud dormancy in perennials, prominently Rosaceae crops widely adapted to varying environmental conditions. RESULTS SVP-like proteins from recently sequenced Rosaceae genomes were identified and characterized using sequence, phylogenetic and synteny analysis tools. SVP-like proteins clustered in three clades (SVP1-3), with known DAM proteins located within SVP2 clade, which also included Arabidopsis AGAMOUS-LIKE 24 (AthAGL24). A more detailed study on these protein sequences led to the identification of a 15-amino acid long motif specific to DAM proteins, which affected protein heteromerization properties by yeast two-hybrid system in peach PpeDAM6, and the unexpected finding of predicted DAM-like genes in loquat, an evergreen species lacking winter dormancy. DAM gene expression in loquat trees was studied by quantitative PCR, associating with inflorescence development and growth in varieties with contrasting flowering behaviour. CONCLUSIONS Phylogenetic, synteny analyses and heterologous overexpression in the model plant Arabidopsis thaliana supported three major conclusions: 1) DAM proteins might have emerged from the SVP2 clade in the Amygdaloideae subfamily of Rosaceae; 2) a short DAM-specific motif affects protein heteromerization, with a likely effect on DAM transcriptional targets and other functional features, providing a sequence signature for the DAM group of dormancy factors; 3) in agreement with other recent studies, DAM associates with inflorescence development and growth, independently of the dormancy habit.
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Affiliation(s)
- Carles Quesada-Traver
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, Km 10.7, 46113 Moncada, Valencia Spain
| | - Alba Lloret
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, Km 10.7, 46113 Moncada, Valencia Spain
| | - Lorenzo Carretero-Paulet
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120 Almería, Spain
- Centro de Investigación de Colecciones Científicas de la Universidad de Almería (CECOUAL), University of Almería, Ctra. Sacramento s/n, 04120 Almería, Spain
| | - María Luisa Badenes
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, Km 10.7, 46113 Moncada, Valencia Spain
| | - Gabino Ríos
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, Km 10.7, 46113 Moncada, Valencia Spain
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11
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Sun L, Nie T, Chen Y, Yin Z. From Floral Induction to Blooming: The Molecular Mysteries of Flowering in Woody Plants. Int J Mol Sci 2022; 23:ijms231810959. [PMID: 36142871 PMCID: PMC9500781 DOI: 10.3390/ijms231810959] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 12/04/2022] Open
Abstract
Flowering is a pivotal developmental process in response to the environment and determines the start of a new life cycle in plants. Woody plants usually possess a long juvenile nonflowering phase followed by an adult phase with repeated flowering cycles. The molecular mechanism underlying flowering regulation in woody plants is believed to be much more complex than that in annual herbs. In this review, we briefly describe the successive but distinct flowering processes in perennial trees, namely the vegetative phase change, the floral transition, floral organogenesis, and final blooming, and summarize in detail the most recent advances in understanding how woody plants regulate flowering through dynamic gene expression. Notably, the florigen gene FLOWERING LOCUS T(FT) and its antagonistic gene TERMINAL FLOWER 1 (TFL1) seem to play a central role in various flowering transition events. Flower development in different taxa requires interactions between floral homeotic genes together with AGL6 conferring floral organ identity. Finally, we illustrate the issues and corresponding measures of flowering regulation investigation. It is of great benefit to the future study of flowering in perennial trees.
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Affiliation(s)
- Liyong Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Department of Biology, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Tangjie Nie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yao Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zengfang Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-025-85427316
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12
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Small RNA Differential Expression Analysis Reveals miRNAs Involved in Dormancy Progression in Sweet Cherry Floral Buds. PLANTS 2022; 11:plants11182396. [PMID: 36145795 PMCID: PMC9500734 DOI: 10.3390/plants11182396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022]
Abstract
In sweet cherry (Prunus avium), as in other temperate woody perennials, bud dormancy allows for survival in adverse environmental conditions during winter. During this process, environmental signals such as short days and/or low temperatures trigger internal signals that enable buds to become tolerant to the cold. The process involves tracking chilling units up to chilling the requirement fulfillment to resume growth, a transition involving transcriptional regulation, metabolic signaling, and epigenetic-related regulatory events. Massive sequencing of small RNAs was performed to identify miRNAs involved in sweet cherry dormancy by comparing their expression in field (regular seasonal) and controlled non-stop (continuous) chilling conditions. miRNAs highlighted by sequencing were validated using specific stem-loop PCR quantification, confirming expression patterns for known miRNAs such as miR156e, miR166c, miR172d, miR391, miR482c, and miR535b, as well as for newly proposed miRNAs. In silico prediction of the target genes was used to construct miRNA/target gene nodes. In particular, the involvement of the sweet cherry version for the miR156/SQUAMOSA PROMOTER-BINDING-LIKE PROTEIN genes whose expression was opposite in the two conditions suggests their involvement on dormancy regulation in sweet cherry. miRNA levels indicate that the regulation of stress-related genes and hormone synthesis modulates the expression of calcium metabolism and cell development-associated genes. Understanding the regulatory networks involved in sweet cherry dormancy, particularly in the context of miRNA involvement, represents the first step in the development of new agricultural strategies that may help overcome the increasing challenges presented by global climate change.
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13
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Morgan BL, Donohue K. Parental
DNA
methylation influences plasticity of early offspring traits, but offspring
DNA
methylation influences trait plasticity throughout life. Ecol Evol 2022. [DOI: 10.1002/ece3.9224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Britany L. Morgan
- University Program in Ecology Duke University Durham North Carolina USA
- Center for Agricultural Synthetic Biology University of Tennessee Knoxville Tennessee USA
| | - Kathleen Donohue
- University Program in Ecology Duke University Durham North Carolina USA
- Biology Department Duke University Durham North Carolina USA
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14
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D’Amico-Willman KM, Ouma WZ, Meulia T, Sideli GM, Gradziel TM, Fresnedo-Ramírez J. Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar 'Nonpareil'. G3 (BETHESDA, MD.) 2022; 12:jkac065. [PMID: 35325123 PMCID: PMC9073694 DOI: 10.1093/g3journal/jkac065] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/19/2022] [Indexed: 01/27/2023]
Abstract
Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including 'Nonpareil,' which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for 'Nonpareil' is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 571X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 49,321 putative genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Furthermore, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of noninfectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several almond tissues, including leaf, flower, endocarp, mesocarp, exocarp, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted % methylation and chromosome-level methylation enrichment.
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Affiliation(s)
| | | | - Tea Meulia
- Molecular and Cellular Imaging Center, The Ohio State University, Wooster, OH 44691, USA
| | - Gina M Sideli
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Thomas M Gradziel
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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15
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Herrera S, Lora J, Fadón E, Hedhly A, Alonso JM, Hormaza JI, Rodrigo J. Male Meiosis as a Biomarker for Endo- to Ecodormancy Transition in Apricot. FRONTIERS IN PLANT SCIENCE 2022; 13:842333. [PMID: 35463418 PMCID: PMC9021868 DOI: 10.3389/fpls.2022.842333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Dormancy is an adaptive strategy in plants to survive under unfavorable climatic conditions during winter. In temperate regions, most fruit trees need exposure to a certain period of low temperatures to overcome endodormancy. After endodormancy release, exposure to warm temperatures is needed to flower (ecodormancy). Chilling and heat requirements are genetically determined and, therefore, are specific for each species and cultivar. The lack of sufficient winter chilling can cause failures in flowering and fruiting, thereby compromising yield. Thus, the knowledge of the chilling and heat requirements is essential to optimize cultivar selection for different edaphoclimatic conditions. However, the lack of phenological or biological markers linked to the dormant and forcing periods makes it difficult to establish the end of endodormancy. This has led to indirect estimates that are usually not valid in different agroclimatic conditions. The increasing number of milder winters caused by climatic change and the continuous release of new cultivars emphasize the necessity of a proper biological marker linked to the endo- to ecodormancy transition for an accurate estimation of the agroclimatic requirements (AR) of each cultivar. In this work, male meiosis is evaluated as a biomarker to determine endodormancy release and to estimate both chilling and heat requirements in apricot. For this purpose, pollen development was characterized histochemically in 20 cultivars over 8 years, and the developmental stages were related to dormancy. Results were compared to three approaches that indirectly estimate the breaking of dormancy: an experimental methodology by evaluating bud growth in shoots collected periodically throughout the winter months and transferred to forcing chambers over 3 years, and two statistical approaches that relate seasonal temperatures and blooming dates in a series of 11-20 years by correlation and partial least square regression. The results disclose that male meiosis is a possible biomarker to determine the end of endodormancy and estimate AR in apricot.
