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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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Girardi F, Canton M, Populin F, Tijero V, Bettio G, Munné-Bosch S, Rasori A, Cardillo V, Costa G, Botton A. A gibberellin-assisted study of the transcriptional and hormonal changes occurring at floral transition in peach buds (Prunus persica L. Batsch). BMC PLANT BIOLOGY 2024; 24:643. [PMID: 38973005 PMCID: PMC11229236 DOI: 10.1186/s12870-024-05360-6] [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: 12/21/2023] [Accepted: 07/01/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND Flower load in peach is an important determinant of final fruit quality and is subjected to cost-effective agronomical practices, such as the thinning, to finely balance the sink-source relationships within the tree and drive the optimal amount of assimilates to the fruits. Floral transition in peach buds occurs as a result of the integration of specific environmental signals, such as light and temperature, into the endogenous pathways that induce the meristem to pass from vegetative to reproductive growth. The cross talk and integration of the different players, such as the genes and the hormones, are still partially unknown. In the present research, transcriptomics and hormone profiling were applied on bud samples at different developmental stages. A gibberellin treatment was used as a tool to identify the different phases of floral transition and characterize the bud sensitivity to gibberellins in terms of inhibition of floral transition. RESULTS Treatments with gibberellins showed different efficacies and pointed out a timeframe of maximum inhibition of floral transition in peach buds. Contextually, APETALA1 gene expression was shown to be a reliable marker of gibberellin efficacy in controlling this process. RNA-Seq transcriptomic analyses allowed to identify specific genes dealing with ROS, cell cycle, T6P, floral induction control and other processes, which are correlated with the bud sensitivity to gibberellins and possibly involved in bud development during its transition to the reproductive stage. Transcriptomic data integrated with the quantification of the main bioactive hormones in the bud allowed to identify the main hormonal regulators of floral transition in peach, with a pivotal role played by endogenous gibberellins and cytokinins. CONCLUSIONS The peach bud undergoes different levels of receptivity to gibberellin inhibition. The stage with maximum responsiveness corresponded to a transcriptional and hormonal crossroad, involving both flowering inhibitors and inductors. Endogenous gibberellin levels increased only at the latest developmental stage, when floral transition was already partially achieved, and the bud was less sensitive to exogenous treatments. A physiological model summarizes the main findings and suggests new research ideas to improve our knowledge about floral transition in peach.
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Affiliation(s)
- Francesco Girardi
- Department of Agronomy, Food, Natural resources, Animals and Environment - DAFNAE, University of Padova, Agripolis, Viale dell'università 16, Legnaro, PD, 35020, Italy
| | - Monica Canton
- Department of Agronomy, Food, Natural resources, Animals and Environment - DAFNAE, University of Padova, Agripolis, Viale dell'università 16, Legnaro, PD, 35020, Italy
| | - Francesca Populin
- Department of Agronomy, Food, Natural resources, Animals and Environment - DAFNAE, University of Padova, Agripolis, Viale dell'università 16, Legnaro, PD, 35020, Italy
- Berry Genetics and Breeding Unit - Research and Innovation Centre (CRI), Fondazione Edmund Mach, San Michele all'Adige, Trento, 38098, Italy
| | - Verónica Tijero
- Department of Agronomy, Food, Natural resources, Animals and Environment - DAFNAE, University of Padova, Agripolis, Viale dell'università 16, Legnaro, PD, 35020, Italy
- Fruit Production Programme, Institute of Agrifood Research and Technology (IRTA), Parc Agrobiotech Lleida, Parc de Gardeny, Edifici Fruitcentre, Lleida, 25003, Spain
| | - Giorgia Bettio
- Department of Agronomy, Food, Natural resources, Animals and Environment - DAFNAE, University of Padova, Agripolis, Viale dell'università 16, Legnaro, PD, 35020, Italy
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Diagonal 643, Barcelona, 08017, Spain
| | - Angela Rasori
- Department of Agronomy, Food, Natural resources, Animals and Environment - DAFNAE, University of Padova, Agripolis, Viale dell'università 16, Legnaro, PD, 35020, Italy
| | - Valerio Cardillo
- Department of Agronomy, Food, Natural resources, Animals and Environment - DAFNAE, University of Padova, Agripolis, Viale dell'università 16, Legnaro, PD, 35020, Italy
| | - Guglielmo Costa
- Department of Agricultural and Food Sciences - DISTAL, University of Bologna, Bologna, 40126, Italy
| | - Alessandro Botton
- Department of Agronomy, Food, Natural resources, Animals and Environment - DAFNAE, University of Padova, Agripolis, Viale dell'università 16, Legnaro, PD, 35020, Italy.
