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Ma Y, Ma C, Zhou P, Gao F, Tan W, Huang X, Bai Y, Li M, Wang Z, Hayat F, Shi T, Ni Z, Gao Z. PmLBD3 links auxin and brassinosteroid signalling pathways on dwarfism in Prunus mume. BMC Biol 2024; 22:184. [PMID: 39183294 PMCID: PMC11346286 DOI: 10.1186/s12915-024-01985-z] [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: 03/12/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Grafting with dwarf rootstock is an efficient method to control plant height in fruit production. However, the molecular mechanism remains unclear. Our previous study showed that plants with Prunus mume (mume) rootstock exhibited a considerable reduction in plant height, internode length, and number of nodes compared with Prunus persica (peach) rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by mume rootstocks through transcriptomic and metabolomic analyses with two grafting combinations, 'Longyan/Mume' and 'Longyan/Peach'. RESULTS There was a significant decrease in brassinolide levels in plants that were grafted onto mume rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased. There was a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto mume rootstocks. Auxin signalling cues promoted PmARF3 transcription, which directly controlled this upregulation. Through its binding to PmBAS1 and PmSAUR36a gene promoters, PmLBD3 promoted endogenous brassinolide inactivation and inhibited cell proliferation. CONCLUSIONS Auxin signalling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and causes dwarf plants in stone fruits.
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Affiliation(s)
- Yufan Ma
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Chengdong Ma
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Pengyu Zhou
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Feng Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wei Tan
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiao Huang
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yang Bai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Minglu Li
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ziqi Wang
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Faisal Hayat
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhaojun Ni
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
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Cai Z, Ruan L, Wei W, He W, Yang H, Chen H, Liang Z, Huang Z, Lan X, Zhang X, Huang R, Zhao C, Li T, He L, Li H. Morphological, anatomical, and transcriptomics analysis reveals the regulatory mechanisms of cassava plant height development. BMC Genomics 2024; 25:699. [PMID: 39020298 PMCID: PMC11253480 DOI: 10.1186/s12864-024-10599-2] [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: 03/21/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Cassava is one of three major potato crops and the sixth most important food crop globally. Improving yield remains a primary aim in cassava breeding. Notably, plant height significantly impacts the yield and quality of crops; however, the mechanisms underlying cassava plant height development are yet to be elucidated. RESULTS In this study, we investigated the mechanisms responsible for cassava plant height development using phenotypic, anatomical, and transcriptomic analyses. Phenotypic and anatomical analysis revealed that compared to the high-stem cassava cultivar, the dwarf-stem cassava cultivar exhibited a significant reduction in plant height and a notable increase in internode tissue xylem area. Meanwhile, physiological analysis demonstrated that the lignin content of dwarf cassava was significantly higher than that of high cassava. Notably, transcriptome analysis of internode tissues identified several differentially expressed genes involved in cell wall synthesis and expansion, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis between the two cassava cultivars. CONCLUSIONS Our findings suggest that internode tissue cell division, secondary wall lignification, and hormone-related gene expression play important roles in cassava plant height development. Ultimately, this study provides new insights into the mechanisms of plant height morphogenesis in cassava and identifies candidate regulatory genes associated with plant height that can serve as valuable genetic resources for future crop dwarfing breeding.
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Affiliation(s)
- Zhaoqin Cai
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Lixia Ruan
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Wanling Wei
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Wen He
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Haixia Yang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Huixian Chen
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Zhenhua Liang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Zhenling Huang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Xiu Lan
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Xiufen Zhang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Ruolan Huang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Chunhui Zhao
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Tianyuan Li
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Longfei He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, PR China.
| | - Hengrui Li
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China.