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Affiliation(s)
- Sara Herrera
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Departamento de Ciencia Vegetal, Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Jorge Lora
- Subtropical Fruit Crops Department, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM La Mayora-CSIC-UMA), Málaga, Spain
| | - Erica Fadón
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Departamento de Ciencia Vegetal, Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Afif Hedhly
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Departamento de Ciencia Vegetal, Zaragoza, Spain
| | - José Manuel Alonso
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Departamento de Ciencia Vegetal, Zaragoza, Spain
| | - José I. Hormaza
- Subtropical Fruit Crops Department, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM La Mayora-CSIC-UMA), Málaga, Spain
| | - Javier Rodrigo
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Departamento de Ciencia Vegetal, Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
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16
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Voogd C, Brian LA, Wu R, Wang T, Allan AC, Varkonyi-Gasic E. A MADS-box gene with similarity to FLC is induced by cold and correlated with epigenetic changes to control budbreak in kiwifruit. THE NEW PHYTOLOGIST 2022; 233:2111-2126. [PMID: 34907541 DOI: 10.1111/nph.17916] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Temperate perennials require exposure to chilling temperatures to resume growth in the following spring. Growth and dormancy cycles are controlled by complex genetic regulatory networks and are governed by epigenetic mechanisms, but the specific genes and mechanisms remain poorly understood. To understand how seasonal changes and chilling regulate dormancy and growth in the woody perennial vine kiwifruit (Ac, Actinidia chinensis), a transcriptome study of kiwifruit buds in the field and controlled conditions was performed. A MADS-box gene with homology to Arabidopsis FLOWERING LOCUS C (FLC) was identified and characterized. Elevated expression of AcFLC-like (AcFLCL) was detected during bud dormancy and chilling. A long noncoding (lnc) antisense transcript with an expression pattern opposite to AcFLCL and shorter sense noncoding RNAs were identified. Chilling induced an increase in trimethylation of lysine-4 of histone H3 (H3K4me3) in the 5' end of the gene, indicating multiple layers of epigenetic regulation in response to cold. Overexpression of AcFLCL in kiwifruit gave rise to plants with earlier budbreak, whilst gene editing using CRISPR-Cas9 resulted in transgenic lines with substantially delayed budbreak, suggesting a role in activation of growth. These results have implications for the future management and breeding of perennials for resilience to changing climate.
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Affiliation(s)
- Charlotte Voogd
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Lara A Brian
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Rongmei Wu
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
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17
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Lempe J, Peil A, Flachowsky H. Time-Resolved Analysis of Candidate Gene Expression and Ambient Temperature During Bud Dormancy in Apple. FRONTIERS IN PLANT SCIENCE 2022; 12:803341. [PMID: 35111181 PMCID: PMC8802299 DOI: 10.3389/fpls.2021.803341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Winter dormancy - a period of low metabolic activity and no visible growth - appears as an adaptation to harsh winter conditions and can be divided into different phases. It is tightly controlled by environmental cues, with ambient temperature playing a major role. During endodormancy, a cultivar-specific amount of cold needs to be perceived, and during ecodormancy, heat hours accumulate before bud burst and anthesis in spring. Expression analysis, performed in several key fruit tree species, proved to be very useful in elucidating the molecular control of onset and release of dormancy. However, the time resolution of these experiments has been limited. Therefore, in this study, dense time-series expression analysis was conducted for 40 candidate genes involved in dormancy control, under the cool-temperate climate conditions in Dresden. Samples were taken from the cultivars 'Pinova' and 'Gala,' which differ in flowering time. The set of candidate genes included well-established dormancy genes such as DAM genes, MdFLC-like, MdICE1, MdPRE 1, and MdPIF4. Furthermore, we tested genes from dormancy-associated pathways including the brassinosteroid, gibberellic acid, abscisic acid (ABA), cytokinin response, and respiratory stress pathways. The expression patterns of well-established dormancy genes were confirmed and could be associated with specific dormancy phases. In addition, less well-known transcription factors and genes of the ABA signaling pathway showed associations with dormancy progression. The three ABA signaling genes HAB1_chr15, HAI3, and ABF2 showed a local minimum of gene expression in proximity of the endodormancy to ecodormancy transition. The number of sampling points allowed us to correlate expression values with temperature data, which revealed significant correlations of ambient temperature with the expression of the Malus domestica genes MdICE1, MdPIF4, MdFLC-like, HAB1chr15, and the type-B cytokinin response regulator BRR9. Interestingly, the slope of the linear correlation of temperature with the expression of MdPIF4 differed between cultivars. Whether the strength of inducibility of MdPIF4 expression by low temperature differs between the 'Pinova' and 'Gala' alleles needs to be tested further.
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18
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Fang ZZ, Lin-Wang K, Dai H, Zhou DR, Jiang CC, Espley RV, Deng C, Lin YJ, Pan SL, Ye XF. The genome of low-chill Chinese plum 'Sanyueli' (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds. Mol Ecol Resour 2022; 22:1919-1938. [PMID: 35032338 DOI: 10.1111/1755-0998.13585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 10/19/2022]
Abstract
Chinese plum (Prunus salicina Lindl.) is a stone fruit that belongs to the Prunus genus and plays an important role in the global production of plum. In this study, we report the genome sequence of the Chinese plum 'Sanyueli', which is known to have a low-chill requirement for flower bud break. The assembled genome size was 282.38 Mb, with a contig N50 of 1.37 Mb. Over 99% of the assembly was anchored to eight pseudochromosomes, with a scaffold N50 of 34.46Mb. A total of 29,708 protein-coding genes were predicted from the genome and 46.85% (132.32 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in 'Sanyueli' revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of 'Sanyueli' was significantly lower than that in the dormant flower buds of the high chill requiring 'Furongli' plum. In addition, the expression of PsDAM6 was repressed by chilling treatment. The genome sequence of 'Sanyueli' plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and it is also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum.
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Affiliation(s)
- Zhi-Zhen Fang
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China.,Fujian Engineering and Technology Research Center for Deciduous Fruit Trees, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert Research Centre, Private Bag, Auckland, 92169, New Zealand
| | - He Dai
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Dan-Rong Zhou
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China.,Fujian Engineering and Technology Research Center for Deciduous Fruit Trees, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
| | - Cui-Cui Jiang
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China.,Fujian Engineering and Technology Research Center for Deciduous Fruit Trees, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert Research Centre, Private Bag, Auckland, 92169, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert Research Centre, Private Bag, Auckland, 92169, New Zealand
| | - Yan-Juan Lin
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China.,Fujian Engineering and Technology Research Center for Deciduous Fruit Trees, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
| | - Shao-Lin Pan
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China.,Fujian Engineering and Technology Research Center for Deciduous Fruit Trees, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
| | - Xin-Fu Ye
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China.,Fujian Engineering and Technology Research Center for Deciduous Fruit Trees, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
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19
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Garighan J, Dvorak E, Estevan J, Loridon K, Huettel B, Sarah G, Farrera I, Leclercq J, Grynberg P, Coiti Togawa R, Mota do Carmo Costa M, Costes E, Andrés F. The Identification of Small RNAs Differentially Expressed in Apple Buds Reveals a Potential Role of the Mir159-MYB Regulatory Module during Dormancy. PLANTS (BASEL, SWITZERLAND) 2021; 10:2665. [PMID: 34961136 PMCID: PMC8703471 DOI: 10.3390/plants10122665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022]
Abstract
Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warmer temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of 17 micro RNAs (miRNAs) that change their pattern of expression in apple buds during dormancy. Furthermore, the functional analysis of their predicted target genes suggests a main role of the 17 miRNAs in phenylpropanoid biosynthesis, gene regulation, plant development and growth, and response to stimulus. Finally, we studied the conservation of the Arabidopsis thaliana regulatory miR159-MYB module in apple in the context of the plant hormone abscisic acid homeostasis.