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Zhao Z, Chen T, Yue J, Pu N, Liu J, Luo L, Huang M, Guo T, Xiao W. Small Auxin Up RNA 56 (SAUR56) regulates heading date in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:62. [PMID: 37521314 PMCID: PMC10374499 DOI: 10.1007/s11032-023-01409-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/16/2023] [Indexed: 08/01/2023]
Abstract
Heading date is a critical agronomic trait that determines crop yield. Although numerous genes associated with heading date have been identified in rice, the mechanisms involving Small Auxin Up RNA (SAUR) family have not been elucidated. In this study, the biological function of several SAUR genes was initially investigated using the CRISPR-Cas9 technology in the Japonica cultivar Zhonghua11 (ZH11) background. Further analysis revealed that the loss-of-function of OsSAUR56 affected heading date in both NLD (natural long-day) and ASD (artificial short-day). OsSAUR56 exhibited predominant expression in the anther, with its protein localized in both the cytoplasm and nucleus. OsSAUR56 regulated flowering time and heading date by modulating the expression of the clock gene OsGI, as well as two repressors Ghd7 and DTH8. Furthermore, haplotype-phenotype association analysis revealed a strong correlation between OsSAUR56 and heading date, suggesting its role in selection during the domestication of rice. In summary, these findings highlights the importance of OsSAUR56 in the regulation of heading date for further potential facilitating genetic engineering for flowering time during rice breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01409-w.
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Affiliation(s)
- Zhe Zhao
- National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Tengkui Chen
- National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Jicheng Yue
- National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Na Pu
- National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Jinzhao Liu
- National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Lixin Luo
- National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Ming Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Tao Guo
- National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
- Heyuan Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Heyuan, 517000 Guangdong China
| | - Wuming Xiao
- National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
- Heyuan Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Heyuan, 517000 Guangdong China
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Liao LY, He ZQ, Zhang L. Cloning and Functional Analysis of the VfRR17 Gene from tung tree ( Vernicia fordii). PLANTS (BASEL, SWITZERLAND) 2023; 12:2474. [PMID: 37447035 DOI: 10.3390/plants12132474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
Tung tree (Vernicia fordii) is one of the four major woody oilseed species in China. However, its fruit yield is severely hampered by the low number of female flowers and the imbalanced male-to-female flower ratio, which is a problem that restricts the development of the oilseed industry. Previous research has demonstrated that the exogenous application of cytokinins can significantly augment the number of female flowers, although the underlying regulatory mechanism remains elusive. To elucidate the involvement of VfRR17, a member of the A-type ARRs family, in the exogenous cytokinin regulation of flower sexual differentiation in tung tree, this study conducted a comprehensive bioinformatic analysis of the physicochemical properties, structural characteristics, and evolutionary relationships of the protein encoded by VfRR17. Additionally, gene function analysis was performed using subcellular localization, qRT-PCR, and genetic transformation techniques. The findings revealed that the VfRR17 gene's coding region spanned 471 bp, encoding an unstable protein of 156 amino acids with a relative molecular mass of 17.4 kDa. Phylogenetic analysis demonstrated a higher similarity between VfRR17 of the tung tree and the RR17 gene of Jatropha curcas, Ricinus communis, Hevea brasiliensis, and other species within the Euphorbiaceae family compared to other species, with the greatest similarity of 86% observed with the RR17 gene of Jatropha curcas. The qRT-PCR analysis indicated that VfRR17 exhibited high expression levels during the early stage of tung tree inflorescence buds following 6-BA treatment, peaking at 24 h and displaying a 3.47-fold increase compared to that at 0 h. In female and male flowers of the tung tree, the expression in female flowers during the 1 DBF period was significantly higher than in male flowers, exhibiting a difference of approximately 47.91-fold. Furthermore, notable differential expression was observed in the root, leaf, and petiole segments of the tung tree under low-temperature stress at the 12-h time point. In transgenic Arabidopsis, the VfRR17 lines and wild-type lines exhibited significantly different flowering times under an exogenous 6-BA treatment at a concentration of 2 mg/L, with the VfRR17 lines experiencing an 11-day delay compared to the wild-type lines. Additionally, the number of fruit pods in VfRR17 transgenic Arabidopsis lines was significantly reduced by 28 compared to the wild-type lines at a 6-BA concentration of 3 mg/L. These findings suggest that VfRR17 likely plays a critical role in regulating flower development in response to exogenous 6-BA, providing valuable insights into the mechanisms underlying exogenous 6-BA-mediated regulation of female flower development in the tung tree.
