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Wu H, Zhang Z, Liu Z, Meng Q, Xu Z, Zhang H, Qian W, She H. Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Bolting Periods in Spinacia oleracea. Genes (Basel) 2023; 15:36. [PMID: 38254926 PMCID: PMC10815260 DOI: 10.3390/genes15010036] [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: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Bolting is a symbol of the transition from vegetative to reproductive growth in plants. Late bolting can effectively prolong the commercial value of spinach and is of great importance for spinach breeding. Bolting has complex regulatory networks, and current research on spinach bolting is relatively weak, with specific regulatory pathways and genes unclear. To clarify the regulatory characteristics and key genes related to bolting in spinach, we conducted a comparative transcriptome analysis. In this study, 18 samples from three periods of bolting-tolerant spinach material 12S3 and bolting-susceptible material 12S4 were analyzed using RNA-seq on, resulting in 10,693 differentially expressed genes (DEGs). Functional enrichment and co-expression trend analysis indicated that most DEGs were enriched in the photoperiod pathway, the hormone signaling pathway, and the cutin, suberin, and wax biosynthetic pathways. According to the weighted gene co-expression network analysis (WGCNA), SpFT (SOV4g003400), SOV4g040250, and SpGASA1 (SOV6g017600) were likely to regulate bolting through the gibberellin and photoperiod pathways, and SpELF4 (SOV1g028600) and SpPAT1 (SOV4g058860) caused differences in early and late bolting among different cultivars. These results provide important insights into the genetic control of bolting in spinach and will help elucidate the molecular mechanisms of bolting in leafy vegetables.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhilong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qing Meng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Jin Y, Luo X, Li Y, Peng X, Wu L, Yang G, Xu X, Pei Y, Li W, Zhang W. Fine mapping and analysis of candidate genes for qBT2 and qBT7.2 locus controlling bolting time in radish (Raphanus sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:4. [PMID: 38085292 DOI: 10.1007/s00122-023-04503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE Two major QTLs for bolting time in radish were mapped to chromosome 02 and 07 in a 0.37 Mb and 0. 52 Mb interval, RsFLC1 and RsFLC2 is the critical genes. Radish (Raphanus sativus L.) is an important vegetable crop of Cruciferae. The premature bolting and flowering reduces the yield and quality of the fleshy root of radish. However, the molecular mechanism underlying bolting and flowering in radish remains unknown. In YZH (early bolting) × XHT (late bolting) F2 population, a high-density genetic linkage map was constructed with genetic distance of 2497.74 cM and an average interval of 2.31 cM. A total of nine QTLs for bolting time and two QTLs for flowering time were detected. Three QTLs associated with bolting time in radish were identified by QTL-seq using radish GDE (early bolting) × GDL (late bolting) F2 population. Fine mapping narrowed down qBT2 and qBT7.2 to an 0.37 Mb and 0.52 Mb region on chromosome 02 and 07, respectively. RNA-seq and qRT-PCR analysis showed that RsFLC1 and RsFLC2 were the candidate gene for qBT7.2 and qBT2 locus, respectively. Subcellular localization exhibited that RsFLC1 and RsFLC2 were mainly expressed in the nucleus. A 1856-bp insertion in the first intron of RsFLC1 was responsible for bolting time. Overexpression of RsFLC2 in Arabidopsis was significantly delayed flowering. These findings will provide new insights into the exploring the molecular mechanism of late bolting and promote the marker-assisted selection for breeding late-bolting varieties in radish.
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Affiliation(s)
- Yueyue Jin
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Xiaobo Luo
- Guizhou Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, 550003, Guizhou, China
| | - Yadong Li
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Xiao Peng
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Linjun Wu
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Guangqian Yang
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Xiuhong Xu
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Yun Pei
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Wei Li
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Guizhou Higher Education Facility Vegetable Engineering Reseach Centre, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Wanping Zhang
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China.
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China.