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Affiliation(s)
- Julio Garighan
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Etienne Dvorak
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Joan Estevan
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Karine Loridon
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Bruno Huettel
- Genome Centre, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany;
| | - Gautier Sarah
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Isabelle Farrera
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Julie Leclercq
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
- UMR AGAP Institute, CIRAD, F-34398 Montpellier, France
| | - Priscila Grynberg
- Bioinformatica Laboratory, Embrapa Recursos Genéticos e Biotecnologia—Cenargen, Brasilia 02372, Brazil; (P.G.); (R.C.T.); (M.M.d.C.C.)
| | - Roberto Coiti Togawa
- Bioinformatica Laboratory, Embrapa Recursos Genéticos e Biotecnologia—Cenargen, Brasilia 02372, Brazil; (P.G.); (R.C.T.); (M.M.d.C.C.)
| | - Marcos Mota do Carmo Costa
- Bioinformatica Laboratory, Embrapa Recursos Genéticos e Biotecnologia—Cenargen, Brasilia 02372, Brazil; (P.G.); (R.C.T.); (M.M.d.C.C.)
| | - Evelyne Costes
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Fernando Andrés
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
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20
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Pan W, Liang J, Sui J, Li J, Liu C, Xin Y, Zhang Y, Wang S, Zhao Y, Zhang J, Yi M, Gazzarrini S, Wu J. ABA and Bud Dormancy in Perennials: Current Knowledge and Future Perspective. Genes (Basel) 2021; 12:genes12101635. [PMID: 34681029 PMCID: PMC8536057 DOI: 10.3390/genes12101635] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
Bud dormancy is an evolved trait that confers adaptation to harsh environments, and affects flower differentiation, crop yield and vegetative growth in perennials. ABA is a stress hormone and a major regulator of dormancy. Although the physiology of bud dormancy is complex, several advancements have been achieved in this field recently by using genetics, omics and bioinformatics methods. Here, we review the current knowledge on the role of ABA and environmental signals, as well as the interplay of other hormones and sucrose, in the regulation of this process. We also discuss emerging potential mechanisms in this physiological process, including epigenetic regulation.
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Affiliation(s)
- Wenqiang Pan
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Jiahui Liang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Juanjuan Sui
- Biology and Food Engineering College, Fuyang Normal University, Fuyang 236037, China;
| | - Jingru Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Chang Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Yin Xin
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Yanmin Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Shaokun Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Yajie Zhao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Jie Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350001, China
| | - Mingfang Yi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto, Toronto, ON M1C 1A4, Canada;
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
- Correspondence:
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21
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Hillmann L, Elsysy M, Goeckeritz C, Hollender C, Rothwell N, Blanke M, Einhorn T. Preanthesis changes in freeze resistance, relative water content, and ovary growth preempt bud phenology and signify dormancy release of sour cherry floral buds. PLANTA 2021; 254:74. [PMID: 34529136 DOI: 10.1007/s00425-021-03722-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Growing degree hours (GDH) predicted floral bud development of 'Montmorency' sour cherry and explained changes in lethal temperatures (LT50) that preempted any visible changes in bud phenology. The gradual warming during late winter and early spring promotes floral bud development and, concomitantly, the de-acclimation of Prunus sp. flowers. In fact, once ecodormancy releases, an approximate 20 °C loss of hardiness occurs prior to any distinguishable changes in external bud phenology. The aim of the following work was to characterize the physiological changes of 'Montmorency' sour cherry floral buds as they transition from endo- and ecodormancy and resume growth, and to determine whether physiological and anatomical characteristics within the buds preempt or signify dormancy release to enable a better prediction of freeze susceptibility. Here, we present a developmental timeline of the preanthesis changes of 'Montmorency' floral buds, ovaries and anthers over 2 years following their completion of chilling and relate these changes to growing degree hours (GDH) and the lethal temperature (LT50) of flowers. Changes in bud dry weight (DW), fresh weight (FW), volume, and external phenology stage including the percentage of green color development of bud scales were predicted by heat accumulation but were not early predictors of the increasing freeze susceptibility of pistils. Between endodormancy and green tip stage, ovary volume increased nearly threefold and relative water content (RWC) increased from ~ 45 to 70% in both years. A linear mixed regression model indicated that RWC and the interaction between RWC and ovary growth were significant predictors of LT50. Importantly, the loss of ~ 20 °C of freeze resistance occurred between 45 and 57% RWC and preceded any detectable changes in bud phenology. Microsporogenesis was observed after dormancy release when measurable changes in the ovary and bud RWC had already occurred. A GDH model estimated freeze sensitivity of pistils and explained 93% of the variation in LT50 during preanthesis development. A simple GDH model to predict critical freeze temperature of pistils should aid producers to manage frost protection.
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Affiliation(s)
- Laura Hillmann
- Department of Horticulture, Michigan State University, Plant and Soil Sciences Bldg., 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Mokhles Elsysy
- Department of Horticulture, Michigan State University, Plant and Soil Sciences Bldg., 1066 Bogue Street, East Lansing, MI, 48824, USA
- Department of Pomology, College of Agriculture, Assiut University, Assiut, 71515, Egypt
| | - Charity Goeckeritz
- Department of Horticulture, Michigan State University, Plant and Soil Sciences Bldg., 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Courtney Hollender
- Department of Horticulture, Michigan State University, Plant and Soil Sciences Bldg., 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Nikki Rothwell
- Northwest Michigan Horticultural Research Center, Michigan State University, 6686 S. Center Highway, Traverse City, MI, USA
| | - Michael Blanke
- Rheinische-Friedrich-Wilhelms-Universität Bonn, INRES Gartenbauwissenschaft, Auf dem Huegel 6, Bonn, Germany
| | - Todd Einhorn
- Department of Horticulture, Michigan State University, Plant and Soil Sciences Bldg., 1066 Bogue Street, East Lansing, MI, 48824, USA.
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22
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Calle A, Grimplet J, Le Dantec L, Wünsch A. Identification and Characterization of DAMs Mutations Associated With Early Blooming in Sweet Cherry, and Validation of DNA-Based Markers for Selection. FRONTIERS IN PLANT SCIENCE 2021; 12:621491. [PMID: 34305957 PMCID: PMC8295754 DOI: 10.3389/fpls.2021.621491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/06/2021] [Indexed: 06/13/2023]
Abstract
Dormancy release and bloom time of sweet cherry cultivars depend on the environment and the genotype. The knowledge of these traits is essential for cultivar adaptation to different growing areas, and to ensure fruit set in the current climate change scenario. In this work, the major sweet cherry bloom time QTL qP-BT1.1 m (327 Kbs; Chromosome 1) was scanned for candidate genes in the Regina cv genome. Six MADS-box genes (PavDAMs), orthologs to peach and Japanese apricot DAMs, were identified as candidate genes for bloom time regulation. The complete curated genomic structure annotation of these genes is reported. To characterize PavDAMs intra-specific variation, genome sequences of cultivars with contrasting chilling requirements and bloom times (N = 13), were then mapped to the 'Regina' genome. A high protein sequence conservation (98.8-100%) was observed. A higher amino acid variability and several structural mutations were identified in the low-chilling and extra-early blooming cv Cristobalina. Specifically, a large deletion (694 bp) upstream of PavDAM1, and various INDELs and SNPs in contiguous PavDAM4 and -5 UTRs were identified. PavDAM1 upstream deletion in 'Cristobalina' revealed the absence of several cis-acting motifs, potentially involved in PavDAMs expression. Also, due to this deletion, a non-coding gene expressed in late-blooming 'Regina' seems truncated in 'Cristobalina'. Additionally, PavDAM4 and -5 UTRs mutations revealed different splicing variants between 'Regina' and 'Cristobalina' PavDAM5. The results indicate that the regulation of PavDAMs expression and post-transcriptional regulation in 'Cristobalina' may be altered due to structural mutations in regulatory regions. Previous transcriptomic studies show differential expression of PavDAM genes during dormancy in this cultivar. The results indicate that 'Cristobalina' show significant amino acid differences, and structural mutations in PavDAMs, that correlate with low-chilling and early blooming, but the direct implication of these mutations remains to be determined. To complete the work, PCR markers designed for the detection of 'Cristobalina' structural mutations in PavDAMs, were validated in an F2 population and a set of cultivars. These PCR markers are useful for marker-assisted selection of early blooming seedlings, and probably low-chilling, from 'Cristobalina', which is a unique breeding source for these traits.
