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Loarca J, Liou M, Dawson JC, Simon PW. Advancing utilization of diverse global carrot ( Daucus carota L.) germplasm with flowering habit trait ontology. FRONTIERS IN PLANT SCIENCE 2024; 15:1342513. [PMID: 38779064 PMCID: PMC11110672 DOI: 10.3389/fpls.2024.1342513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/26/2024] [Indexed: 05/25/2024]
Abstract
Biennial vegetable crops are challenging to breed due to long breeding cycle times. At the same time, it is important to preserve a strong biennial growth habit, avoiding premature flowering that renders the crop unmarketable. Gene banks carry important genetic variation which may be essential to improve crop resilience, but these collections are underutilized due to lack of characterization for key traits like bolting tendency for biennial vegetable crops. Due to concerns about introducing undesirable traits such as premature flowering into elite germplasm, many accessions may not be considered for other key traits that benefit growers, leaving crops more vulnerable to pests, diseases, and abiotic stresses. In this study, we develop a method for characterizing flowering to identify accessions that are predominantly biennial, which could be incorporated into biennial breeding programs without substantially increasing the risk of annual growth habits. This should increase the use of these accessions if they are also sources of other important traits such as disease resistance. We developed the CarrotOmics flowering habit trait ontology and evaluated flowering habit in the largest (N=695), and most diverse collection of cultivated carrots studied to date. Over 80% of accessions were collected from the Eurasian supercontinent, which includes the primary and secondary centers of carrot diversity. We successfully identified untapped genetic diversity in biennial carrot germplasm (n=197 with 0% plants flowering) and predominantly-biennial germplasm (n=357 with <15% plants flowering). High broad-sense heritability for flowering habit (0.81 < H2< 0.93) indicates a strong genetic component of this trait, suggesting that these carrot accessions should be consistently biennial. Breeders can select biennial plants and eliminate annual plants from a predominantly biennial population. The establishment of the predominantly biennial subcategory nearly doubles the availability of germplasm with commercial potential and accounts for 54% of the germplasm collection we evaluated. This subcollection is a useful source of genetic diversity for breeders. This method could also be applied to other biennial vegetable genetic resources and to introduce higher levels of genetic diversity into commercial cultivars, to reduce crop genetic vulnerability. We encourage breeders and researchers of biennial crops to optimize this strategy for their particular crop.
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Affiliation(s)
- Jenyne Loarca
- Vegetable Crops Research Unit, United States Department of Agriculture, Madison, WI, United States
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael Liou
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, United States
| | - Julie C. Dawson
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Philipp W. Simon
- Vegetable Crops Research Unit, United States Department of Agriculture, Madison, WI, United States
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
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Godwin A, McGill C, Ward A, Sofkova-Bobcheva S, Pieralli S. Phenological phase affects carrot seed production sensitivity to climate change - A panel data analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 892:164502. [PMID: 37268143 DOI: 10.1016/j.scitotenv.2023.164502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/04/2023]
Abstract
New Zealand is a major producer of carrot seeds globally. Carrots are an important nutritional crop for human consumption. Since the growth and development of carrot seed crops mainly depend on climatic factors, seed yield is extremely susceptible to climate change. This modeling study was undertaken using a panel data approach to determine the impact of the atmospheric conditions (proxied by maximum and minimum temperature) and precipitation during the critical growth stages for seed production in carrot, viz., juvenile phase, vernalization phase, floral development phase, and flowering and seed development phase on carrot seed yield. The panel dataset was created using cross-sections from 28 locations within the Canterbury and Hawke's Bay regions of New Zealand that cultivate carrot seed crops and time series from 2005 to 2022. Pre-diagnostic tests were performed to test the model assumptions, and a fixed effect model was selected subsequently. There was significant (p < 0.01) variability in temperature and rainfall throughout different growing phases, except for precipitation at the vernalization phase. The highest rate of changes in maximum temperature, minimum temperature, and precipitation were recorded during the vernalization phase (+0.254 °C per year), floral development phase (+0.18 °C per year), and juvenile phase (-6.508 mm per year), respectively. Based on marginal effect analysis, the highest significant influence of minimum (187.724 kg/ha of seed yield decrease for each 1 °C increment) and maximum temperature (1 °C rise increases seed yield by 132.728 kg/ha), and precipitation (1 mm increment of rainfall decreases the seed yield by 1.745 kg/ha) on carrot seed yield were reported at vernalization, and flowering and seed development, respectively. The minimum and maximum temperatures have a higher marginal effect on carrot seed production. Analysis of the panel data demonstrates that the production of carrot seeds will be vulnerable to climatic change.