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Ma F, Jiang Y, Li B, Zeng Y, Shang H, Wang F, Sun Z. The Dynamic Accumulation Rules of Chemical Components during the Medicine Formation Period of Angelica sinensis and Chemometric Classifying Analysis for Different Bolting Times Using ATR-FTIR. Molecules 2023; 28:7292. [PMID: 37959713 PMCID: PMC10649412 DOI: 10.3390/molecules28217292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The dried roots of the perennial herb Angelica sinensis (Oliv.) Diels (AS) are commonly used as medicinal and edible resources. In commercial planting, early bolting and flowering (EB) of ca. 60% in the medicine formation period reduces root yield and quality, becoming a significant bottleneck in agricultural production. In the cultivation process, summer bolting (SB) occurs from June to July, and autumn bolting (AB) occurs in September. The AB root is often mistaken for the AS root due to its similar morphological characteristics. Few studies have involved whether the root of AB could be used as herbal medicine. This study explored and compared the accumulation dynamics of primary and secondary metabolites in AS and EB roots during the vegetative growth stage (from May to September) by light microscopy, ultraviolet spectrometry, and HPLC methods. Under a microscope, the amount of free starch granules and oil chamber in the AS root increased. On the contrary, they decreased further from EB-Jul to EB-Sep. By comparison, the wall of the xylem vessel was slightly thickened and stacked, and the cell walls of parenchyma and root cortex tissue were thickened in the EB root. Early underground bolting reduces soluble sugar, soluble protein, free amino acids, total C element, total N element, ferulic acid, and ligustilide accumulation, accompanied by the lignification of the root during the vegetative growth stage. Furthermore, a total of 55 root samples from different bolting types of AS root (29 samples), SB root (14 samples), and AB root (12 samples) were collected from Gansu Province during the harvesting period (October). The later the bolting occurred, the less difference there was between unbolted and bolted roots in terms of morphological appearance and efficacy components. Fourier transform infrared spectroscopy with the attenuated total reflection mode (ATR-FTIR) provides a "holistic" spectroscopic fingerprinting of all compositions in the tested sample. The ATR-FTIR spectrum of the AB root was similar to that of the AS root. However, the number and location of absorption peaks in the spectra of SB were different, and only one strong absorption peak at 1021 cm-1 was regarded as the characteristic peak of C-O stretching vibration in lignin. The ATR-FTIR spectra can be effectively differentiated based on their various characteristics using orthogonal partial least squares discrimination analysis (OPLS-DA). Results were assessed using multiple statistical techniques, including Spearman's correlation, principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and OPLS-DA. Among these methods, the ATR-FTIR data demonstrated the most effective outcomes in differentiating between viable and non-viable roots for their application in herbal medicine. Essential substances are ferulic acid and flavonoid, which are much more abundant in the AB root. It provides a material basis for the pharmacological action of the AB roots and a theoretical basis for improving their availability.
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Affiliation(s)
- Fang Ma
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China; (F.M.); (Y.J.); (B.L.); (Y.Z.)
| | - Yuan Jiang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China; (F.M.); (Y.J.); (B.L.); (Y.Z.)
| | - Baoshan Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China; (F.M.); (Y.J.); (B.L.); (Y.Z.)
| | - Yuxin Zeng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China; (F.M.); (Y.J.); (B.L.); (Y.Z.)
| | - Hushan Shang
- Dingxi Academy of Agricultural Sciences, Dingxi 743002, China; (H.S.); (F.W.)
| | - Fusheng Wang
- Dingxi Academy of Agricultural Sciences, Dingxi 743002, China; (H.S.); (F.W.)
| | - Zhirong Sun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China; (F.M.); (Y.J.); (B.L.); (Y.Z.)
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Mitsui Y, Yokoyama H, Nakaegawa W, Tanaka K, Komatsu K, Koizuka N, Okuzaki A, Matsumoto T, Takahara M, Tabei Y. Epistatic interactions among multiple copies of FLC genes with naturally occurring insertions correlate with flowering time variation in radish. AOB PLANTS 2023; 15:plac066. [PMID: 36751367 PMCID: PMC9893874 DOI: 10.1093/aobpla/plac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Brassicaceae crops, which underwent whole-genome triplication during their evolution, have multiple copies of flowering-related genes. Interactions among multiple gene copies may be involved in flowering time regulation; however, this mechanism is poorly understood. In this study, we performed comprehensive, high-throughput RNA sequencing analysis to identify candidate genes involved in the extremely late-bolting (LB) trait in radish. Then, we examined the regulatory roles and interactions of radish FLOWERING LOCUS C (RsFLC) paralogs, the main flowering repressor candidates. Seven flowering integrator genes, five vernalization genes, nine photoperiodic/circadian clock genes and eight genes from other flowering pathways were differentially expressed in the early-bolting (EB) cultivar 'Aokubinagafuto' and LB radish cultivar 'Tokinashi' under different vernalization conditions. In the LB cultivar, RsFLC1 and RsFLC2 expression levels were maintained after 40 days of cold exposure. Bolting time was significantly correlated with the expression rates of RsFLC1 and RsFLC2. Using the EB × LB F2 population, we performed association analyses of genotypes with or without 1910- and 1627-bp insertions in the first introns of RsFLC1 and RsFLC2, respectively. The insertion alleles prevented the repression of their respective FLC genes under cold conditions. Interestingly, genotypes homozygous for RsFLC2 insertion alleles maintained high RsFLC1 and RsFLC3 expression levels under cold conditions, and two-way analysis of variance revealed that RsFLC1 and RsFLC3 expression was influenced by the RsFLC2 genotype. Our results indicate that insertions in the first introns of RsFLC1 and RsFLC2 contribute to the late-flowering trait in radish via different mechanisms. The RsFLC2 insertion allele conferred a strong delay in bolting by inhibiting the repression of all three RsFLC genes, suggesting that radish flowering time is determined by epistatic interactions among multiple FLC gene copies.
