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Tang C, Zhai Y, Wang Z, Zhao X, Yang C, Zhao Y, Zeng LB, Zhang DY. Metabolomics and transcriptomics reveal the effect of hetero-chitooligosaccharides in promoting growth of Brassica napus. Sci Rep 2022; 12:21197. [PMID: 36482110 PMCID: PMC9731942 DOI: 10.1038/s41598-022-25850-7] [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: 05/08/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The hetero-chitooligosaccharide (HTCOS) is a naturally occurring biopolymer in the exoskeleton of crustaceans and insects. Although some studies have been carried out on HTCOS in inducing plant resistance and promoting growth, the molecular mechanism of HTCOS in plants is not clear. In this study, an integrated analysis of metabolomics and transcriptomics was performed to analyze the response of Brassica napus to hetero-chitooligosaccharides treatment. The levels of 26 metabolites in B. napus were significantly changed under the HTCOS treatment. Amongst these metabolites, 9 metabolites were significantly up-regulated, including pentonic acid, indole-3-acetate, and γ-aminobutyric acid. Transcriptome data showed that there were 817 significantly up-regulated genes and 1064 significantly down-regulated genes in B. napus under the HTCOS treatment. Interestingly, the indole-3-acetate (IAA) content under the HTCOS treatment was about five times higher than that under the control condition. Moreover, four genes related to plant hormone signal transduction, three AUX/IAA genes, and one ARF gene, were significantly up-regulated under the HTCOS treatment. Furthermore, the plant height, branching number, and biomass of B. napus under the HTCOS treatment were significantly increased compared to that in the control condition. This evidence indicated that the HTCOS treatment contributed to accumulating the content of plant hormone IAA in the B. napus, up-regulating the expression of key genes in the signaling pathway of plant growth and improving the agronomic traits of B. napus.
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Affiliation(s)
- Chao Tang
- grid.257160.70000 0004 1761 0331College of Plant Protection, Hunan Agricultural University, No. 1, Nongda Road, Furong District, Changsha City, 410208 Hunan Province China ,grid.410727.70000 0001 0526 1937Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Xianjiahu West Road, Yuelu District, Changsha, 410205 Hunan Province China
| | - Yang Zhai
- grid.410727.70000 0001 0526 1937Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Xianjiahu West Road, Yuelu District, Changsha, 410205 Hunan Province China
| | - Zhuo Wang
- grid.9227.e0000000119573309State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190 China
| | - Xin Zhao
- grid.410727.70000 0001 0526 1937Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Xianjiahu West Road, Yuelu District, Changsha, 410205 Hunan Province China
| | - Chen Yang
- grid.410727.70000 0001 0526 1937Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Xianjiahu West Road, Yuelu District, Changsha, 410205 Hunan Province China
| | - Yong Zhao
- ZhongkeRunxin (Suzhou) Biotechnology Co., Ltd., Suzhou, 215152 Jiangsu China
| | - Liang-bin Zeng
- grid.410727.70000 0001 0526 1937Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Xianjiahu West Road, Yuelu District, Changsha, 410205 Hunan Province China
| | - De-yong Zhang
- grid.257160.70000 0004 1761 0331College of Plant Protection, Hunan Agricultural University, No. 1, Nongda Road, Furong District, Changsha City, 410208 Hunan Province China
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Zeng Z, Zhu S, Wang Y, Bai X, Liu C, Chen J, Zhang T, Wei Y, Li F, Bao Z, Yan L, Wang H, Liu T. Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:323-334. [PMID: 34558775 PMCID: PMC8753365 DOI: 10.1111/pbi.13714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/13/2021] [Indexed: 05/27/2023]
Abstract
Ramie is an important fibre-producing crop in China; however, the genetic basis of its agronomic traits remains poorly understood. We produced a comprehensive map of genomic variation in ramie based on resequencing of 301 landraces and cultivars. Genetic analysis produced 129 signals significantly associated with six fibre yield-related traits, and several genes were identified as candidate genes for respective traits. Furthermore, we found that natural variations in the promoter region of Bnt14G019616 were associated with extremely low fibre abundance, providing the first evidence for the role of pectin methylesterase in fibre growth of plants. Additionally, nucleotide diversity analysis revealed that breeding selection has been markedly focussed on chromosome 9 in which ~ 39.6% sequence underwent selection, where one gibberellin-signalling-repressed DELLA gene showed distinct selection signatures in the cultivars. This study provides insights into the genetic architecture and breeding history of fibre yield traits in ramie. Moreover, the identification of fibre yield-related genetic loci and large-scale genomic variation represent valuable resources for genomics-assisted breeding of this crop.