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Affiliation(s)
- Alejandro Calle
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, CITA-Universidad de Zaragoza, Zaragoza, Spain
| | - Jérôme Grimplet
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, CITA-Universidad de Zaragoza, Zaragoza, Spain
| | - Loïck Le Dantec
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Villenave d'Ornon, France
| | - Ana Wünsch
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, CITA-Universidad de Zaragoza, Zaragoza, Spain
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23
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Rothkegel K, Espinoza A, Sanhueza D, Lillo-Carmona V, Riveros A, Campos-Vargas R, Meneses C. Identification of DNA Methylation and Transcriptomic Profiles Associated With Fruit Mealiness in Prunus persica (L.) Batsch. FRONTIERS IN PLANT SCIENCE 2021; 12:684130. [PMID: 34178003 PMCID: PMC8222998 DOI: 10.3389/fpls.2021.684130] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 05/27/2023]
Abstract
Peach (Prunus persica) fruits have a fast ripening process and a shelf-life of days, presenting a challenge for long-distance consuming markets. To prolong shelf-life, peach fruits are stored at low temperatures (0 to 7 °C) for at least two weeks, which can lead to the development of mealiness, a physiological disorder that reduces fruit quality and decreases consumer acceptance. Several studies have been made to understand this disorder, however, the molecular mechanisms underlying mealiness are not fully understood. Epigenetic factors, such as DNA methylation, modulate gene expression according to the genetic background and environmental conditions. In this sense, the aim of this work was to identify differentially methylated regions (DMRs) that could affect gene expression in contrasting individuals for mealiness. Peach flesh was studied at harvest time (E1 stage) and after cold storage (E3 stage) for 30 days. The distribution of DNA methylations within the eight chromosomes of P. persica showed higher methylation levels in pericentromeric regions and most differences between mealy and normal fruits were at Chr1, Chr4, and Chr8. Notably, differences in Chr4 co-localized with previous QTLs associated with mealiness. Additionally, the number of DMRs was higher in CHH cytosines of normal and mealy fruits at E3; however, most DMRs were attributed to mealy fruits from E1, increasing at E3. From RNA-Seq data, we observed that differentially expressed genes (DEGs) between normal and mealy fruits were associated with ethylene signaling, cell wall modification, lipid metabolism, oxidative stress and iron homeostasis. When integrating the annotation of DMRs and DEGs, we identified a CYP450 82A and an UDP-ARABINOSE 4 EPIMERASE 1 gene that were downregulated and hypermethylated in mealy fruits, coinciding with the co-localization of a transposable element (TE). Altogether, this study indicates that genetic differences between tolerant and susceptible individuals is predominantly affecting epigenetic regulation over gene expression, which could contribute to a metabolic alteration from earlier stages of development, resulting in mealiness at later stages. Finally, this epigenetic mark should be further studied for the development of new molecular tools in support of breeding programs.
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Affiliation(s)
- Karin Rothkegel
- Facultad Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
| | - Alonso Espinoza
- Facultad Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
| | - Dayan Sanhueza
- Facultad Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
| | - Victoria Lillo-Carmona
- Facultad Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
| | - Aníbal Riveros
- Facultad Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
| | - Reinaldo Campos-Vargas
- Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Centro de Estudios Postcosecha, Universidad de Chile, Santiago, Chile
| | - Claudio Meneses
- Facultad Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
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24
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Yang Q, Gao Y, Wu X, Moriguchi T, Bai S, Teng Y. Bud endodormancy in deciduous fruit trees: advances and prospects. HORTICULTURE RESEARCH 2021; 8:139. [PMID: 34078882 PMCID: PMC8172858 DOI: 10.1038/s41438-021-00575-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 05/12/2023]
Abstract
Bud endodormancy is a complex physiological process that is indispensable for the survival, growth, and development of deciduous perennial plants. The timely release of endodormancy is essential for flowering and fruit production of deciduous fruit trees. A better understanding of the mechanism of endodormancy will be of great help in the artificial regulation of endodormancy to cope with climate change and in creating new cultivars with different chilling requirements. Studies in poplar have clarified the mechanism of vegetative bud endodormancy, but the endodormancy of floral buds in fruit trees needs further study. In this review, we focus on the molecular regulation of endodormancy induction, maintenance and release in floral buds of deciduous fruit trees. We also describe recent advances in quantitative trait loci analysis of chilling requirements in fruit trees. We discuss phytohormones, epigenetic regulation, and the detailed molecular network controlling endodormancy, centered on SHORT VEGETATIVE PHASE (SVP) and Dormancy-associated MADS-box (DAM) genes during endodormancy maintenance and release. Combining previous studies and our observations, we propose a regulatory model for bud endodormancy and offer some perspectives for the future.
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Affiliation(s)
- Qinsong Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Haidian District, Beijing, 100083, China
| | - Yuhao Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyue Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Takaya Moriguchi
- Shizuoka Professional University of Agriculture, Iwata, Shizuoka, 438-0803, Japan
| | - Songling Bai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Yuanwen Teng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, 572000, China
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25
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Yu J, Bennett D, Dardick C, Zhebentyayeva T, Abbott AG, Liu Z, Staton ME. Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach. Front Mol Biosci 2021; 8:612881. [PMID: 33968979 PMCID: PMC8098804 DOI: 10.3389/fmolb.2021.612881] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/15/2021] [Indexed: 11/15/2022] Open
Abstract
Bud dormancy is under the regulation of complex mechanisms including genetic and epigenetic factors. To study the function of regulatory non-coding RNAs in winter dormancy release, we analyzed the small RNA and long non-coding RNA (lncRNA) expression from peach (Prunus persica) floral buds in endodormancy, ecodormancy and bud break stages. Small RNAs underwent a major shift in expression primarily between dormancy and flowering with specific pairs of microRNAs and their mRNA target genes undergoing coordinated differential expression. From endodormancy to ecodormancy, ppe-miR6285 was significantly upregulated while its target gene, an ASPARAGINE-RICH PROTEIN involved in the regulation of abscisic acid signaling, was downregulated. At ecodormancy, ppe-miR2275, a homolog of meiosis-specific miR2275 across angiosperms, was significantly upregulated, supporting microsporogenesis in anthers at a late stage of dormancy. The expression of 785 lncRNAs, unlike the overall expression pattern in the small RNAs, demonstrated distinctive expression signatures across all dormancy and flowering stages. We predicted that a subset of lncRNAs were targets of microRNAs and found 18 lncRNA/microRNA target pairs with both differentially expressed across time points. The genome-wide differential expression and network analysis of non-coding RNAs and mRNAs from the same tissues provide new candidate loci for dormancy regulation and suggest complex noncoding RNA interactions control transcriptional regulation across these key developmental time points.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
| | - Dennis Bennett
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Christopher Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, The Pennsylvania State University, University Park, PA, United States
| | - Albert G Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
| | - Zongrang Liu
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Margaret E Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States.,Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
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26
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Fadón E, Herrera S, Herrero M, Rodrigo J. Male meiosis in sweet cherry is constrained by the chilling and forcing phases of dormancy. TREE PHYSIOLOGY 2021; 41:619-630. [PMID: 32453409 DOI: 10.1093/treephys/tpaa063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 03/23/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Male meiosis in temperate fruit trees occurs in the anthers once a year, synchronized with the seasons. The alternation of dormant and growth cycles determines the optimum moment for the male gametophyte formation, a process sensitive to both cold and warm temperatures. This ensures pollen viability and subsequent reproduction success that guarantee fruit production. In this work, we explore how male meiosis is framed by seasonality in sweet cherry. For this purpose, the dormant phases, male meiosis and blooming dates were established in four cultivars with different flowering dates and chilling requirements over 7 years. The chilling and heat requirements for each cultivar were empirically estimated, and chilling and heat temperatures were quantified according to the Dynamic and Growing Degree Hours (GDH) models, respectively. Endodormancy was overcome approximately a fortnight earlier during the colder winters than during the milder winters. Against our initial hypothesis, these differences were not clearly reflected in the time of male meiosis. The period between chilling fulfillment and meiosis lasted several weeks, during which a high amount of GDH accumulated. Results showed that male meiosis is conditioned by endodormancy but especially by warm temperatures, during the forcing period. This differs from what has been described in other related species and creates a framework for further studies to understand the strategies of synchronizing dormancy with seasons.