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Affiliation(s)
- Asharp Godwin
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; Department of Agronomy, Faculty of Agriculture, University of Jaffna, Ariviyal Nagar, Kilinochchi, Sri Lanka.
| | - Craig McGill
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Andrew Ward
- AsureQuality Limited, Batchelar Agriculture Centre, Tennent Drive, PO Box 609, Palmerston North 4440, New Zealand
| | - Svetla Sofkova-Bobcheva
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Simone Pieralli
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; European Commission Joint Research Centre, 41092 Seville, Spain
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Li M, Li M, Wang L, Li M, Wei J. Apiaceae Medicinal Plants in China: A Review of Traditional Uses, Phytochemistry, Bolting and Flowering (BF), and BF Control Methods. Molecules 2023; 28:molecules28114384. [PMID: 37298861 DOI: 10.3390/molecules28114384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Apiaceae plants have been widely used in traditional Chinese medicine (TCM) for the removing dampness, relieving superficies, and dispelling cold, etc. In order to exploit potential applications as well as improve the yield and quality of Apiaceae medicinal plants (AMPs), the traditional use, modern pharmacological use, phytochemistry, effect of bolting and flowering (BF), and approaches for controlling BF were summarized. Currently, about 228 AMPs have been recorded as TCMs, with 6 medicinal parts, 79 traditional uses, 62 modern pharmacological uses, and 5 main kinds of metabolites. Three different degrees (i.e., significantly affected, affected to some extent, and not significantly affected) could be classed based on the yield and quality. Although the BF of some plants (e.g., Angelica sinensis) could be effectively controlled by standard cultivation techniques, the mechanism of BF has not yet been systemically revealed. This review will provide useful references for the reasonable exploration and high-quality production of AMPs.
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Affiliation(s)
- Meiling Li
- State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Min Li
- State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Li Wang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen 518120, China
| | - Mengfei Li
- State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
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Liu X, Zhao D, Ou C, Hao W, Zhao Z, Zhuang F. Genome-wide identification and characterization profile of phosphatidy ethanolamine-binding protein family genes in carrot. Front Genet 2022; 13:1047890. [PMID: 36437940 PMCID: PMC9696379 DOI: 10.3389/fgene.2022.1047890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2023] Open
Abstract
Members of the family of Phosphatidy Ethanolamine-Binding Protein (PEBP) have been shown to be key regulators of the transition of plants from vegetative to reproductive phases. Here, a total of 12 PEBP proteins were identified in the carrot (Daucus carota L.) genome and classified into FT-like (4), TFL1-like (6), and MFT-like 2) subfamilies, that had different lengths (110-267 aa) and were distributed unevenly across seven chromosomes. Moreover, 13 and 31 PEBP proteins were identified in other two Apiaceae species, celery (Apium graveolens L.) and coriander (Coriandrum sativum L.). The phylogenetic and evolutionary results of these PEBP family proteins were obtained based on the protein sequences. In the three Apiaceae species, purifying selection was the main evolutionary force, and WGD, segmental duplication, and dispersed duplication have played key roles in the PEBP family expansion. The expression analysis showed that carrot PEBP genes exhibited relatively broad expression patterns across various tissues. In the period of bolting to flowering, the carrot FT-like subfamily genes were upregulated as positive regulators, and TFL1-like subfamily genes remained at lower expression levels as inhibitors. More interestingly, the members of carrot FT-like genes had different temporal-spatial expression characteristics, suggesting that they have different regulatory functions in the carrot reproductive phase. In summary, this study contributes to our understanding of the PEBP family proteins and provides a foundation for exploring the mechanism of carrot bolting and flowering for the breeding of cultivars with bolting resistance.