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Affiliation(s)
| | - Hinano Yokoyama
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Atsugi, Kanagawa 243-0034, Japan
| | - Wataru Nakaegawa
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Atsugi, Kanagawa 243-0034, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kenji Komatsu
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Atsugi, Kanagawa 243-0034, Japan
| | - Nobuya Koizuka
- College of Agriculture, Tamagawa University, 6-1-1 Tamagawa Gakuen, Machida, Tokyo 194-8610, Japan
| | - Ayako Okuzaki
- College of Agriculture, Tamagawa University, 6-1-1 Tamagawa Gakuen, Machida, Tokyo 194-8610, Japan
| | - Takashi Matsumoto
- Faculty of Applied Biology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Manabu Takahara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8634, Japan
| | - Yutaka Tabei
- Faculty of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma 374-0193, Japan
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Chen L, Xu M, Liu C, Hao J, Fan S, Han Y. LsMYB15 Regulates Bolting in Leaf Lettuce ( Lactuca sativa L.) Under High-Temperature Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:921021. [PMID: 35837450 PMCID: PMC9275828 DOI: 10.3389/fpls.2022.921021] [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: 04/15/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
High temperature is one of the primary environmental stress factors affecting the bolting of leaf lettuce. To determine the potential role of melatonin in regulating high-temperature induced bolting in leaf lettuce (Lactuca sativa L.), we conducted melatonin treatment of the bolting-sensitive cultivar "S39." The results showed that 100 μmol L-1 melatonin treatment significantly promoted growth, and melatonin treatment delayed high-temperature-induced bolting in lettuce. RNA-seq analysis revealed that the differentially expressed genes (DEGs) involved in "plant hormone signal transduction" and "phenylpropanoid biosynthesis" were significantly enriched during high-temperature and melatonin treatment. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis suggested that the expression patterns of abscisic acid (ABA)-related genes positively correlated with stem length during leaf lettuce development. Furthermore, weighted gene co-expression network analysis (WGCNA) demonstrated that MYB15 may play an important role in melatonin-induced resistance to high temperatures. Silencing the LsMYB15 gene in leaf lettuce resulted in early bolting, and exogenous melatonin delayed early bolting in leaf lettuce at high temperatures. Our study provides valuable data for future studies of leaf lettuce quality.
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Wei Q, Hu T, Xu X, Tian Z, Bao C, Wang J, Pang H, Hu H, Yan Y, Liu T, Wang W. The New Variation in the Promoter Region of FLOWERING LOCUS T Is Involved in Flowering in Brassica rapa. Genes (Basel) 2022; 13:genes13071162. [PMID: 35885945 PMCID: PMC9317459 DOI: 10.3390/genes13071162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 12/10/2022] Open
Abstract
Flowering time is an important agronomic trait in Brassica rapa and has a wide range of variation. The change from vegetative to reproductive development is a major transition period, especially in flowering vegetable crops. In this study, two non-heading Chinese cabbage varieties with significantly different flowering times, Pak-choi (B. rapa var. communis Tesn et Lee) and Caitai (B. rapa var. tsaitai Hort.), were used to construct segregated F2 populations. The bulk-segregant approach coupled with whole genome re-sequencing was used for QTL sequencing (QTL-seq) analysis to map flowering time traits. The candidate genes controlling flowering time in B. rapa were predicted by homologous gene alignment and function annotation. The major-effect QTL ft7.1 was detected on chromosome A07 of B. rapa, and the FT family gene BrFT was predicted as the candidate gene. Moreover, a new promoter regional difference of 1577 bp was revealed by analyzing the sequence of the BrFT gene. The promoter region activity analysis and divergent gene expression levels indicated that the difference in the promoter region may contribute to different flowering times. These findings provide insights into the mechanisms underlying the flowering time in Brassica and the candidate genes regulating flowering in production.