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Affiliation(s)
- Erica Fadón
- INRES - Gartenbauwissenschaft, Universität Bonn, Bonn, Germany
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Departamento de Pomología, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD - CSIC), Zaragoza, Spain
| | - Sara Herrera
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
| | - María Herrero
- Departamento de Pomología, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD - CSIC), Zaragoza, Spain
| | - Javier Rodrigo
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón - IA2 (CITA - Universidad de Zaragoza), Zaragoza, Spain
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27
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Prudencio ÁS, Hoeberichts FA, Dicenta F, Martínez-Gómez P, Sánchez-Pérez R. Identification of early and late flowering time candidate genes in endodormant and ecodormant almond flower buds. TREE PHYSIOLOGY 2021; 41:589-605. [PMID: 33200186 PMCID: PMC8033246 DOI: 10.1093/treephys/tpaa151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/22/2020] [Accepted: 10/23/2020] [Indexed: 05/13/2023]
Abstract
Flower bud dormancy in temperate fruit tree species, such as almond [Prunus dulcis (Mill.) D.A. Webb], is a survival mechanism that ensures that flowering will occur under suitable weather conditions for successful flower development, pollination and fruit set. Dormancy is divided into three sequential phases: paradormancy, endodormancy and ecodormancy. During the winter, buds need cultivar-specific chilling requirements (CRs) to overcome endodormancy and heat requirements to activate the machinery to flower in the ecodormancy phase. One of the main factors that enables the transition from endodormancy to ecodormancy is transcriptome reprogramming. In this work, we therefore monitored three almond cultivars with different CRs and flowering times by RNA sequencing during the endodormancy release of flower buds and validated the data by quantitative real-time PCR in two consecutive seasons. We were thus able to identify early and late flowering time candidate genes in endodormant and ecodormant almond flower buds associated with metabolic switches, transmembrane transport, cell wall remodeling, phytohormone signaling and pollen development. These candidate genes were indeed involved in the overcoming of the endodormancy in almond. This information may be used for the development of dormancy molecular markers, increasing the efficiency of temperate fruit tree breeding programs in a climate-change context.
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Affiliation(s)
- Ángela S Prudencio
- Department of Plant Breeding, Fruit Breeding Group, CEBAS-CSIC, PO Box 164, 30100 Espinardo, Murcia, Spain
| | | | - Federico Dicenta
- Department of Plant Breeding, Fruit Breeding Group, CEBAS-CSIC, PO Box 164, 30100 Espinardo, Murcia, Spain
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, Fruit Breeding Group, CEBAS-CSIC, PO Box 164, 30100 Espinardo, Murcia, Spain
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28
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Zhang Y, Zhang T, Si F, Wang X, Liu C, Yuan Y, Feng W, Gai S. Changes of DNA Methylation Patterns Reveal Epigenetic Modification of Dormancy Release-Related Genes Is Induced by Chilling in Tree Peony. DNA Cell Biol 2021; 40:606-617. [PMID: 33493084 DOI: 10.1089/dna.2020.6142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
DNA methylation is an important epigenetic regulator of gene expression. Application of 5-azacytidine (a methylation inhibitor) significantly promoted bud sprouting rate and the elongation of branches and leaves in "Luhehong" and "Fengdanbai." In total, 11,166 and 11,443 fragments were obtained by methylation-sensitive amplified polymorphism (MSAP) analysis during chilling-induced dormancy release in the two varieties, respectively. Total methylation levels were high in dormant buds, mainly for hemimethylation, which were slowly increased by short-term chilling (7 days) and decreased by long-term chilling. Compared with 0 day, the ratio of the methylation downregulated group increased during dormancy release, whereas that of the upregulated group declined gradually. These variations were consistent with the dynamic expressions of DNA methyltransferase/demethylase genes and their enzyme activity changes. In total, 13 polymorphic MSAP fragments were similar to known proteins (E-value <1e-5), and their methylation statuses were consistent with their expression patterns. The expression change of PsCWH, encoding cell wall hydrolase, might be due to DNA methylation ratios of CpG sites identified by bisulfite sequencing. These results indicated that chilling accumulation promoted bud dormancy release and sprouting through DNA methylation modification of specific genes. This study would provide new insights into the molecular mechanism underlying dormancy release in tree peony.
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Affiliation(s)
- Yuxi Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Tao Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Fuhui Si
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Xueting Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Chunying Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Yanchao Yuan
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Weirong Feng
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Shupeng Gai
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
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29
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Soppe WJJ, Viñegra de la Torre N, Albani MC. The Diverse Roles of FLOWERING LOCUS C in Annual and Perennial Brassicaceae Species. FRONTIERS IN PLANT SCIENCE 2021; 12:627258. [PMID: 33679840 PMCID: PMC7927791 DOI: 10.3389/fpls.2021.627258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/25/2021] [Indexed: 05/07/2023]
Abstract
Most temperate species require prolonged exposure to winter chilling temperatures to flower in the spring. In the Brassicaceae, the MADS box transcription factor FLOWERING LOCUS C (FLC) is a major regulator of flowering in response to prolonged cold exposure, a process called vernalization. Winter annual Arabidopsis thaliana accessions initiate flowering in the spring due to the stable silencing of FLC by vernalization. The role of FLC has also been explored in perennials within the Brassicaceae family, such as Arabis alpina. The flowering pattern in A. alpina differs from the one in A. thaliana. A. alpina plants initiate flower buds during vernalization but only flower after subsequent exposure to growth-promoting conditions. Here we discuss the role of FLC in annual and perennial Brassicaceae species. We show that, besides its conserved role in flowering, FLC has acquired additional functions that contribute to vegetative and seed traits. PERPETUAL FLOWERING 1 (PEP1), the A. alpina FLC ortholog, contributes to the perennial growth habit. We discuss that PEP1 directly and indirectly, regulates traits such as the duration of the flowering episode, polycarpic growth habit and shoot architecture. We suggest that these additional roles of PEP1 are facilitated by (1) the ability of A. alpina plants to form flower buds during long-term cold exposure, (2) age-related differences between meristems, which enable that not all meristems initiate flowering during cold exposure, and (3) differences between meristems in stable silencing of PEP1 after long-term cold, which ensure that PEP1 expression levels will remain low after vernalization only in meristems that commit to flowering during cold exposure. These features result in spatiotemporal seasonal changes of PEP1 expression during the A. alpina life cycle that contribute to the perennial growth habit. FLC and PEP1 have also been shown to influence the timing of another developmental transition in the plant, seed germination, by influencing seed dormancy and longevity. This suggests that during evolution, FLC and its orthologs adopted both similar and divergent roles to regulate life history traits. Spatiotemporal changes of FLC transcript accumulation drive developmental decisions and contribute to life history evolution.