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Affiliation(s)
| | | | | | | | | | - Feiyun Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, China
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Ou C, Sun T, Liu X, Li C, Li M, Wang X, Ren H, Zhao Z, Zhuang F. Detection of Chromosomal Segments Introgressed from Wild Species of Carrot into Cultivars: Quantitative Trait Loci Mapping for Morphological Features in Backcross Inbred Lines. PLANTS (BASEL, SWITZERLAND) 2022; 11:391. [PMID: 35161370 PMCID: PMC8840429 DOI: 10.3390/plants11030391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although several studies have focused on identifying genetic loci that contribute to the morphology of storage roots. A backcross inbred line (BIL) population derived from a cross between the wild species Daucus carota ssp. carota "Songzi" and the orange cultivar "Amsterdam forcing" was developed. The morphological features in the BIL population became more diverse after several generations of selfing BC2F1 plants. Only few lines retained features of wild parent. Genomic resequencing of the two parental lines and the BILs resulted in 3,223,651 single nucleotide polymorphisms (SNPs), and 13,445 bin markers were generated using a sliding window approach. We constructed a genetic map with 2027 bins containing 154,776 SNPs; the total genetic distance was 1436.43 cM and the average interval between the bins was 0.71 cm. Five stable QTLs related to root length, root shoulder width, dry material content of root, and ratio of root shoulder width to root middle width were consistently detected on chromosome 2 in both years and explained 23.4-66.9% of the phenotypic variance. The effects of introgressed genomic segments from the wild species on the storage root are reported and will enable the identification of functional genes that control root morphological traits in carrot.
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Affiliation(s)
- Chenggang Ou
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Tingting Sun
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Xing Liu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Chengjiang Li
- Suzhou Academy of Agricultural Science, Suzhou 234000, China; (C.L.); (H.R.)
| | - Min Li
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Xuewei Wang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Huaifu Ren
- Suzhou Academy of Agricultural Science, Suzhou 234000, China; (C.L.); (H.R.)
| | - Zhiwei Zhao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Feiyun Zhuang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
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Ghorbani F, Abolghasemi R, Haghighi M, Etemadi N, Wang S, Karimi M, Soorni A. Global identification of long non-coding RNAs involved in the induction of spinach flowering. BMC Genomics 2021; 22:704. [PMID: 34587906 PMCID: PMC8482690 DOI: 10.1186/s12864-021-07989-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait. Results In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. Conclusions This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07989-1.
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Affiliation(s)
- Fatemeh Ghorbani
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Reza Abolghasemi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Maryam Haghighi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Shui Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Marzieh Karimi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.,Department of Plant Breeding and Biotechnology, College of Agriculture, University of Shahrekord, Shahrekord, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
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Abolghasemi R, Haghighi M, Etemadi N, Wang S, Soorni A. Transcriptome architecture reveals genetic networks of bolting regulation in spinach. BMC PLANT BIOLOGY 2021; 21:179. [PMID: 33853527 PMCID: PMC8045288 DOI: 10.1186/s12870-021-02956-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/31/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Bolting refers to the early flowering stem production on agricultural and horticultural crops before harvesting. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components, which cause a large reduction in the quality and productivity of vegetable crops like spinach. However, little is known about the signaling pathways and molecular functions involved in bolting mechanisms in spinach. The genetic information regarding the transition from vegetative growth to the reproductive stage in spinach would represent an advantage to regulate bolting time and improvement of resistant cultivars to minimize performance loss. RESULTS To investigate the key genes and their genetic networks controlling spinach bolting, we performed RNA-seq analysis on early bolting accession Kashan and late-bolting accession Viroflay at both vegetative and reproductive stages and found a significant number of differentially expressed genes (DEGs) ranging from 195 to 1230 in different comparisons. These genes were mainly associated with the signaling pathways of vernalization, photoperiod/circadian clock, gibberellin, autonomous, and aging pathways. Gene ontology analysis uncovered terms associated with carbohydrate metabolism, and detailed analysis of expression patterns for genes of Fructose-1, 6-bisphosphate aldolase, TREHALOSE-6-PHOSPHATE SYNTHASE 1, FLOWERING PROMOTING FACTOR 1, EARLY FLOWERING, GIGANTEA, and MADS-box proteins revealed their potential roles in the initiating or delaying of bolting. CONCLUSION This study is the first report on identifying bolting and flowering-related genes based on transcriptome sequencing in spinach, which provides insight into bolting control and can be useful for molecular breeding programs and further study in the regulation of the genetic mechanisms related to bolting in other vegetable crops.