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Affiliation(s)
- Qingzhen Wei
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Tianhua Hu
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Xinfeng Xu
- Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing 210095, China;
| | - Zhen Tian
- College of Ecology, Lishui University, Lishui 323000, China;
| | - Chonglai Bao
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Jinglei Wang
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Hongtao Pang
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Haijiao Hu
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Yaqin Yan
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Tongkun Liu
- Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing 210095, China;
- Correspondence: (T.L.); (W.W.); Tel.: +86-571-86409722 (W.W.)
| | - Wuhong Wang
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
- Correspondence: (T.L.); (W.W.); Tel.: +86-571-86409722 (W.W.)
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Genome-Wide Characterization Analysis of CCT Genes in Raphanus sativus and Their Potential Role in Flowering and Abiotic Stress Response. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
CCT genes play vital roles in flowering, plant growth, development, and response to abiotic stresses. Although they have been reported in many plants, the characterization and expression pattern of CCT genes is still limited in R. sativus. In this study, a total of 58 CCT genes were identified in R. sativus. Phylogenetic tree, gene structure, and conserved domains revealed that all CCT genes were classified into three groups: COL, CMF, and PRR. Genome-wide identification and evolutionary analysis showed that segmental duplication expanded the CCT gene families considerably, with the LF subgenome retaining more CCT genes. We observed strong purifying selection pressure for CCT genes. RsCCT genes showed tissue specificity, and some genes (such as RsCCT22, RsCCT36, RsCCT42 and RsCCT51) were highly expressed in flowers. Promoter cis-elements and RNA-seq data analysis showed that RsCCT genes could play roles in controlling flowering through the photoperiodic pathway and vernalization pathway. The expression profiles of RsCCT genes under Cd, Cr, Pb, and heat and salt stresses revealed that many RsCCT genes could respond to one or more abiotic stresses. Our findings could provide essential information for further studies on the function of RsCCT genes.
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Wang P, Liu D, Yang FH, Ge H, Zhao X, Chen HG, Du T. Identification of key gene networks controlling vernalization development characteristics of Isatis indigotica by full-length transcriptomes and gene expression profiles. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2679-2693. [PMID: 34975240 PMCID: PMC8703213 DOI: 10.1007/s12298-021-01110-2] [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: 09/14/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Isatis indigotica Fort., as a common Chinese medicinal raw material, will lose its medicinal value if it blooms early, so it is highly valuable to clarify the induction mechanism of the vernalization of I. indigotica at low temperature. In this study, the concentrations of soluble sugar, proline, glutathione and zeatin in two germplasms of I. indigotica with different degrees of low temperature tolerance (Y1 and Y2) were determined at 10 days, 20 days and 30 days of low-temperature treatment, and the full-length transcriptome of 24 samples was sequenced by Nanopore sequencing with Oxford Nanopore Technologies (ONT). After that, the data of transcripts involved in the vernalization of I. indigotica at low temperature were obtained, and these transcripts were identified using weighted gene co-expression network analysis (WGCNA). The results revealed the massive accumulation of soluble sugar and proline in Y1 and Y2 after low temperature induction. A total of 18,385 new transcripts, 6168 transcription factors and 470 lncRNAs were obtained. Differential expression analysis showed that gibberellin, flavonoids, fatty acids and some processes related to low temperature response were significantly enriched. Eight key transcripts were identified by WGCNA, among which ONT.14640.1, ONT.9119.1, ONT.13080.2 and ONT.16007.1 encodes a flavonoid transporter, 9-cis-epoxycarotenoid dioxygenase 3 (NCED3), growth factor gene and L-aspartate oxidase in plants, respectively. It indicated that secondary metabolites such as hormones and flavonoids play an important role in the vernalization of I. indigotica. qRT-PCR proved the reliability of transcriptome results. These results provide important insights on the low-temperature vernalization of I. indigotica, and provide a research basis for analyzing the vernalization mechanism of I. indigotica. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01110-2.