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Affiliation(s)
| | - Natanael Viñegra de la Torre
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maria C. Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- *Correspondence: Maria C. Albani, ;
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Zhang M, Yang Q, Yuan X, Yan X, Wang J, Cheng T, Zhang Q. Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume. FRONTIERS IN PLANT SCIENCE 2021; 12:690841. [PMID: 34335659 PMCID: PMC8319914 DOI: 10.3389/fpls.2021.690841] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/28/2021] [Indexed: 05/12/2023]
Abstract
Prunus mume is one of the most important woody perennials for edible and ornamental use. Despite a substantial variation in the flowering phenology among the P. mume germplasm resources, the genetic control for flowering time remains to be elucidated. In this study, we examined five blooming time-related traits of 235 P. mume landraces for 2 years. Based on the phenotypic data, we performed genome-wide association studies, which included a combination of marker- and gene-based association tests, and identified 1,445 candidate genes that are consistently linked with flowering time across multiple years. Furthermore, we assessed the global transcriptome change of floral buds from the two P. mume cultivars exhibiting contrasting bloom dates and detected 617 associated genes that were differentially expressed during the flowering process. By integrating a co-expression network analysis, we screened out 191 gene candidates of conserved transcriptional pattern during blooming across cultivars. Finally, we validated the temporal expression profiles of these candidates and highlighted their putative roles in regulating floral bud break and blooming time in P. mume. Our findings are important to expand the understanding of flowering time control in woody perennials and will boost the molecular breeding of novel varieties in P. mume.
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Affiliation(s)
- Man Zhang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qingqing Yang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xi Yuan
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | | | - Jia Wang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- *Correspondence: Qixiang Zhang
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Liu J, Ren M, Chen H, Wu S, Yan H, Jalal A, Wang C. Evolution of SHORT VEGETATIVE PHASE (SVP) genes in Rosaceae: Implications of lineage-specific gene duplication events and function diversifications with respect to their roles in processes other than bud dormancy. THE PLANT GENOME 2020; 13:e20053. [PMID: 33217197 DOI: 10.1002/tpg2.20053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
MADS-box genes that are homologous to Arabidopsis SHORT VEGETATIVE PHASE (SVP) have been shown to play key roles in the regulation of bud dormancy in perennial species, particularly in the deciduous fruit trees of Rosaceae. However, their evolutionary profiles in Rosaceae have not yet been analyzed systematically. Here, The SVP genes were found to be significantly expanded in Rosaceae when compared with annual species from Brassicaceae. Phylogenetic analysis showed that Rosaceae SVP genes could be classified into five clades, namely, SVP1, SVP2-R1, SVP2-R2, SVP2-R3 and SVP3. The SVP1 clade genes were retained in most of the species, whereas the SVP2-R2 and SVP2-R3 clades were found to be Maleae- and Amygdaleae-specific (Both of the lineages belong to Amygdaloideae), respectively, and SVP2-R1 was Rosoideae-specific in Rosaceae. Furthermore, 10 lineage-specific gene duplication (GD) events (GD1-10) were proposed for the expansion of SVP genes, suggesting that the expansion and divergence of Rosaceae SVP genes were mainly derived by lineage-specific manner during evolution. Moreover, tandem and segmental duplications were the major reasons for the expansion of SVP genes, and interestingly, tandem duplications, a well-known evolutionary feature of SVP genes, were found to be mainly Amygdaloideae-specific. Sequence alignment, selection pressure, and cis-acting element analysis suggested large functional innovations and diversification of SVP genes in different lineages of Rosaceae. Finally, the different growth cycle of Rosa multiflora and their novel expression patterns of RmSVP genes provided new insights into the functional diversification of SVP genes in terms of their roles in processes other than bud dormancy.
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Affiliation(s)
- Jinyi Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Min Ren
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- Shanghai Forestry Station, Shanghai, 200072, China
| | - Hui Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Silin Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Huijun Yan
- Yunnan Academy of Agricultural Sciences, Flower Research Institute, Kunming, Yunnan, 650200, China
| | - Abdul Jalal
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Changquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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Yang Q, Yang B, Li J, Wang Y, Tao R, Yang F, Wu X, Yan X, Ahmad M, Shen J, Bai S, Teng Y. ABA-responsive ABRE-BINDING FACTOR3 activates DAM3 expression to promote bud dormancy in Asian pear. PLANT, CELL & ENVIRONMENT 2020; 43:1360-1375. [PMID: 32092154 DOI: 10.1111/pce.13744] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 05/22/2023]
Abstract
Bud dormancy is indispensable for the survival of perennial plants in cold winters. Abscisic acid (ABA) has essential functions influencing the endo-dormancy status. Dormancy-associated MADS-box/SHORT VEGETATIVE PHASE-like genes function downstream of the ABA signalling pathway to regulate bud dormancy. However, the regulation of DAM/SVP expression remains largely uncharacterized. In this study, we confirmed that endo-dormancy maintenance and PpyDAM3 expression are controlled by the ABA content in pear (Pyrus pyrifolia) buds. The expression of pear ABRE-BINDING FACTOR3 (PpyABF3) was positively correlated with PpyDAM3 expression. Furthermore, PpyABF3 directly bound to the second ABRE in the PpyDAM3 promoter to activate its expression. Interestingly, both PpyABF3 and PpyDAM3 repressed the cell division and growth of transgenic pear calli. Another ABA-induced ABF protein, PpyABF2, physically interacted with PpyABF3 and disrupted the activation of the PpyDAM3 promoter by PpyABF3, indicating DAM expression was precisely controlled. Additionally, our results suggested that the differences in the PpyDAM3 promoter in two pear cultivars might be responsible for the diversity in the chilling requirements. In summary, our data clarify the finely tuned regulatory mechanism underlying the effect of ABA on DAM gene expression and provide new insights into ABA-related bud dormancy regulation.
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Affiliation(s)
- Qinsong Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Bo Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Jianzhao Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Yan Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Ruiyan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Feng Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Xinyue Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Xinhui Yan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Mudassar Ahmad
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Jiaqi Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Songling Bai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
| | - Yuanwen Teng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang, China
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Xanthopoulou A, Manioudaki M, Bazakos C, Kissoudis C, Farsakoglou AM, Karagiannis E, Michailidis M, Polychroniadou C, Zambounis A, Kazantzis K, Tsaftaris A, Madesis P, Aravanopoulos F, Molassiotis A, Ganopoulos I. Whole genome re-sequencing of sweet cherry ( Prunus avium L.) yields insights into genomic diversity of a fruit species. HORTICULTURE RESEARCH 2020; 7:60. [PMID: 32377351 PMCID: PMC7193578 DOI: 10.1038/s41438-020-0281-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/17/2020] [Accepted: 02/18/2020] [Indexed: 05/30/2023]
Abstract
Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. In this study, whole-genome resequencing (WGRS) was employed to characterize genetic variation, population structure and allelic variants in a panel of 20 sweet cherry and one wild cherry genotypes, embodying the majority of cultivated Greek germplasm and a representative of a local wild cherry elite phenotype. The 21 genotypes were sequenced in an average depth of coverage of 33.91×. and effective mapping depth, to the genomic reference sequence of 'Satonishiki' cultivar, between 22.21× to 36.62×. Discriminant analysis of principal components (DAPC) with SNPs revealed two clusters of genotypes. There was a rapid linkage disequilibrium decay, as the majority of SNP pairs with r2 in near complete disequilibrium (>0.8) were found at physical distances less than 10 kb. Functional analysis of the variants showed that the genomic ratio of non-synonymous/synonymous (dN/dS) changes was 1.78. The higher dN frequency in the Greek cohort of sweet cherry could be the result of artificial selection pressure imposed by breeding, in combination with the vegetative propagation of domesticated cultivars through grafting. The majority of SNPs with high impact (e.g., stop codon gaining, frameshift), were identified in genes involved in flowering time, dormancy and defense reactions against pathogens, providing promising resources for future breeding programs. Our study has established the foundation for further large scale characterization of sweet cherry germplasm, enabling breeders to incorporate diverse germplasm and allelic variants to fine tune flowering and maturity time and disease resistance in sweet cherry cultivars.