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Affiliation(s)
- Reza Abolghasemi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Maryam Haghighi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Shui Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
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Regulation of flowering under short photoperiods based on transcriptomic and metabolomic analysis in Phaseolus vulgaris L. Mol Genet Genomics 2021; 296:379-390. [PMID: 33449160 DOI: 10.1007/s00438-020-01751-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
Common bean (Phaseolus vulgaris L.) is a short-day plant and its flowering time, and consequently, pod yield and quality is influenced by photoperiod. In this study, the photoperiodic-sensitive variety 'Hong jin gou', which flowers 31 days (d) earlier in short-day than in long-day, was used as the experimental material. Samples were collected to determine the growth and photosynthetic parameters in each daylength treatment, and transcriptome and metabolome data were conducted. We identified eight genes related to flowering by further screening for differentially expressed genes. These genes function to regulate the biological clock. The combination of differentially expressed genes and metabolites, together with the known regulation network of flowering time and the day-night expression pattern of related genes allow us to speculate on the regulation of flowering time in the common bean and conclude that TIMING OF CAB EXPRESSION1 (TOC1) plays a pivotal role in the network and its upregulation or downregulation causes corresponding changes in the expression of downstream genes. The regulatory network is also influenced by gibberellic acid (GA) and jasmonic acid (JA). These regulatory pathways jointly comprise the flowering regulatory network in common bean.
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The Response of COL and FT Homologues to Photoperiodic Regulation in Carrot (Daucus carota L.). Sci Rep 2020; 10:9984. [PMID: 32561786 PMCID: PMC7305175 DOI: 10.1038/s41598-020-66807-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/22/2020] [Indexed: 11/13/2022] Open
Abstract
Carrot (Daucus carota L.) is a biennial plant requiring vernalization to induce flowering, but long days can promote its premature bolting and flowering. The basic genetic network controlling the flowering time has been constructed for carrot, but there is limited information on the molecular mechanisms underlying the photoperiodic flowering response. The published carrot genome could provide an effective tool for systematically retrieving the key integrator genes of GIGANTEA (GI), CONSTANS-LIKE (COL), FLOWERING LOCUS T (FT), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) homologues in the photoperiod pathway. In this study, the bolting time of wild species “Songzi” (Ws) could be regulated by different photoperiods, but the orange cultivar “Amsterdam forcing” (Af) displayed no bolting phenomenon. According to the carrot genome and previous de novo transcriptome, 1 DcGI, 15 DcCOLs, 2 DcFTs, and 3 DcSOC1s were identified in the photoperiod pathway. The circadian rhythm peaks of DcGI, DcCOL2, DcCOL5a, and DcCOL13b could be delayed under long days (LDs). The peak value of DcCOL2 in Af (12.9) was significantly higher than that in Ws (6.8) under short day (SD) conditions, and was reduced under LD conditions (5.0). The peak values of DcCOL5a in Ws were constantly higher than those in Af under the photoperiod treatments. The expression levels of DcFT1 in Ws (463.0) were significantly upregulated under LD conditions compared with those in Af (1.4). These responses of DcCOL2, DcCOL5a, and DcFT1 might be related to the different bolting responses of Ws and Af. This study could provide valuable insights into understanding the key integrator genes in the carrot photoperiod pathway.
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Differentially Expressed Genes between Carrot Petaloid Cytoplasmic Male Sterile and Maintainer during Floral Development. Sci Rep 2019; 9:17384. [PMID: 31757985 PMCID: PMC6874560 DOI: 10.1038/s41598-019-53717-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/31/2019] [Indexed: 11/09/2022] Open
Abstract
Petaloid cytoplasmic male sterility (CMS) is a maternally inherited loss of male fertility due to the complete conversion of stamens into petal-like organs, and CMS lines have been widely utilized in carrot breeding. Petaloid CMS is an ideal model not only for studying the mitochondrial-nuclear interaction but also for discovering genes that are essential for floral organ development. To investigate the comprehensive mechanism of CMS and homeotic organ alternation during carrot flower development, we conducted transcriptome analysis between the petaloid CMS line (P2S) and its maintainer line (P2M) at four flower developmental stages (T1-T4). A total of 2838 genes were found to be differentially expressed, among which 1495 genes were significantly downregulated and 1343 genes were significantly upregulated in the CMS line. Functional analysis showed that most of the differentially expressed genes (DEGs) were involved in protein processing in the endoplasmic reticulum, plant hormone signal transduction, and biosynthesis. A total of 16 MADS-box genes were grouped into class A, B, C, and E, but not class D, genes. Several key genes associated with oxidative phosphorylation showed continuously low expression from stage T2 in P2S, and the expression of DcPI and DcAG-like genes also greatly decreased at stage T2 in P2S. This indicated that energy deficiency might inhibit the expression of B- and C-class MADS-box genes resulting in the conversion of stamens into petals. Stamen petaloidy may act as an intrinsic stress, upregulating the expression of heat shock protein (HSP) genes and MADS-box genes at stages T3 and T4 in P2S, which results in some fertile revertants. This study will provide a better understanding of carrot petaloid CMS and floral development as a basis for further research.
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