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Affiliation(s)
- Zheng Zeng
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Siyuan Zhu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Yanzhou Wang
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Xuehua Bai
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Chan Liu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Jianrong Chen
- College of Biological and Environmental EngineeringChangsha UniversityChangshaChina
| | - Ting Zhang
- Shanghai OE Biotech. Co., LtdShanghaiChina
| | - Yiping Wei
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Fu Li
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Zhigui Bao
- Shanghai OE Biotech. Co., LtdShanghaiChina
| | - Li Yan
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | | | - Touming Liu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
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Identification of proteins associated with bast fiber growth of ramie by differential proteomic analysis. BMC Genomics 2021; 22:865. [PMID: 34856929 PMCID: PMC8638140 DOI: 10.1186/s12864-021-08195-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Background Ramie is an important fiber-producing crop in China, and its fibers are widely used as textile materials. Fibers contain specialized secondary cellular walls that are mainly composed of cellulose, hemicelluloses, and lignin. Understanding the mechanism underlying the secondary wall biosynthesis of fibers will benefit the improvement of fiber yield and quality in ramie. Results Here, we performed a proteomic analysis of the bark from the top and middle parts of the stem, where fiber growth is at different stages. We identified 6971 non-redundant proteins from bast bark. Proteomic comparison revealed 983 proteins with differential expression between the two bark types. Of these 983 proteins, 46 were identified as the homolog of known secondary wall biosynthetic proteins of Arabidopsis, indicating that they were potentially associated with fiber growth. Then, we proposed a molecular model for the secondary wall biosynthesis of ramie fiber. Furthermore, interaction analysis of 46 candidate proteins revealed two interacting networks that consisted of eight cellulose biosynthetic enzymes and seven lignin biosynthetic proteins, respectively. Conclusion This study sheds light on the proteomic basis underlying bast fiber growth in ramie, and the identification of many candidates associated with fiber growth provides important basis for understanding the fiber growth in this crop. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08195-9.
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Zeng Z, Li F, Huang R, Wang Y, Liu T. Phosphoproteome analysis reveals an extensive phosphorylation of proteins associated with bast fiber growth in ramie. BMC PLANT BIOLOGY 2021; 21:473. [PMID: 34656094 PMCID: PMC8520194 DOI: 10.1186/s12870-021-03252-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Phosphorylation modification, one of the most common post-translational modifications of proteins, widely participates in the regulation of plant growth and development. Fibers extracted from the stem bark of ramie are important natural textile fibers; however, the role of phosphorylation modification in the growth of ramie fibers is largely unknown. RESULTS Here, we report a phosphoproteome analysis for the barks from the top and middle section of ramie stems, in which the fiber grows at different stages. A total of 10,320 phosphorylation sites from 9,170 unique phosphopeptides that were assigned to 3,506 proteins was identified, and 458 differentially phosphorylated sites from 323 proteins were detected in the fiber developmental barks. Twelve differentially phosphorylated proteins were the homologs of Arabidopsis fiber growth-related proteins. We further focused on the function of the differentially phosphorylated KNOX protein whole_GLEAN_10029667, and found that this protein dramatically repressed the fiber formation in Arabidopsis. Additionally, using a yeast two-hybridization assay, we identified a kinase and a phosphatase that interact with whole_GLEAN_10029667, indicating that they potentially target this KNOX protein to regulate its phosphorylation level. CONCLUSION The finding of this study provided insights into the involvement of phosphorylation modification in ramie fiber growth, and our functional characterization of whole_GLEAN_10029667 provide the first evidence to indicate the involvement of phosphorylation modification in the regulation of KNOX protein function in plants.