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Affiliation(s)
- Aliki Xanthopoulou
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria Manioudaki
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Thermi, Thessaloniki, 570001 Greece
| | | | - Anna-Maria Farsakoglou
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelos Karagiannis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Michail Michailidis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Chrysanthi Polychroniadou
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonios Zambounis
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Department of Deciduous Fruit Growing, Naoussa, 59035 Greece
| | - Konstantinos Kazantzis
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Department of Deciduous Fruit Growing, Naoussa, 59035 Greece
| | | | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki, 570 01 Greece
| | - Filippos Aravanopoulos
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Thermi, Thessaloniki, 570001 Greece
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Quesada-Traver C, Guerrero BI, Badenes ML, Rodrigo J, Ríos G, Lloret A. Structure and Expression of Bud Dormancy-Associated MADS-Box Genes ( DAM) in European Plum. FRONTIERS IN PLANT SCIENCE 2020; 11:1288. [PMID: 32973847 PMCID: PMC7466548 DOI: 10.3389/fpls.2020.01288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/07/2020] [Indexed: 05/22/2023]
Abstract
Bud dormancy in temperate perennials ensures the survival of growing meristems under the harsh environmental conditions of autumn and winter, and facilitates an optimal growth and development resumption in the spring. Although the molecular pathways controlling the dormancy process are still unclear, DORMANCY-ASSOCIATED MADS-BOX genes (DAM) have emerged as key regulators of the dormancy cycle in different species. In the present study, we have characterized the orthologs of DAM genes in European plum (Prunus domestica L.). Their expression patterns together with sequence similarities are consistent with a role of PdoDAMs in dormancy maintenance mechanisms in European plum. Furthermore, other genes related to dormancy, flowering, and stress response have been identified in order to obtain a molecular framework of these three different processes taking place within the dormant flower bud in this species. This research provides a set of candidate genes to be genetically modified in future research, in order to better understand dormancy regulation in perennial species.
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Affiliation(s)
- Carles Quesada-Traver
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Brenda Ivette Guerrero
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
| | - María Luisa Badenes
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Javier Rodrigo
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, CITA-Universidad de Zaragoza, Zaragoza, Spain
| | - Gabino Ríos
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Alba Lloret
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
- *Correspondence: Alba Lloret,
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Rothkegel K, Sandoval P, Soto E, Ulloa L, Riveros A, Lillo-Carmona V, Cáceres-Molina J, Almeida AM, Meneses C. Dormant but Active: Chilling Accumulation Modulates the Epigenome and Transcriptome of Prunus avium During Bud Dormancy. FRONTIERS IN PLANT SCIENCE 2020; 11:1115. [PMID: 32765576 PMCID: PMC7380246 DOI: 10.3389/fpls.2020.01115] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/06/2020] [Indexed: 05/22/2023]
Abstract
Temperate deciduous fruit tree species like sweet cherry (Prunus avium) require long periods of low temperatures to trigger dormancy release and flowering. In addition to sequence-based genetic diversity, epigenetic variation may contribute to different chilling requirements among varieties. For the low chill variety 'Royal Dawn' and high chill variety 'Kordia', we studied the methylome of floral buds during chilling accumulation using MethylC-seq to identify differentially methylated regions (DMRs) during chilling hours (CH) accumulation, followed by transcriptome analysis to correlate changes in gene expression with DNA methylation. We found that during chilling accumulation, DNA methylation increased from 173 CH in 'Royal Dawn' and 443 CH in 'Kordia' and was mostly associated with the CHH context. In addition, transcriptional changes were observed from 443 CH in 'Kordia' with 1,210 differentially expressed genes, increasing to 4,292 genes at 1,295 CH. While 'Royal Dawn' showed approximately 5,000 genes differentially expressed at 348 CH and 516 CH, showing a reprogramming that was specific for each genotype. From conserved upregulated genes that overlapped with hypomethylated regions and downregulated genes that overlapped with hypermethylated regions in both varieties, we identified genes related to cold-sensing, cold-signaling, oxidation-reduction process, metabolism of phenylpropanoids and lipids, and a MADS-box SVP-like gene. As a complementary analysis, we used conserved and non-conserved DEGs that presented a negative correlation between DNA methylations and mRNA levels across all chilling conditions, obtaining Gene Ontology (GO) categories related to abiotic stress, metabolism, and oxidative stress. Altogether, this data indicates that changes in DNA methylation precedes transcript changes and may occur as an early response to low temperatures to increase the cold tolerance in the endodormancy period, contributing with the first methylome information about the effect of environmental cues over two different genotypes of sweet cherry.
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Affiliation(s)
- Karin Rothkegel
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Paula Sandoval
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Esteban Soto
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Lissette Ulloa
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Anibal Riveros
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Victoria Lillo-Carmona
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Javier Cáceres-Molina
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Andrea Miyasaka Almeida
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- ;*Correspondence: Andrea Miyasaka Almeida, ; Claudio Meneses,
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- FONDAP, Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
- ;*Correspondence: Andrea Miyasaka Almeida, ; Claudio Meneses,
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Vimont N, Fouché M, Campoy JA, Tong M, Arkoun M, Yvin JC, Wigge PA, Dirlewanger E, Cortijo S, Wenden B. From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy. BMC Genomics 2019; 20:974. [PMID: 31830909 PMCID: PMC6909552 DOI: 10.1186/s12864-019-6348-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/28/2019] [Indexed: 12/22/2022] Open
Abstract
Background Bud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during bud dormancy in trees. However, they usually examined bud development or bud dormancy in isolation. In this work, we aimed to further explore the global transcriptional changes happening throughout bud development and dormancy onset, progression and release. Results Using next-generation sequencing and modelling, we conducted an in-depth transcriptomic analysis for all stages of flower buds in several sweet cherry (Prunus avium L.) cultivars that are characterized for their contrasted dates of dormancy release. We find that buds in organogenesis, paradormancy, endodormancy and ecodormancy stages are defined by the expression of genes involved in specific pathways, and these are conserved between different sweet cherry cultivars. In particular, we found that DORMANCY ASSOCIATED MADS-box (DAM), floral identity and organogenesis genes are up-regulated during the pre-dormancy stages while endodormancy is characterized by a complex array of signalling pathways, including cold response genes, ABA and oxidation-reduction processes. After dormancy release, genes associated with global cell activity, division and differentiation are activated during ecodormancy and growth resumption. We then went a step beyond the global transcriptomic analysis and we developed a model based on the transcriptional profiles of just seven genes to accurately predict the main bud dormancy stages. Conclusions Overall, this study has allowed us to better understand the transcriptional changes occurring throughout the different phases of flower bud development, from bud formation in the summer to flowering in the following spring. Our work sets the stage for the development of fast and cost effective diagnostic tools to molecularly define the dormancy stages. Such integrative approaches will therefore be extremely useful for a better comprehension of complex phenological processes in many species.
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Affiliation(s)
- Noémie Vimont
- INRA, UMR1332 BFP, Univ. Bordeaux, 33882, Villenave d'Ornon, Cedex, France.,Agro Innovation International, Centre Mondial d'Innovation, Groupe Roullier, 35400, St Malo, France.,The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Mathieu Fouché
- INRA, UMR1332 BFP, Univ. Bordeaux, 33882, Villenave d'Ornon, Cedex, France
| | - José Antonio Campoy
- Universidad Politécnica de Cartagena, Cartagena, Spain.,Universidad de Murcia, Murcia, Spain.,Present address: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Meixuezi Tong
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Mustapha Arkoun
- Agro Innovation International, Centre Mondial d'Innovation, Groupe Roullier, 35400, St Malo, France
| | - Jean-Claude Yvin
- Agro Innovation International, Centre Mondial d'Innovation, Groupe Roullier, 35400, St Malo, France
| | - Philip A Wigge
- Leibniz-Institute für Gemüse- und Zierpflanzenbau (IGZ), Plant Adaptation, Grossbeeren, Germany
| | | | - Sandra Cortijo
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.
| | - Bénédicte Wenden
- INRA, UMR1332 BFP, Univ. Bordeaux, 33882, Villenave d'Ornon, Cedex, France.