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Affiliation(s)
- Pan Wang
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Dong Liu
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Fu-Hong Yang
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
- Pingliang Academy of Agricultural Sciences, Pingliang, 744000 China
| | - Hui Ge
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Xin Zhao
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Hong-Gang Chen
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Tao Du
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
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Xie Y, Ying J, Tang M, Wang Y, Xu L, Liu M, Liu L. Genome-wide identification of AUX/IAA in radish and functional characterization of RsIAA33 gene during taproot thickening. Gene 2021; 795:145782. [PMID: 34146634 DOI: 10.1016/j.gene.2021.145782] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/17/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Auxin/indole-3-acetic acid (Aux/IAA) genes encode short lived nuclear proteins that cooperated with auxin or auxin response factor (ARF), which are involved in plant growth and developmental processes. However, it's still ambiguous how the Aux/IAA genes regulate the process governing taproot thickening in radish. Herein, 65 Aux/IAA genes were identified from the radish genome. Gene duplication analysis showed that two pairs of tandem duplication and 17 (27%) segmental duplication events were identified among Aux/IAA family genes in radish. Transcriptomic analysis revealed that most of Aux/IAA genes (52/65) exhibited differential expression pattern in different root tissues, and six root-specific genes were highly expressed in root cortex, cambium, xylem, and root tip in radish. RT-qPCR analysis showed that the expression level of RsIAA33 was the highest at cortex splitting stage (CSS), and early expanding stage (ES). Furthermore, amiRNA-mediated gene silencing of RsIAA33 indicated that it could inhibit the reproductive growth, thus promoting taproot thickening and development. These results would provide valuable information for elucidating the molecular function of Aux/IAA genes involved in taproot thickening in radish.
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Affiliation(s)
- Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China; Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Jiali Ying
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
| | - Meiyan Liu
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
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10
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Braynen J, Yang Y, Yuan J, Xie Z, Cao G, Wei X, Shi G, Zhang X, Wei F, Tian B. Comparative transcriptome analysis revealed differential gene expression in multiple signaling pathways at flowering in polyploid Brassica rapa. Cell Biosci 2021; 11:17. [PMID: 33436051 PMCID: PMC7802129 DOI: 10.1186/s13578-021-00528-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/03/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Polyploidy is widespread in angiosperms and has a significant impact on plant evolution, diversity, and breeding program. However, the changes in the flower development regulatory mechanism in autotetraploid plants remains relatively limited. In this study, RNA-seq analysis was used to investigate changes in signaling pathways at flowering in autotetraploid Brassica rapa. RESULTS The study findings showed that the key genes such as CO, CRY2, and FT which promotes floral formation were down-regulated, whereas floral transition genes FPF1 and FD were up-regulated in autotetraploid B. rapa. The data also demonstrated that the positive regulators GA1 and ELA1 in the gibberellin's biosynthesis pathway were negatively regulated by polyploidy in B. rapa. Furthermore, transcriptional factors (TFs) associated with flower development were significantly differentially expressed including the up-regulated CIB1 and AGL18, and the down-regulated AGL15 genes, and by working together such genes affected the expression of the down-stream flowering regulator FLOWERING LOCUS T in polyploid B. rapa. Compared with that in diploids autotetrapoid plants consist of differential expression within the signaling transduction pathway, with 13 TIFY gens up-regulated and 17 genes related to auxin pathway down-regulated. CONCLUSION Therefore, polyploidy is more likely to integrate multiple signaling pathways to influence flowering in B. rapa after polyploidization. In general, the present results shed new light on our global understanding of flowering regulation in polyploid plants during breeding program.