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Bai Y, Xie Y, Cai M, Jiang J, Wu C, Zheng H, Gao J. GA20ox Family Genes Mediate Gibberellin and Auxin Crosstalk in Moso bamboo ( Phyllostachys edulis). PLANTS (BASEL, SWITZERLAND) 2023; 12:2842. [PMID: 37570996 PMCID: PMC10421110 DOI: 10.3390/plants12152842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Moso bamboo (Phyllostachys edulis) is one of the fastest growing plants. Gibberellin (GA) is a key phytohormone regulating growth, but there are few studies on the growth of Moso bamboo regulated by GA. The gibberellin 20 oxidase (GA20ox) gene family was targeted in this study. Chromosomal distribution and collinearity analysis identified 10 GA20ox genes evenly distributed on chromosomes, and the family genes were relatively conservative in evolution. The genetic relationship of GA20ox genes had been confirmed to be closest in different genera of plants in a phylogenetic and selective pressure analysis between Moso bamboo and rice. About 1/3 GA20ox genes experienced positive selective pressure with segmental duplication being the main driver of gene family expansion. Analysis of expression patterns revealed that only six PheGA20ox genes were expressed in different organs of shoot development and flowers, that there was redundancy in gene function. Underground organs were not the main site of GA synthesis in Moso bamboo, and floral organs are involved in the GA biosynthesis process. The auxin signaling factor PheARF47 was located upstream of PheGA20ox3 and PheGA20ox6 genes, where PheARF47 regulated PheGA20ox3 through cis-P box elements and cis-AuxRR elements, based on the result that promoter analysis combined with yeast one-hybrid and dual luciferase detection analysis identified. Overall, we identified the evolutionary pattern of PheGA20ox genes in Moso bamboo and the possible major synthesis sites of GA, screened for key genes in the crosstalk between auxin and GA, and laid the foundation for further exploration of the synergistic regulation of growth by GA and auxin in Moso bamboo.
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Affiliation(s)
| | | | | | | | | | | | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China; (Y.B.); (Y.X.); (M.C.); (J.J.); (C.W.); (H.Z.)
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Xia X, Fan M, Liu Y, Chang X, Wang J, Qian J, Yang Y. Genome-wide alternative polyadenylation dynamics underlying plant growth retardant-induced dwarfing of pomegranate. FRONTIERS IN PLANT SCIENCE 2023; 14:1189456. [PMID: 37223801 PMCID: PMC10200943 DOI: 10.3389/fpls.2023.1189456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023]
Abstract
Dwarfed stature is a desired agronomic trait for pomegranate (Punica granatum L.), with its advantages such as lower cost and increased yield. A comprehensive understanding of regulatory mechanisms underlying the growth repression would provide a genetic foundation to molecular-assisted dwarfing cultivation of pomegranate. Our previous study induced dwarfed pomegranate seedlings via exogenous application of plant growth retardants (PGRs) and highlighted the important roles of differential expression of plant growth-related genes in eliciting the dwarfed phenotype of pomegranate. Alternative polyadenylation (APA) is an important post-transcriptional mechanism and has been demonstrated to act as a key regulator in plant growth and development. However, no attention has been paid to the role of APA in PGR-induced dwarfing in pomegranate. In this study, we characterized and compared APA-mediated regulation events underlying PGR-induced treatments and normal growth condition. Genome-wide alterations in the usage of poly(A) sites were elicited by PGR treatments, and these changes were involved in modulating the growth and development of pomegranate seedlings. Importantly, ample specificities were observed in APA dynamics among the different PGR treatments, which mirrors their distinct nature. Despite the asynchrony between APA events and differential gene expression, APA was found to regulate transcriptome via influencing microRNA (miRNA)-mediated mRNA cleavage or translation inhibition. A global preference for lengthening of 3' untranslated regions (3' UTRs) was observed under PGR treatments, which was likely to host more miRNA target sites in 3' UTRs and thus suppress the expression of the corresponding genes, especially those associated with developmental growth, lateral root branching, and maintenance of shoot apical meristem. Together, these results highlighted the key role of APA-mediated regulations in fine-tuning the PGR-induced dwarfed stature of pomegranate, which provides new insights into the genetic basis underlying the growth and development of pomegranate.
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Affiliation(s)
- Xinhui Xia
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Minhong Fan
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuqi Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Xinyue Chang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Jingting Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Jingjing Qian
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
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5
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Zha R, Chen T, Liu Q, Wei Q, Que F. Morphological and Anatomical Analysis of the Internodes of a New Dwarf Variant of Moso Bamboo, Phyllostachys edulis f. exaurita. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091759. [PMID: 37176817 PMCID: PMC10180987 DOI: 10.3390/plants12091759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The lack of mutants due to the long periods between flowering of bamboo plants is one of the limiting factors inhibiting research progress in the culm development of bamboo plants. In this study, a stable new dwarf variant of Phyllostachys edulis (Moso bamboo), Phyllostachys edulis f. exaurita T. G. Chen, was discovered and was characterized morphologically, anatomically, and physiologically. The height, diameter at breast height, number of internodes, length and wall thickness of internodes, length, width and number of parenchyma cells of internodes, and morphology of the wide-type (WT) and dwarf variant vascular bundles were compared. The height of the variant was only 49% that of the WT Moso bamboo. It was concluded that the decrease in internode number and length was the cause of dwarfism in P. edulis f. exaurita. The decreased internode length was the result of a decrease in cell number and cell length in the internode. In addition, the laws of change of internode length, internode thickness, cell length, and cell number differed between the WT Moso bamboo and the variant. Furthermore, lower IAA and zeatin concentrations were detected in the buds of the variant. These results suggest that P. edulis f. exaurita is a variant with inhibited primary thickening growth, which is valuable for interpretating the molecular mechanisms underlying the primary thickening growth of bamboo that are still largely unknown.