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Affiliation(s)
- Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Renyan Huang
- Hunan Institute of Plant protection, Changsha, 410205, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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A New Method for Exonuclease Activity Analysis of Apurinic/Apyrimidinic Endonuclease 1 and Application in Heavy-polluted Ramie. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2021. [DOI: 10.1016/s1872-2040(21)60117-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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He Q, Zeng Z, Li F, Huang R, Wang Y, Liu T. Ubiquitylome analysis reveals the involvement of ubiquitination in the bast fiber growth of ramie. PLANTA 2021; 254:1. [PMID: 34081200 DOI: 10.1007/s00425-021-03652-x] [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: 04/08/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
A total of 249 sites from 197 proteins showed a differential ubiquitination level in the fiber development of ramie barks. The function of two differentially ubiquitinated proteins for fiber growth was demonstrated. Ubiquitination is one of the most common post-translational modifications of proteins, and it plays essential roles in plant growth and development. However, the involvement of ubiquitination in the growth of plant fibers remains largely unknown. We compared the ubiquitylome of the top and middle stems of ramie bark, with different fiber growth stages. We identified 249 differentially ubiquitinated sites in 197 proteins in fiber-developing barks in the stems and found that seven were homologs of Arabidopsis proteins associated with fiber growth. Overexpression of the differentially ubiquitinated proteins, RWA3 homolog whole_GLEAN_10024150 and MYB protein whole_GLEAN_10015497, significantly promoted fiber growth in transgenic Arabidopsis, indicating their involvement in this process. We also found that the abundance of these proteins decreased when their ubiquitination levels increased and vice versa in the fiber-developing bark. These results indicated that the abundance of these two proteins was adjusted through ubiquitin-dependent degradation. Collectively, our findings provide important insights into the involvement of ubiquitination in the growth of ramie fibers.
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Affiliation(s)
- Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Renyan Huang
- Hunan Institute of Plant Protection, Changsha, 410125, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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Yu Y, Zhang G, Chen Y, Bai Q, Gao C, Zeng L, Li Z, Cheng Y, Chen J, Sun X, Guo L, Xu J, Yan Z. Selection of Reference Genes for qPCR Analyses of Gene Expression in Ramie Leaves and Roots across Eleven Abiotic/Biotic Treatments. Sci Rep 2019; 9:20004. [PMID: 31882847 PMCID: PMC6934855 DOI: 10.1038/s41598-019-56640-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/16/2019] [Indexed: 12/25/2022] Open
Abstract
Quantitative real-time PCR (qPCR) is commonly used for deciphering gene functions. For effective qPCR analyses, suitable reference genes are needed for normalization. The objective of this study is to identify the appropriate reference gene(s) for qPCR analyses of the leaves and roots of ramie (Boehmeria nivea L.), an important natural fiber crop. To accomplish this goal, we investigated the expression patterns of eight common plant qPCR reference genes in ramie leaves and roots under five abiotic stresses, five hormonal treatments, and one biotic stress. The relative expression stabilities of the eight genes were evaluated using four common but different approaches: geNorm, NormFinder, BestKeeper, and RefFinder. Across the 11 tested conditions, ACT1 was the most stably expressed among the eight genes while GAPDH displayed the biggest variation. Overall, while variations in the suggested reference genes were found for different tissue x treatment combinations, our analyses revealed that together, genes ACT1, CYP2, and UBQ can provide robust references for gene expression studies of ramie leaves under most conditions, while genes EF-1α, TUB, and ACT1 can be used for similar studies of ramie roots. Our results should help future functional studies of the genes in ramie genome across tissues and environmental conditions.