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The Role of EjSVPs in Flower Initiation in Eriobotrya japonica. Int J Mol Sci 2019; 20:ijms20235933. [PMID: 31779080 PMCID: PMC6928820 DOI: 10.3390/ijms20235933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/16/2019] [Accepted: 11/22/2019] [Indexed: 12/22/2022] Open
Abstract
Flowering plants have evolved different flowering habits to sustain long-term reproduction. Most woody trees experience dormancy and then bloom in the warm spring, but loquat blooms in the cold autumn and winter. To explore its mechanism of flowering regulation, we cloned two SHORT VEGETATIVE PHASE (SVP) homologous genes from 'Jiefanzhong' loquat (Eriobotrya japonica Lindl.), namely, EjSVP1 and EjSVP2. Sequence analysis revealed that the EjSVPs were typical MADS-box transcription factors and exhibited a close genetic relationship with other plant SVP/DORMANCY-ASSOCIATED MADS-BOX (DAM) proteins. The temporal and spatial expression patterns showed that EjSVP1 and EjSVP2 were mainly expressed in the shoot apical meristem (SAM) after the initiation of flowering; after reaching their highest level, they gradually decreased with the development of the flower until they could not be detected. EjSVP1 expression levels were relatively high in young tissues, and EjSVP2 expression levels were relatively high in young to mature transformed tissues. Interestingly, EjSVP2 showed relatively high expression levels in various flower tissues. We analyzed the EjSVP promoter regions and found that they did not contain the C-repeat/dehydration-responsive element. Finally, we overexpressed the EjSVPs in wild-type Arabidopsis thaliana Col-0 and found no significant changes in the number of rosette leaves of Arabidopsis thaliana; however, overexpression of EjSVP2 affected the formation of Arabidopsis thaliana flower organs. In conclusion, EjSVPs were found to play an active role in the development of loquat flowering. These findings may provide a reference for exploring the regulation mechanisms of loquat flowering and the dormancy mechanisms of other plants.
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Aranzana MJ, Decroocq V, Dirlewanger E, Eduardo I, Gao ZS, Gasic K, Iezzoni A, Jung S, Peace C, Prieto H, Tao R, Verde I, Abbott AG, Arús P. Prunus genetics and applications after de novo genome sequencing: achievements and prospects. HORTICULTURE RESEARCH 2019; 6:58. [PMID: 30962943 PMCID: PMC6450939 DOI: 10.1038/s41438-019-0140-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 05/04/2023]
Abstract
Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.
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Affiliation(s)
- Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Véronique Decroocq
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Elisabeth Dirlewanger
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Zhong Shan Gao
- Allergy Research Center, Zhejiang University, 310058 Hangzhou, China
| | | | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1325 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, Instituto de Investigaciones Agropecuarias, Santa Rosa, 11610 La Pintana, Santiago Chile
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Rome, Italy
| | - Albert G. Abbott
- University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY 40546-0073 USA
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Conde D, Perales M, Sreedasyam A, Tuskan GA, Lloret A, Badenes ML, González-Melendi P, Ríos G, Allona I. Engineering Tree Seasonal Cycles of Growth Through Chromatin Modification. FRONTIERS IN PLANT SCIENCE 2019; 10:412. [PMID: 31024588 PMCID: PMC6459980 DOI: 10.3389/fpls.2019.00412] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/19/2019] [Indexed: 05/21/2023]
Abstract
In temperate and boreal regions, perennial trees arrest cell division in their meristematic tissues during winter dormancy until environmental conditions become appropriate for their renewed growth. Release from the dormant state requires exposure to a period of chilling temperatures similar to the vernalization required for flowering in Arabidopsis. Over the past decade, genomic DNA (gDNA) methylation and transcriptome studies have revealed signatures of chromatin regulation during active growth and winter dormancy. To date, only a few chromatin modification genes, as candidate regulators of these developmental stages, have been functionally characterized in trees. In this work, we summarize the major findings of the chromatin-remodeling role during growth-dormancy cycles and we explore the transcriptional profiling of vegetative apical bud and stem tissues during dormancy. Finally, we discuss genetic strategies designed to improve the growth and quality of forest trees.
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Affiliation(s)
- Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Gerald A. Tuskan
- Oak Ridge National Laboratory, Center for Bioenergy Innovation, Oak Ridge, TN, United States
| | - Alba Lloret
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - María L. Badenes
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Pablo González-Melendi
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
- *Correspondence: Isabel Allona, orcid.org/0000-0002-7012-2850
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Liu J, Sherif SM. Hormonal Orchestration of Bud Dormancy Cycle in Deciduous Woody Perennials. FRONTIERS IN PLANT SCIENCE 2019; 10:1136. [PMID: 31620159 PMCID: PMC6759871 DOI: 10.3389/fpls.2019.01136] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/19/2019] [Indexed: 05/03/2023]
Abstract
Woody perennials enter seasonal dormancy to avoid unfavorable environmental conditions. Plant hormones are the critical mediators regulating this complex process, which is subject to the influence of many internal and external factors. Over the last two decades, our knowledge of hormone-mediated dormancy has increased considerably, primarily due to advancements in molecular biology, omics, and bioinformatics. These advancements have enabled the elucidation of several aspects of hormonal regulation associated with bud dormancy in various deciduous tree species. Plant hormones interact with each other extensively in a context-dependent manner. The dormancy-associated MADS (DAM) transcription factors appear to enable hormones and other internal signals associated with the transition between different phases of bud dormancy. These proteins likely hold a great potential in deciphering the underlying mechanisms of dormancy initiation, maintenance, and release. In this review, a recent understanding of the roles of plant hormones, their cross talks, and their potential interactions with DAM proteins during dormancy is discussed.
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Prudencio ÁS, Werner O, Martínez-García PJ, Dicenta F, Ros RM, Martínez-Gómez P. DNA Methylation Analysis of Dormancy Release in Almond ( Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing. Int J Mol Sci 2018; 19:ijms19113542. [PMID: 30423798 PMCID: PMC6274898 DOI: 10.3390/ijms19113542] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 01/26/2023] Open
Abstract
DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.
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Affiliation(s)
- Ángela S Prudencio
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Olaf Werner
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | | | - Federico Dicenta
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Rosa M Ros
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
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Prudencio ÁS, Werner O, Martínez-García PJ, Dicenta F, Ros RM, Martínez-Gómez P. DNA Methylation Analysis of Dormancy Release in Almond ( Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing. Int J Mol Sci 2018. [PMID: 30423798 DOI: 10.3542/ijms19113542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.
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Affiliation(s)
- Ángela S Prudencio
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Olaf Werner
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | | | - Federico Dicenta
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Rosa M Ros
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
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Lloret A, Badenes ML, Ríos G. Modulation of Dormancy and Growth Responses in Reproductive Buds of Temperate Trees. FRONTIERS IN PLANT SCIENCE 2018; 9:1368. [PMID: 30271422 PMCID: PMC6146825 DOI: 10.3389/fpls.2018.01368] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/29/2018] [Indexed: 05/20/2023]
Abstract
During autumn perennial trees cease growth and form structures called buds in order to protect meristems from the unfavorable environmental conditions, including low temperature and desiccation. In addition to increased tolerance to these abiotic stresses, reproductive buds modulate developmental programs leading to dormancy induction to avoid premature growth resumption, and flowering pathways. Stress tolerance, dormancy, and flowering processes are thus physically and temporarily restricted to a bud, and consequently forced to interact at the regulatory level. We review recent genomic, genetic, and molecular contributions to the knowledge of these three processes in trees, highlighting the role of epigenetic modifications, phytohormones, and common regulatory factors. Finally, we emphasize the utility of transcriptomic approaches for the identification of key structural and regulatory genes involved in bud processes, illustrated with our own experience using peach as a model.
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Sánchez E, Tricon D, Mora R, Quiroz D, Decroocq V, Prieto H. A fast and efficient protocol for small RNA extraction in Japanese plum and other Prunus species. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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