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Affiliation(s)
- Li-Yu Liao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- Key Lab of Non-Wood Forest Products of State Forestry and Grassland Administration, Central South University of Forestry and Technology, Changsha 410004, China
| | - Zhang-Qi He
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- Key Lab of Non-Wood Forest Products of State Forestry and Grassland Administration, Central South University of Forestry and Technology, Changsha 410004, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- Key Lab of Non-Wood Forest Products of State Forestry and Grassland Administration, Central South University of Forestry and Technology, Changsha 410004, China
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Liu X, Yuan M, Dang S, Zhou J, Zhang Y. Comparative transcriptomic analysis of transcription factors and hormones during flower bud differentiation in 'Red Globe' grape under red‒blue light. Sci Rep 2023; 13:8932. [PMID: 37264033 DOI: 10.1038/s41598-023-29402-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/03/2023] [Indexed: 06/03/2023] Open
Abstract
Grape is a globally significant fruit-bearing crop, and the grape flower bud differentiation essential to fruit production is closely related to light quality. To investigate the regulatory mechanism of grape flower bud differentiation under red‒blue light, the transcriptome and hormone content were determined at four stages of flower bud differentiation. The levels of indole-3-acetic acid (IAA) and abscisic acid (ABA) in grape flower buds at all stages of differentiation under red‒blue light were higher than those in the control. However, the levels of cytokinins (CKs) and gibberellic acid (giberellins, GAs) fluctuated continuously over the course of flower bud differentiation. Moreover, many differentially expressed genes were involved in auxin, CK, GA, and the ABA signal transduction pathways. There were significant differences in the AUX/IAA, SAUR, A-RR, and ABF gene expression levels between the red‒blue light treatment and the control buds, especially in regard to the ABF genes, the expression levels of which were completely different between the two groups. The expression of GBF4 and AI5L2 in the control was always low, while the expression under red‒blue light increased. AI5L7 and AI5L5 expression levels showed an upwards trend in the control plant buds and gradually decreased in red‒blue light treatment plant buds. Through weighted gene coexpression network analysis, we determined that the transcription factors WRK48 (WRKY family), EF110 (ERF family), ABR1, CAMTA3 (CAMTA family), and HSFA3 (HSF family) may be involved in the regulation of the GBF4 gene. This study lays a foundation for further analysis of grape flower bud differentiation regulation under red‒blue light.
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Affiliation(s)
- Xin Liu
- College of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Miao Yuan
- College of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Shizhuo Dang
- College of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Juan Zhou
- College of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Yahong Zhang
- College of Agriculture, Ningxia University, Yinchuan, 750021, China.