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Affiliation(s)
- Yongting Yu
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Gang Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712406, China
| | - Yikun Chen
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Qingqing Bai
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712406, China
| | - Chunsheng Gao
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Liangbin Zeng
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Zhimin Li
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Yi Cheng
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Jia Chen
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Xiangping Sun
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Litao Guo
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Jianping Xu
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China. .,Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
| | - Zhun Yan
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
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Chen J, Rao J, Wang Y, Zeng Z, Liu F, Tang Y, Chen X, Liu C, Liu T. Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis. Genes (Basel) 2019; 10:genes10110842. [PMID: 31653111 PMCID: PMC6896145 DOI: 10.3390/genes10110842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/12/2022] Open
Abstract
Ramie fibers, one of the most important natural fibers in China, are mainly composed of lignin, cellulose, and hemicellulose. As the high lignin content in the fibers results in a prickly texture, the lignin content is deemed to be an important trait of the fiber quality. In this study, the genetic basis of the fiber lignin content was evaluated, resulting in the identification of five quantitative trait loci (QTLs). Three genes, whole_GLEAN_10021050, whole_GLEAN_10026962, and whole_GLEAN_10009464 that were identified on the QTL regions of qLC7, qLC10, and qLC13, respectively, were found to be homologs of the Arabidopsis lignin biosynthetic genes. Moreover, all three genes displayed differential expression in the barks located in the top and middle parts of the stem, where lignin was not being synthesized and where it was being biosynthesized, respectively. Sequence comparison found that these three genes had wide variations in their coding sequences (CDSs) and putative promoter regions between the two parents, especially the MYB gene whole_GLEAN_10021050, whose protein had insertions/deletions of five amino acids and substitutions of two amino acids in the conserved domain. This evidence indicates that these three genes are potentially involved in lignin biosynthesis in ramie fibers. The QTLs identified from this study provide a basis for the improvement of lignin content and fiber quality in ramie breeding. The characterization of the three candidate genes here will be helpful for the future clarification of their functions in ramie.
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Affiliation(s)
- Jianrong Chen
- College of Biological and Environmental Engineering, Changsha University, Changsha 410003, China.
| | - Jing Rao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Fang Liu
- College of Biological and Environmental Engineering, Changsha University, Changsha 410003, China.
| | - Yinghong Tang
- College of biological and environmental sciences, Hunan University of Arts and Science, Changde 410128, China.
| | - Xiaorong Chen
- Laboratory of ramie, Yichun Institute of Agricultural Sciences, Yichun 336000, China.
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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Liu C, Zeng L, Zhu S, Wu L, Wang Y, Tang S, Wang H, Zheng X, Zhao J, Chen X, Dai Q, Liu T. Draft genome analysis provides insights into the fiber yield, crude protein biosynthesis, and vegetative growth of domesticated ramie (Boehmeria nivea L. Gaud). DNA Res 2018; 25:173-181. [PMID: 29149285 PMCID: PMC5909428 DOI: 10.1093/dnares/dsx047] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/01/2017] [Indexed: 12/26/2022] Open
Abstract
Plentiful bast fiber, a high crude protein content, and vigorous vegetative growth make ramie a popular fiber and forage crop. Here, we report the draft genome of ramie, along with a genomic comparison and evolutionary analysis. The draft genome contained a sequence of approximately 335.6 Mb with 42,463 predicted genes. A high-density genetic map with 4,338 single nucleotide polymorphisms (SNPs) was developed and used to anchor the genome sequence, thus, creating an integrated genetic and physical map containing a 58.2-Mb genome sequence and 4,304 molecular markers. A genomic comparison identified 1,075 unique gene families in ramie, containing 4,082 genes. Among these unique genes, five were cellulose synthase genes that were specifically expressed in stem bark, and 3 encoded a WAT1-related protein, suggesting that they are probably related to high bast fiber yield. An evolutionary analysis detected 106 positively selected genes, 22 of which were related to nitrogen metabolism, indicating that they are probably responsible for the crude protein content and vegetative growth of domesticated varieties. This study is the first to characterize the genome and develop a high-density genetic map of ramie and provides a basis for the genetic and molecular study of this crop.