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Affiliation(s)
- Janeen Braynen
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.,Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Jiachen Yuan
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Gangqiang Cao
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiaochun Wei
- Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Gongyao Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.,Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiaowei Zhang
- Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Fang Wei
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China. .,Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Baoming Tian
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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11
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Identification and differential expression analysis of anthocyanin biosynthetic genes in root-skin color variants of radish (Raphanus sativus L.). Genes Genomics 2020; 42:413-424. [PMID: 31997158 DOI: 10.1007/s13258-020-00915-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 01/14/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Taproot skin color is a major trait for assessing the commercial and nutritional quality of radish, and red-skinned radish is confirmed to improve consumer's interest and health. However, little is known about the molecular mechanisms responsible for controlling the formation of red-skinned radish. OBJECTIVE This study aimed to identify the differentially expressed anthocyanin biosynthetic genes between red- and white-skinned radishes and understand the molecular regulatory mechanism underlying red-skinned radish formation. METHODS Based on the published complete genome sequence of radish, the digital gene expression profiles of Yangzhouyuanbai (YB, white-skinned) and Sading (SD, red-skinned) were analyzed using Illumina sequencing. RESULTS A total of 3666 DEGs were identified in SD compared with YB. Interestingly, 46 genes encoded enzymes related to anthocyanin biosynthesis and 241 genes encoded transcription factors were identified. KEGG pathway analysis showed that the formation of red-skinned radish was mainly controlled by pelargonidin-derived anthocyanin biosynthetic pathway genes. This process included the upregulation of PAL, C4H, 4CL, CHS, CHI, F3H, DFR, LDOX, and UGT enzymes in SD. CHS genes were specifically expressed in SD, and it might be the key point for red pigment accumulation in red-skinned radish. Furthermore, MYB1/2/75, bHLH (TT8), and WD 40 showed higher expression in SD than in YB. Meanwhile, the corresponding low-abundance anthocyanin biosynthesis enzymes and upregulation of MYB4 might be the factors influencing the formation of white-skinned radish. CONCLUSION These findings provide new insights into the molecular mechanisms and regulatory network of anthocyanin biosynthesis in red-skinned radish.
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12
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Motoki K, Kinoshita Y, Hosokawa M. Non-vernalization Flowering and Seed Set of Cabbage Induced by Grafting Onto Radish Rootstocks. FRONTIERS IN PLANT SCIENCE 2019; 9:1967. [PMID: 30687362 PMCID: PMC6335391 DOI: 10.3389/fpls.2018.01967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Cabbage (Brassica oleracea var. capitata) requires a long-term low-temperature exposure for floral induction, causing a delay in the breeding cycle. The objective of this study is to develop a method to induce flowering in cabbage without low-temperature treatment, using a grafting method. We conducted grafting experiments using two flower-induced Chinese kale cultivars (B. oleracea var. alboglabra) and seven radish cultivars/accessions as rootstocks and investigated the flowering response of grafted cabbage scions without low-temperature treatment. "Watanabe-seiko No.1" cabbage, when grafted onto the two Chinese kale cultivars, did not formed flower buds. Flowering was successfully induced in "Watanabe-seiko No.1" by grafting onto three out of the seven tested radish cultivars, and in "Kinkei No.201" and "Red cabbage" by grafting onto one tested radish cultivar. In "Watanabe-seiko No.1," the earliest flower bud appearance was observed at 29 days after grafting. Seeds were also obtained from the three cabbage cultivars that flowered by grafting. Gene expression analysis of "Watanabe-seiko No.1" cabbage scions which formed flower buds by grafting, revealed high expression of the homolog of the floral integrator, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (BoSOC1), at the time of flower bud appearance. However, in the same leaf samples, we observed low expression of two homologs of florigen, FLOWERING LOCUS T (BoFT.C2 and BoFT.C6). In addition, two homologs of the floral repressor FLOWERING LOCUS C (BoFLC3 and BoFLC4), which are known to be down-regulated before flower bud differentiation in the vernalization pathway, were highly expressed, indicating that grafting onto radish induces cabbage flowering independently of the vernalization pathway. The expression level of the radish FT homolog (RsFT) in "Rat's tail-G2," which had highly induced flowering in the grafted cabbage scion, was higher than in the other radish cultivars. However, although "Rat's tail-CH" effectively induced flowering in the cabbage scion, the expression of RsFT was low in this cultivar. In this study, floral induction of non-vernalized cabbage cannot be explained by the expression levels of RsFT in rootstock plants, alone. The flowering of non-vernalized cabbage would be induced by transmissible agents from rootstocks and not by the expression of cabbage FT, BoFT, from the scion itself.