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Cross-Talk between Transcriptome Analysis and Dynamic Changes of Carbohydrates Identifies Stage-Specific Genes during the Flower Bud Differentiation Process of Chinese Cherry ( Prunus pseudocerasus L.). Int J Mol Sci 2022; 23:ijms232415562. [PMID: 36555203 PMCID: PMC9778666 DOI: 10.3390/ijms232415562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Flower bud differentiation is crucial to reproductive success in plants. In the present study, RNA-Seq and nutrients quantification were used to identify the stage-specific genes for flower bud differentiation with buds which characterize the marked change during flower bud formation from a widely grown Chinese cherry (Prunus pseudocerasus L.) cultivar 'Manaohong'. A KEGG enrichment analysis revealed that the sugar metabolism pathways dynamically changed. The gradually decreasing trend in the contents of total sugar, soluble sugar and protein implies that the differentiation was an energy-consuming process. Changes in the contents of D-glucose and sorbitol were conformed with the gene expression trends of bglX and SORD, respectively, which at least partially reflects a key role of the two substances in the transition from physiological to morphological differentiation. Further, the WRKY and SBP families were also significantly differentially expressed during the vegetative-to-reproductive transition. In addition, floral meristem identity genes, e.g., AP1, AP3, PI, AGL6, SEP1, LFY, and UFO demonstrate involvement in the specification of the petal and stamen primordia, and FPF1 might promote the onset of morphological differentiation. Conclusively, the available evidence justifies the involvement of sugar metabolism in the flower bud differentiation of Chinese cherry, and the uncovered candidate genes are beneficial to further elucidate flower bud differentiation in cherries.
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7
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Wang Q, Gao G, Chen X, Liu X, Dong B, Wang Y, Zhong S, Deng J, Fang Q, Zhao H. Genetic studies on continuous flowering in woody plant Osmanthus fragrans. FRONTIERS IN PLANT SCIENCE 2022; 13:1049479. [PMID: 36407607 PMCID: PMC9671776 DOI: 10.3389/fpls.2022.1049479] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Continuous flowering is a key horticultural trait in ornamental plants, whereas the specific molecular regulation mechanism remains largely unknown. In sweet osmanthus (Osmanthus fragrans Lour.), plants based on their flowering characteristics are divided into once-flowering (OF) habit and continuous flowering (CF) habit. Here, we first described the flowering phenology shifts of OF and CF habits in sweet osmanthus through paraffin section and microscope assay. Phenotypic characterization showed that CF plants had constant new shoot growth, floral transition, and blooming for 1 year, which might lead to a continuous flowering trait. We performed the transcriptome sequencing of OF and CF sweet osmanthus and analyzed the transcriptional activity of flowering-related genes. Among the genes, three floral integrators, OfFT, OfTFL1, and OfBFT, had a differential expression during the floral transition process in OF and CF habits. The expression patterns of the three genes in 1 year were revealed. The results suggested that their accumulations corresponded to the new shoots occurring and the floral transition process. Function studies suggested that OfFT acted as a flowering activator, whereas OfBFT was a flowering inhibitor. Yeast one-hybrid assay indicated that OfSPL8 was a common upstream transcription factor of OfFT and OfBFT, suggesting the vital role of OfSPL8 in continuous flowering regulation. These results provide a novel insight into the molecular mechanism of continuous flowering.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Qiu Fang
- *Correspondence: Hongbo Zhao, ; Qiu Fang,
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Transcriptome Analysis Reveals Putative Induction of Floral Initiation by Old Leaves in Tea-Oil Tree (Camellia oleifera ‘changlin53’). Int J Mol Sci 2022; 23:ijms232113021. [PMID: 36361817 PMCID: PMC9655362 DOI: 10.3390/ijms232113021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Floral initiation is a major phase change in the spermatophyte, where developmental programs switch from vegetative growth to reproductive growth. It is a key phase of flowering in tea-oil trees that can affect flowering time and yield, but very little is known about the molecular mechanism of floral initiation in tea-oil trees. A 12-year-old Camellia oleifera (cultivar ‘changlin53’) was the source of experimental materials in the current study. Scanning electron microscopy was used to identify the key stage of floral initiation, and transcriptome analysis was used to reveal the transcriptional regulatory network in old leaves involved in floral initiation. We mined 5 DEGs related to energy and 55 DEGs related to plant hormone signal transduction, and we found floral initiation induction required a high level of energy metabolism, and the phytohormones signals in the old leaves regulate floral initiation, which occurred at stage I and II. Twenty-seven rhythm-related DEGs and 107 genes associated with flowering were also identified, and the circadian rhythm interacted with photoperiod pathways to induce floral initiation. Unigene0017292 (PSEUDO-RESPONSE REGULATOR), Unigene0046809 (LATE ELONGATED HYPOCOTYL), Unigene0009932 (GIGANTEA), Unigene0001842 (CONSTANS), and Unigene0084708 (FLOWER LOCUS T) were the key genes in the circadian rhythm-photoperiod regulatory network. In conjunction with morphological observations and transcriptomic analysis, we concluded that the induction of floral initiation by old leaves in C. oleifera ‘changlin53’ mainly occurred during stages I and II, floral initiation was completed during stage III, and rhythm–photoperiod interactions may be the source of the main signals in floral initiation induced by old leaves.