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Affiliation(s)
- Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Liangbin Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Lingqing Wu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Shouwei Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Hongwu Wang
- Xianning Agriculture Academy of sciences, Hubei, China
| | - Xia Zheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jian Zhao
- Novogene Bioinformatics Institute, Beijing, China
| | - Xiaorong Chen
- Yichun Institute of Agricultural Sciences, Jiangxi, China
| | - Qiuzhong Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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Guo P, Zheng Y, Peng D, Liu L, Dai L, Chen C, Wang B. Identification and expression characterization of the Phloem Protein 2 (PP2) genes in ramie (Boehmeria nivea L. Gaudich). Sci Rep 2018; 8:10734. [PMID: 30013165 PMCID: PMC6048116 DOI: 10.1038/s41598-018-28953-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 06/28/2018] [Indexed: 11/20/2022] Open
Abstract
Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in sieve elements and companion cells, which play important roles in the maintenance of morphology, photoassimilate transportation and wound protection in higher plants, but to date, no PP2 (BnPP2) genes had been identified in ramie. Here, a total of 15 full-length BnPP2 genes were identified. These BnPP2 genes exhibited different responses to abiotic stresses. Interestingly, the BnPP2 genes are more sensitive to insect pests than to other stresses. A study of the BnPP2-15 promoter revealed that pBnPP2-15 could drive specific GUS expression in the petiole, root and stamen and could also be induced by mechanical wounding and aphid infection in transgenic Arabidopsis lines. The subcellular localization of six BnPP2 proteins showed that GFP-BnPP2-1, GFP-BnPP2-6, GFP-BnPP2-7, GFP-BnPP2-9, GFP-BnPP2-11 and GFP-BnPP2-12 were predominantly located in the cytoplasm. These results provide useful information elucidating the functions of BnPP2 genes in ramie.
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Affiliation(s)
- Pingan Guo
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Yancheng Zheng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Lijun Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Lunjin Dai
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Cong Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Bo Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China.
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Zheng X, Tang S, Zhu S, Dai Q, Liu T. Identification of an NAC Transcription Factor Family by Deep Transcriptome Sequencing in Onion (Allium cepa L.). PLoS One 2016; 11:e0157871. [PMID: 27331904 PMCID: PMC4917099 DOI: 10.1371/journal.pone.0157871] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/06/2016] [Indexed: 01/29/2023] Open
Abstract
Although onion has been used extensively in the past for cytogenetic studies, molecular analysis has been lacking because the availability of genetic resources is limited. NAM, ATAF, and CUC (NAC) transcription factors (TFs) are plant-specific proteins, and they play key roles in plant growth, development, and stress tolerance. However, none of the onion NAC (CepNAC) genes had been identified thus far. In this study, the transcriptome of onion leaves was analyzed by Illumina paired-end sequencing. Approximately 102.9 million clean sequence reads were produced and used for de novo assembly, which generated 117,189 non-redundant transcripts. Of these transcripts, 39,472 were annotated for their function. In order to mine the CepNAC TFs, CepNAC genes were searched from the transcripts assembled, resulting in the identification of all 39 CepNAC genes. These 39 CepNAC proteins were subjected to phylogenetic analysis together with 47 NAC proteins of known function that were previously identified in other species. The results showed that they can be divided into five groups (NAC-I–V). Interestingly, the NAC-IV and -V groups were found to be likely related to the processes of secondary wall synthesis and stress response, respectively. The transcriptome analysis generated a substantial amount of transcripts, which will aid immensely in identifying important genes and accelerating our understanding of onion growth and development. Moreover, the discovery of 39 CepNAC TFs and the identification of the sequence conservation between them and NAC proteins published will provide a basis for further characterization and validation of their functions in the future.
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Affiliation(s)
- Xia Zheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Shouwei Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Qiuzhong Dai
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- * E-mail:
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12
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Transcriptome Analysis of Ramie (Boehmeria nivea L. Gaud.) in Response to Ramie Moth (Cocytodes coerulea Guenée) Infestation. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3702789. [PMID: 27034936 PMCID: PMC4789370 DOI: 10.1155/2016/3702789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/13/2015] [Accepted: 02/01/2016] [Indexed: 11/27/2022]
Abstract
The ramie moth Cocytodes coerulea Guenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore, de novo assembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.