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Affiliation(s)
- Ko Motoki
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yu Kinoshita
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Munetaka Hosokawa
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Laboratory of Floriculture, Department of Agriculture, Kindai University, Nara, Japan
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13
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Hu T, Wei Q, Wang W, Hu H, Mao W, Zhu Q, Bao C. Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus). PLoS One 2018; 13:e0204137. [PMID: 30248137 PMCID: PMC6152963 DOI: 10.1371/journal.pone.0204137] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022] Open
Abstract
Floral induction that initiates bolting and flowering is crucial for reproductive fitness in radishes. CONSTANS-like (CO-like, COL) genes play an important role in the circadian clock, which ensures regular development through complicated time-keeping mechanisms. However, the specific biological and functional roles of each COL transcription factor gene in the radish remain unknown. In this study, we performed a genome-wide identification of COL genes in the radish genome of three cultivars including ‘Aokubi’, ‘kazusa’ and ‘WK10039’, and we analyzed their exon-intron structure, gene phylogeny and synteny, and expression levels in different tissues. The bioinformatics analysis identified 20 COL transcription factors in the radish genome, which were divided into three subgroups (Group I to Group III). RsaCOL-09 and RsaCOL-12 might be tandem duplicated genes, whereas the others may have resulted from segmental duplication. The Ka/Ks ratio indicated that all the COL genes in radish, Arabidopsis, Brassica rapa, Brassica oleracea, Capsella rubella and rice were under purifying selection. We identified 6 orthologous and 19 co-orthologous COL gene pairs between the radish and Arabidopsis, and we constructed an interaction network among these gene pairs. The expression values for each COL gene during vegetable and flower development showed that the majority of Group I members had similar expression patterns. In general, the expression of radish COL genes in Groups I and III decreased during development, whereas the expression of radish COL genes in Group II first increased and then decreased. Substantial numbers of radish COL genes were differentially expressed after vernalization treatment. The expression levels of RsaCOL-02 and RsaCOL-04 were significantly increased during vernalization treatment, while the expression of RsaCOL-10 was significantly decreased. These outcomes provide insights for improving the genetic control of bolting and flowering in radish and other root vegetable crops, and they facilitate genetic improvements to radish yields and quality.
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Affiliation(s)
- Tianhua Hu
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qingzhen Wei
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wuhong Wang
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haijiao Hu
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Weihai Mao
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qinmei Zhu
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Chonglai Bao
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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14
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Zhang J, Li D, Shi X, Zhang D, Qiu S, Wei J, Zhang J, Zhou J, Zhu K, Xia Y. Mining and expression analysis of candidate genes involved in regulating the chilling requirement fulfillment of Paeonia lactiflora 'Hang Baishao'. BMC PLANT BIOLOGY 2017; 17:262. [PMID: 29273002 PMCID: PMC5741883 DOI: 10.1186/s12870-017-1205-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/06/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND The artificial enlargement of the planting area and ecological amplitude of ornamentals for horticultural and landscape applications are significant. Herbaceous peony (Paeonia lactiflora Pall.) is a world-famous ornamental with attractive and fragrant flowers and is mainly planted in temperate and cool areas. Comparatively higher winter temperatures in the subtropical and tropical Northern Hemisphere result in a deficit of chilling accumulation for bud dormancy release, which severely hinders "The southward plantation of herbaceous peony". Studies on the dormancy, chilling requirement (CR) and relevant molecular mechanisms of peony are needed to enhance our ability to extend the range of this valuable horticultural species. RESULTS Based on natural and artificial chilling experiments, and chilling hour (CH) and chilling unit (CU) evaluation systems, the lowest CR of 'Hang Baishao' was between 504.00 and 672.00 CHs and the optimal CR was 672.00 CHs and 856.08 CUs for achieving strong sprouting, growth and flowering performance. Transcriptome sequencing and gene identification by RNA-Seq were performed on 'Hang Baishao' buds during the dormancy and sprouting periods. Six gene libraries were constructed, and 66 temperature- and photoperiod-associated unigenes were identified as the potential candidate genes that may regulate or possibly determine CR characteristics. The difference in the expression patterns of SUPPRESSPOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) between the winters of 2012-2013 and 2015-2016, and the difference of CR fulfillment periods also between these two winters represented the interesting congruent relationships. This correlation was also observed for WRKY DNA-BINDING PROTEIN 33 (WRKY 33). CONCLUSIONS Combined with the results acquired from all of experiments, 'Hang Baishao' was confirmed to be a superb peony resource that have significantly low CR characteristics. The two genes of SOC1 and WRKY33 are likely involved in determining the CR amount and fulfillment period of 'Hang Baishao'. HEAT SHOCK PROTEIN, OSMOTIN and TIMING OF CAB EXPRESSION 1 also deserve attention for the CR research. This study could contribute to the knowledge of the deep factors and mechanisms that regulate CR characteristics, and may be beneficial for breeding new germplasms that have low CRs for landscape or horticulture applications in subtropical regions.