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Identification of Key Genes Related to Dormancy Control in Prunus Species by Meta-Analysis of RNAseq Data. PLANTS 2022; 11:plants11192469. [PMID: 36235335 PMCID: PMC9573011 DOI: 10.3390/plants11192469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/18/2022]
Abstract
Bud dormancy is a genotype-dependent mechanism observed in Prunus species in which bud growth is inhibited, and the accumulation of a specific amount of chilling (endodormancy) and heat (ecodormancy) is necessary to resume growth and reach flowering. We analyzed publicly available transcriptome data from fifteen cultivars of four Prunus species (almond, apricot, peach, and sweet cherry) sampled at endo- and ecodormancy points to identify conserved genes and pathways associated with dormancy control in the genus. A total of 13,018 genes were differentially expressed during dormancy transitions, of which 139 and 223 were of interest because their expression profiles correlated with endo- and ecodormancy, respectively, in at least one cultivar of each species. The endodormancy-related genes comprised transcripts mainly overexpressed during chilling accumulation and were associated with abiotic stresses, cell wall modifications, and hormone regulation. The ecodormancy-related genes, upregulated after chilling fulfillment, were primarily involved in the genetic control of carbohydrate regulation, hormone biosynthesis, and pollen development. Additionally, the integrated co-expression network of differentially expressed genes in the four species showed clusters of co-expressed genes correlated to dormancy stages and genes of breeding interest overlapping with quantitative trait loci for bloom time and chilling and heat requirements.
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10
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Wu Z, Huang L, Huang F, Lu G, Wei S, Liu C, Deng H, Liang G. Temporal transcriptome analysis provides molecular insights into flower development in red-flesh pitaya. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Liang J, Zheng J, Wu Z, Wang H. Time-Course Transcriptomic Profiling of Floral Induction in Cultivated Strawberry. Int J Mol Sci 2022; 23:ijms23116126. [PMID: 35682808 PMCID: PMC9181015 DOI: 10.3390/ijms23116126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 12/04/2022] Open
Abstract
The initiation and quality of flowering directly affect the time to market and economic benefit of cultivated strawberries, but the underlying mechanisms of these processes are largely unknown. To investigate the gene activity during the key period of floral induction in strawberries, time-course transcriptome analysis was performed on the shoot apex of the strawberry cultivar ‘Benihoppe.’ A total of 7177 differentially expressed genes (DEGs) were identified through pairwise comparisons. These DEGs were grouped into four clusters with dynamic expression patterns. By analyzing the key genes in the potential flowering pathways and the development of the leaf and flower, at least 73 DEGs that may be involved in the regulatory network of floral induction in strawberries were identified, some of which belong to the NAC, MYB, MADS, and SEB families. A variety of eight hormone signaling pathway genes that might play important roles in floral induction were analyzed. In particular, the gene encoding DELLA, a key inhibitor of the gibberellin signaling pathway, was found to be significantly differentially expressed during the floral induction. Furthermore, the differential expression of some important candidate genes, such as TFL1, SOC1, and GAI-like, was further verified by qRT-PCR. Therefore, we used this time-course transcriptome data for a preliminary exploration of the regulatory network of floral induction and to provide potential candidate genes for future studies of flowering in strawberries.