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Identification of 7 stress-related NAC transcription factor members in maize (Zea mays L.) and characterization of the expression pattern of these genes. Biochem Biophys Res Commun 2015; 462:144-50. [PMID: 25937463 DOI: 10.1016/j.bbrc.2015.04.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 11/20/2022]
Abstract
NAC proteins are plant-specific transcription factors that play essential roles in plant development and various abiotic stress responses. A comprehensive analysis of maize NAC genes was performed in this study. A total of 157 non-redundant maize NAC genes including seven membrane-bound members were identified and found to be unevenly distributed on 10 maize chromosomes. Motif composition analysis indicated that the maize NAC proteins share three relatively conserved motifs in the NAC domain within the N-terminal region. Phylogenetic analysis of 157 maize NAC proteins accompanied by 117 NAC proteins from Arabidopsis and 151 from rice were presented. The NAC proteins evaluated were divided into two large groups including 18 subgroups. Gene duplication analysis indicated that gene loss occurred during maize evolution. Seven NAC members that belong to the same clade of maize NAC domain genes were isolated, and overlapping expression patterns were observed under various abiotic stresses, including low temperature, high salinity and dehydration, and phytohormone abscisic acid treatments. This suggested that NAC members function as stress-responsive transcription factors in ABA-dependent signaling pathways. Relatively higher expression levels of these selected maize NAC genes were detected in roots. The stress responsive NAC genes may have applications in molecular breeding to improve crop stress tolerance.
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Liu T, Zhu S, Tang Q, Tang S. Identification of a CONSTANS homologous gene with distinct diurnal expression patterns in varied photoperiods in ramie (Boehmeria nivea L. Gaud). Gene 2015; 560:63-70. [PMID: 25623329 DOI: 10.1016/j.gene.2015.01.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 01/06/2015] [Accepted: 01/21/2015] [Indexed: 10/24/2022]
Abstract
Ramie is an important natural fiber and forage crop in China. Breeding of late- or non-flowering varieties, with higher vegetative yields, is an important goal in ramie improvement. However, the ramie genes involved in flowering regulation have not previously been identified. In model plants, such as rice and Arabidopsis, the CONSTANS (CO) and CONSTANS-like (COL) genes play key roles in flowering regulation. In the present study, six ramie COL genes (BnCOL1-BnCOL6) with a full-length open reading frame (ORF) were identified. Sequence alignment revealed that all six BnCOL proteins contained conserved CCT (CO, COL, TOC1) and B-box I domains, but that only four of these proteins contained the B-box II domain. Expression pattern analysis showed that BnCOL1-BnCOL6 were mainly expressed in the stem xylem, flowers, and leaves. Phylogenetic analysis classified the six newly identified BnCOL proteins, and also 16 COL proteins with known functions in other species, into three groups. The BnCOL2-encoded protein was assigned to the same group as the CO- and Hd1-encoded proteins, suggesting that this BnCOL2-encoded protein showed the highest level of homology with the CO/Hd1-encoded proteins. Photoperiodic experiments showed that BnCOL2 exhibited a diurnal expression pattern under long- and short-day conditions. Subcellular localization examination revealed that the BnCOL2 protein fused with YFP was localized in the nucleus. Because the homologous sequence and similar expression pattern between BnCOL2 and CO/Hd1, the BnCOL2 possibly has a role in flowering modulation, and can be used as a candidate gene for research in the flowering regulation of ramie.
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Affiliation(s)
- Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Qingming Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Shouwei Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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15
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Liu T, Zhu S, Tang Q, Tang S. Genome-wide transcriptomic profiling of ramie (Boehmeria nivea L. Gaud) in response to cadmium stress. Gene 2014; 558:131-7. [PMID: 25550046 DOI: 10.1016/j.gene.2014.12.057] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/19/2014] [Accepted: 12/24/2014] [Indexed: 12/15/2022]
Abstract
Cadmium (Cd) contamination in agricultural soils has become a major environmental problem in China. Ramie, a fiber crop, has frequently been proposed for use as a phytoremediation crop for the restoration of Cd-contaminated farmlands. However, high levels of Cd can greatly inhibit stem growth in ramie, which reduces its economic value as a crop. To understand the potential mechanisms behind this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing on two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2). Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequence reads were generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, and de novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels in CO and CdS ramie revealed 155 differentially expressed genes (DEGs) between treatment and control conditions. Sixteen DEGs were further analyzed for expression differences by using real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase (a major enzyme for deactivating bioactive gibberellins [GAs]) showed markedly up-regulated expression in Cd stressed ramie. This might be responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that the cutin, suberine and wax biosynthesis pathway was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful in further understanding the mechanism of Cd-stress response and improving Cd stress tolerance in ramie.