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Affiliation(s)
- Jiaping Zhang
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Danqing Li
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Xiaohua Shi
- Research & Development Centre of Flower, Zhejiang Academy of Agricultural Sciences, Hangzhou, 311202 China
| | - Dong Zhang
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Shuai Qiu
- Research & Development Center, Hangzhou Landscaping Incorporated, Hangzhou, 310020 China
| | - Jianfen Wei
- Research & Development Center, Hangzhou Landscaping Incorporated, Hangzhou, 310020 China
| | - Jiao Zhang
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Jianghua Zhou
- Research & Development Centre of Flower, Zhejiang Academy of Agricultural Sciences, Hangzhou, 311202 China
| | - Kaiyuan Zhu
- Research & Development Centre of Flower, Zhejiang Academy of Agricultural Sciences, Hangzhou, 311202 China
| | - Yiping Xia
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
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15
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Wang J, Qiu Y, Cheng F, Chen X, Zhang X, Wang H, Song J, Duan M, Yang H, Li X. Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.). BMC Genomics 2017; 18:981. [PMID: 29258434 PMCID: PMC5738175 DOI: 10.1186/s12864-017-4377-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus. The release of the R. sativus genome sequence provides an opportunity to identify and characterize the flowering genes using a comparative genomics approach. RESULTS We identified 254 R. sativus flowering genes based on sequence similarities and analyses of syntenic regions. The genes were unevenly distributed on the various chromosomes. Furthermore, we discovered the existence of R. sativus core function genes in the flowering regulatory network, which revealed that basic flowering pathways are relatively conserved between Arabidopsis thaliana and R. sativus. Additional comparisons with Brassica oleracea and Brassica rapa indicated that the retained flowering genes differed among species after genome triplication events. The R. sativus flowering genes were preferentially retained, especially those associated with gibberellin signaling and metabolism. Moreover, analyses of selection pressures suggested that the genes in vernalization and autonomous pathways were more variable than the genes in other R. sativus flowering pathways. CONCLUSIONS Our results revealed that the core flowering genes are conserved between R. sativus and A. thaliana to a certain extent. Moreover, the copy number variation and functional differentiation of the homologous genes in R. sativus increased the complexity of the flowering regulatory networks after genome polyploidization. Our study provides an integrated framework for the R. sativus flowering pathways and insights into the evolutionary relationships between R. sativus flowering genes and the genes from A. thaliana and close relatives.
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Affiliation(s)
- Jinglei Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yang Qiu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Xiaohua Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Xiaohui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Haiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Jiangping Song
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Mengmeng Duan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Haohui Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Xixiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China.
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Huang X, Lei Y, Guan H, Hao Y, Liu H, Sun G, Chen R, Song S. Transcriptomic analysis of the regulation of stalk development in flowering Chinese cabbage (Brassica campestris) by RNA sequencing. Sci Rep 2017; 7:15517. [PMID: 29138433 PMCID: PMC5686075 DOI: 10.1038/s41598-017-15699-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022] Open
Abstract
Flowering Chinese cabbage is a stalk vegetable whose quality and yield are directly related to stalk development. However, no comprehensive investigations on stalk development have been performed. To address this issue, the present study used RNA sequencing to investigate transcriptional regulation at three key stages (seedling, bolting, and flowering) of stalk development in flowering Chinese cabbage. Anatomical analysis revealed that cell division was the main mode of stalk thickening and elongation at all key stages. Among the 35,327 genes expressed in shoot apices, 34,448 were annotated and 879 were identified as novel transcripts. We identified 11,514 differentially expressed genes (DEGs) among the three stages of stalk development. Functional analysis revealed that these DEGs were significantly enriched in ‘ribosome’ and ‘plant hormone signal transduction’ pathways and were involved in hormone signal transduction, cell cycle progression, and the regulation of flowering time. The roles of these genes in stalk development were explored, and a putative gene-regulation network for the stalk flowering time was established. These findings provide insight into the molecular mechanisms of stalk development in flowering Chinese cabbage that provides a new theoretical basis for stalk vegetable breeding.
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Affiliation(s)
- Xinmin Huang
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yuling Lei
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Hongling Guan
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yanwei Hao
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Houcheng Liu
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Guangwen Sun
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Riyuan Chen
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
| | - Shiwei Song
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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