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Affiliation(s)
- Jiahui Liang
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (J.L.); (J.Z.)
| | - Jing Zheng
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (J.L.); (J.Z.)
| | - Ze Wu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Hongqing Wang
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (J.L.); (J.Z.)
- Correspondence: ; Tel.: +86-136-8301-8901
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Characterization of Phytohormones and Transcriptomic Profiling of the Female and Male Inflorescence Development in Manchurian Walnut ( Juglans mandshurica Maxim.). Int J Mol Sci 2022; 23:ijms23105433. [PMID: 35628244 PMCID: PMC9143237 DOI: 10.3390/ijms23105433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 12/18/2022] Open
Abstract
Flowers are imperative reproductive organs and play a key role in the propagation of offspring, along with the generation of several metabolic products in flowering plants. In Juglans mandshurica, the number and development of flowers directly affect the fruit yield and subsequently its commercial value. However, owing to the lack of genetic information, there are few studies on the reproductive biology of Juglans mandshurica, and the molecular regulatory mechanisms underlying the development of female and male inflorescence remain unclear. In this study, phytohormones and transcriptomic sequencing analyses at the three stages of female and male inflorescence growth were performed to understand the regulatory functions underlying flower development. Gibberellin is the most dominant phytohormone that regulates flower development. In total, 14,579 and 7188 differentially expressed genes were identified after analyzing the development of male and female flowers, respectively, wherein, 3241 were commonly expressed. Enrichment analysis for significantly enriched pathways suggested the roles of MAPK signaling, phytohormone signal transduction, and sugar metabolism. Genes involved in floral organ transition and flowering were obtained and analyzed; these mainly belonged to the M-type MADS-box gene family. Three flowering-related genes (SOC1/AGL20, ANT, and SVP) strongly interacted with transcription factors in the co-expression network. Two key CO genes (CO3 and CO1) were identified in the photoperiod pathway. We also identified two GA20xs genes, one SVP gene, and five AGL genes (AGL8, AGL9, AGL15, AGL19, and AGL42) that contributed to flower development. The findings are expected to provide a genetic basis for the studies on the regulatory networks and reproductive biology in inflorescence development for J. mandshurica.
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Xanthopoulou A, Moysiadis T, Bazakos C, Karagiannis E, Karamichali I, Stamatakis G, Samiotaki M, Manioudaki M, Michailidis M, Madesis P, Ganopoulos I, Molassiotis A, Tanou G. The perennial fruit tree proteogenomics atlas: a spatial map of the sweet cherry proteome and transcriptome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1319-1336. [PMID: 34842310 DOI: 10.1111/tpj.15612] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Genome-wide transcriptome analysis provides systems-level insights into plant biology. Due to the limited depth of quantitative proteomics our understanding of gene-protein-complex stoichiometry is largely unknown in plants. Recently, the complexity of the proteome and its cell-/tissue-specific distribution have boosted the research community to the integration of transcriptomics and proteomics landscapes in a proteogenomic approach. Herein, we generated a quantitative proteome and transcriptome abundance atlas of 15 major sweet cherry (Prunus avium L., cv 'Tragana Edessis') tissues represented by 29 247 genes and 7584 proteins. Additionally, 199 984 alternative splicing events, particularly exon skipping and alternative 3' splicing, were identified in 23 383 transcribed regions of the analyzed tissues. Common signatures as well as differences between mRNA and protein quantities, including genes encoding transcription factors and allergens, within and across the different tissues are reported. Using our integrated dataset, we identified key putative regulators of fruit development, notably genes involved in the biosynthesis of anthocyanins and flavonoids. We also provide proteogenomic-based evidence for the involvement of ethylene signaling and pectin degradation in cherry fruit ripening. Moreover, clusters of genes and proteins with similar and different expression and suppression trends across diverse tissues and developmental stages revealed a relatively low RNA abundance-to-protein correlation. The present proteogenomic analysis allows us to identify 17 novel sweet cherry proteins without prior protein-level annotation evidenced in the currently available databases. To facilitate use by the community, we also developed the Sweet Cherry Atlas Database (https://grcherrydb.com/) for viewing and data mining these resources. This work provides new insights into the proteogenomics workflow in plants and a rich knowledge resource for future investigation of gene and protein functions in Prunus species.