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Affiliation(s)
- Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Qingming Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Shouwei Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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Huang X, Chen J, Bao Y, Liu L, Jiang H, An X, Dai L, Wang B, Peng D. Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of Ramie (Boehmeria nivea L. Gaud). PLoS One 2014; 9:e113768. [PMID: 25415356 PMCID: PMC4240604 DOI: 10.1371/journal.pone.0113768] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/28/2014] [Indexed: 12/13/2022] Open
Abstract
In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.
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Affiliation(s)
- Xing Huang
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
| | - Jie Chen
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
| | - Yaning Bao
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
| | - Lijun Liu
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
| | - Hui Jiang
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
| | - Xia An
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
| | - Lunjin Dai
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
| | - Bo Wang
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
| | - Dingxiang Peng
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
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Zhu S, Tang S, Tang Q, Liu T. Genome-wide transcriptional changes of ramie (Boehmeria nivea L. Gaud) in response to root-lesion nematode infection. Gene 2014; 552:67-74. [PMID: 25218245 DOI: 10.1016/j.gene.2014.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 12/27/2022]
Abstract
Ramie fiber extracted from stem bark is one of the most important natural fibers. The root-lesion nematode (RLN) Pratylenchus coffeae is a major ramie pest and causes large fiber yield losses in China annually. The response mechanism of ramie to RLN infection is poorly understood. In this study, we identified genes that are potentially involved in the RLN-resistance in ramie using Illumina pair-end sequencing in two RLN-infected plants (Inf1 and Inf2) and two control plants (CO1 and CO2). Approximately 56.3, 51.7, 43.4, and 45.0 million sequencing reads were generated from the libraries of CO1, CO2, Inf1, and Inf2, respectively. De novo assembly for these 196 million reads yielded 50,486 unigenes with an average length of 853.3bp. A total of 24,820 (49.2%) genes were annotated for their function. Comparison of gene expression levels between CO and Inf ramie revealed 777 differentially expressed genes (DEGs). The expression levels of 12 DEGs were further confirmed by real-time quantitative PCR (qRT-PCR). Pathway enrichment analysis showed that three pathways (phenylalanine metabolism, carotenoid biosynthesis, and phenylpropanoid biosynthesis) were strongly influenced by RLN infection. A series of candidate genes and pathways that may contribute to the defense response against RLN in ramie will be helpful for further improving resistance to RLN infection.
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Affiliation(s)
- Siyuan Zhu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Shouwei Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Qingming Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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Transcriptome-wide analysis of WRKY transcription factors in wheat and their leaf rust responsive expression profiling. Mol Genet Genomics 2014; 289:1289-306. [PMID: 25098419 DOI: 10.1007/s00438-014-0890-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/18/2014] [Indexed: 12/13/2022]
Abstract
WRKY, a plant-specific transcription factor family, has important roles in pathogen defense, abiotic cues and phytohormone signaling, yet little is known about their roles and molecular mechanism of function in response to rust diseases in wheat. We identified 100 TaWRKY sequences using wheat Expressed Sequence Tag database of which 22 WRKY sequences were novel. Identified proteins were characterized based on their zinc finger motifs and phylogenetic analysis clustered them into six clades consisting of class IIc and class III WRKY proteins. Functional annotation revealed major functions in metabolic and cellular processes in control plants; whereas response to stimuli, signaling and defense in pathogen inoculated plants, their major molecular function being binding to DNA. Tag-based expression analysis of the identified genes revealed differential expression between mock and Puccinia triticina inoculated wheat near isogenic lines. Gene expression was also performed with six rust-related microarray experiments at Gene Expression Omnibus database. TaWRKY10, 15, 17 and 56 were common in both tag-based and microarray-based differential expression analysis and could be representing rust specific WRKY genes. The obtained results will bestow insight into the functional characterization of WRKY transcription factors responsive to leaf rust pathogenesis that can be used as candidate genes in molecular breeding programs to improve biotic stress tolerance in wheat.
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