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Affiliation(s)
- Aliki Xanthopoulou
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
| | - Theodoros Moysiadis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
- Department of Computer Science, School of Sciences and Engineering, University of Nicosia, Nicosia, 2417, Cyprus
| | - Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Evangelos Karagiannis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
| | - Ioanna Karamichali
- Institute of Applied Biosciences, CERTH, Thessaloniki-Thermi, 57001, Greece
| | - George Stamatakis
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Vari, 16672, Greece
| | - Martina Samiotaki
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Vari, 16672, Greece
| | - Maria Manioudaki
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
| | - Michail Michailidis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thessaloniki-Thermi, 57001, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
| | - Georgia Tanou
- Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
- Institute of Soil and Water Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
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Hou Q, Li S, Shang C, Wen Z, Cai X, Hong Y, Qiao G. Genome-wide characterization of chalcone synthase genes in sweet cherry and functional characterization of CpCHS1 under drought stress. FRONTIERS IN PLANT SCIENCE 2022; 13:989959. [PMID: 36061761 PMCID: PMC9437463 DOI: 10.3389/fpls.2022.989959] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/03/2022] [Indexed: 05/22/2023]
Abstract
Cherries are one of the important fruit trees. The growth of cherry is greatly affected by abiotic stresses such as drought, which hinders its development. Chalcone synthase (CHS, EC 2.3.1.74) is a crucial rate-limiting enzyme in the flavonoid biosynthetic pathway that plays an important role in regulating plant growth, development, and abiotic stress tolerance. In the current study, three genes encoding chalcone synthase were identified in the genome of sweet cherry (Prunus avium L.). The three genes contained fewer introns and showed high homology with CHS genes of other Rosaceae members. All members are predicted to localize in the cytoplasm. The conserved catalytic sites may be located at the Cys163, Phe214, His302, and Asn335 residues. These genes were differentially expressed during flower bud dormancy and fruit development. The total flavonoid content of Chinese cherry (Cerasus pseudocerasus Lindl.) was highest in the leaves and slightly higher in the pulp than in the peel. No significant difference in total flavonoid content was detected between aborted kernels and normally developing kernels. Overexpression of Chinese cherry CpCHS1 in tobacco improved the germination frequency of tobacco seeds under drought stress, and the fresh weight of transgenic seedlings under drought stress was higher than that of the wild type, and the contents of SOD, POD, CAT, and Pro in OE lines were significantly increased and higher than WT under drought stress. These results indicate cherry CHS genes are conserved and functionally diverse and will assist in elucidating the functions of flavonoid synthesis pathways in cherry and other Rosaceae species under drought stress.
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Affiliation(s)
- Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Shuang Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Chunqiong Shang
- College of Forestry, Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, China
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Xiaowei Cai
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Yi Hong
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- *Correspondence: Guang Qiao,
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Gómez-Ocampo G, Ploschuk EL, Mantese A, Crocco CD, Botto JF. BBX21 reduces abscisic acid sensitivity, mesophyll conductance and chloroplast electron transport capacity to increase photosynthesis and water use efficiency in potato plants cultivated under moderated drought. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1131-1144. [PMID: 34606658 DOI: 10.1111/tpj.15499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 09/11/2021] [Indexed: 05/14/2023]
Abstract
The B-box (BBX) proteins are zinc-finger transcription factors with a key role in growth and developmental regulatory networks mediated by light. AtBBX21 overexpressing (BBX21-OE) potato (Solanum tuberosum) plants, cultivated in optimal water conditions, have a higher photosynthesis rate and stomatal conductance without penalty in water use efficiency (WUE) and with a higher tuber yield. In this work, we cultivated potato plants in two water regimes: 100 and 35% field capacity of water restriction that imposed leaf water potentials between -0.3 and -1.2 MPa for vegetative and tuber growth during 14 or 28 days, respectively. We found that 42-day-old plants of BBX21-OE were more tolerant to water restriction with higher levels of chlorophylls and tuber yield than wild-type spunta (WT) plants. In addition, the BBX21-OE lines showed higher photosynthesis rates and WUE under water restriction during the morning. Mechanistically, we found that BBX21-OE lines were more tolerant to moderated drought by enhancing mesophyll conductance (gm ) and maximum capacity of electron transport (Jmax ), and by reducing abscisic acid (ABA) sensitivity in plant tissues. By RNA-seq analysis, we found 204 genes whose expression decreased by drought in WT plants and expressed independently of the water condition in BBX21-OE lines as SAP12, MYB73, EGYP1, TIP2-1 and DREB2A, and expressions were confirmed by quantitative polymerase chain reaction. These results suggest that BBX21 interplays with the ABA and growth signaling networks, improving the photosynthetic behavior in suboptimal water conditions with an increase in potato tuber yield.
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Affiliation(s)
- Gabriel Gómez-Ocampo
- Universidad de Buenos Aires, Facultad de Agronomía, IFEVA, CONICET., Av. San Martín 4453, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Edmundo L Ploschuk
- Universidad de Buenos Aires, Facultad de Agronomía, Cátedra de Cultivos Industriales, Av. San Martín 4453, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Anita Mantese
- Universidad de Buenos Aires, Facultad de Agronomía, Cátedra de Botánica General, Av. San Martín 4453, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Carlos D Crocco
- Universidad de Buenos Aires, Facultad de Agronomía, IFEVA, CONICET., Av. San Martín 4453, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Javier F Botto
- Universidad de Buenos Aires, Facultad de Agronomía, IFEVA, CONICET., Av. San Martín 4453, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
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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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Goeckeritz C, Hollender CA. There is more to flowering than those DAM genes: the biology behind bloom in rosaceous fruit trees. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101995. [PMID: 33444911 DOI: 10.1016/j.pbi.2020.101995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 05/06/2023]
Abstract
The regulation of bloom time in deciduous fruit trees is an area of increasing interest due to the negative impact of climate change on fruit production. Although flower development has been well-studied in model species, there are many knowledge gaps about this process in perennial fruit trees, whose floral development spans the four seasons and includes many temperature-driven transitions. To develop solutions for minimizing crop loss, a comprehensive research strategy is needed to understand flower development and bloom time in deciduous fruit trees. This approach must incorporate genetic, physiological, and phenological strategies which include morphological and molecular analyses. Here, we describe key floral development events for rosaceae family fruit trees, highlight recent molecular and genetic discoveries, and discuss future directions for this field.
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Affiliation(s)
- Charity Goeckeritz
- Michigan State University Department of Horticulture, East Lansing, MI 48824, United States
| | - Courtney A Hollender
- Michigan State University Department of Horticulture, East Lansing, MI 48824, United States.
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Convergence and Divergence of Sugar and Cytokinin Signaling in Plant Development. Int J Mol Sci 2021; 22:ijms22031282. [PMID: 33525430 PMCID: PMC7865218 DOI: 10.3390/ijms22031282] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/19/2021] [Accepted: 01/24/2021] [Indexed: 02/06/2023] Open
Abstract
Plants adjust their growth and development through a sophisticated regulatory system integrating endogenous and exogenous cues. Many of them rely on intricate crosstalk between nutrients and hormones, an effective way of coupling nutritional and developmental information and ensuring plant survival. Sugars in their different forms such as sucrose, glucose, fructose and trehalose-6-P and the hormone family of cytokinins (CKs) are major regulators of the shoot and root functioning throughout the plant life cycle. While their individual roles have been extensively investigated, their combined effects have unexpectedly received little attention, resulting in many gaps in current knowledge. The present review provides an overview of the relationship between sugars and CKs signaling in the main developmental transition during the plant lifecycle, including seed development, germination, seedling establishment, root and shoot branching, leaf senescence, and flowering. These new insights highlight the diversity and the complexity of the crosstalk between sugars and CKs and raise several questions that will open onto further investigations of these regulation networks orchestrating plant growth and development.
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