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Affiliation(s)
- Ruofei Zha
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Tianguo Chen
- Changzhou Agricultural Comprehensive Technology Extension Center, Changzhou 213022, China
| | - Qingnan Liu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Feng Que
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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Wu C, Bai Y, Cao Z, Xu J, Xie Y, Zheng H, Jiang J, Mu C, Cheng W, Fang H, Gao J. Plasticity in the Morphology of Growing Bamboo: A Bayesian Analysis of Exogenous Treatment Effects on Plant Height, Internode Length, and Internode Numbers. PLANTS (BASEL, SWITZERLAND) 2023; 12:1713. [PMID: 37111934 PMCID: PMC10145155 DOI: 10.3390/plants12081713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 06/19/2023]
Abstract
Sucrose (Suc) and gibberellin (GA) can promote the elongation of certain internodes in bamboo. However, there is a lack of field studies to support these findings and no evidence concerning how Suc and GA promote the plant height of bamboo by regulating the internode elongation and number. We investigated the plant height, the length of each internode, and the total number of internodes of Moso bamboo (Phyllostachys edulis) under exogenous Suc, GA, and control group (CTRL) treatments in the field and analyzed how Suc and GA affected the height of Moso bamboo by promoting the internode length and number. The lengths of the 10th-50th internodes were significantly increased under the exogenous Suc and GA treatments, and the number of internodes was significantly increased by the exogenous Suc treatment. The increased effect of Suc and GA exogenous treatment on the proportion of longer internodes showed a weakening trend near the plant height of 15-16 m compared with the CTRL, suggesting that these exogenous treatments may be more effective in regions where bamboo growth is suboptimal. This study demonstrated that both the exogenous Suc and GA treatments could promote internode elongation of Moso bamboo in the field. The exogenous GA treatment had a stronger effect on internode elongation, and the exogenous Suc treatment had a stronger effect on increasing the internode numbers. The increase in plant height by the exogenous Suc and GA treatments was promoted by the co-elongation of most internodes or the increase in the proportion of longer internodes.
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Affiliation(s)
- Chongyang Wu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
| | - Zhihua Cao
- Anhui Academy of Forestry, Hefei 230036, China
| | - Junlei Xu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
| | - Yali Xie
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
| | - Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
| | - Jutang Jiang
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
| | - Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
| | - Hui Fang
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing 100102, China; (C.W.); (Y.B.); (J.X.); (Y.X.); (J.J.); (C.M.); (W.C.); (H.F.)
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Gu Q, Wei Q, Hu Y, Chen M, Chen Z, Zheng S, Ma Q, Luo Z. Physiological and Full-Length Transcriptome Analyses Reveal the Dwarfing Regulation in Trifoliate Orange ( Poncirus trifoliata L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:271. [PMID: 36678984 PMCID: PMC9860739 DOI: 10.3390/plants12020271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Dwarfing rootstocks are capable of high-density planting and are therefore urgently needed in the modern citrus cultivation system. However, little is known about the physiological relevance and molecular basis underlying citrus height. This study aimed to comprehensively analyze phytohormone, carbohydrate, and associated transcriptome changes in the stem of two weak growth rootstocks ('TO' and 'FD') relative to the vigorous 'CC' rootstock. The phenotypic observation revealed that the plant height, plant weight, and internode length were reduced in dwarfing rootstocks. Moreover, the contents of indole-3-acetic acid (IAA), trans-zeatin (tZ), and abscisic acid (ABA), were higher in TO and FD rootstocks, whereas the gibberellin 3 (GA3) content was higher in the CC rootstocks. The carbohydrate contents, including sucrose, fructose, glucose, starch, and lignin significantly decreased in both the TO and FD rootstocks. The full-length transcriptome analysis revealed a potential mechanism regulating dwarfing phenotype that was mainly related to the phytohormone signaling transduction, sugar and starch degradation, lignin synthesis, and cellulose and hemicellulose degradation processes. In addition, many transcription factors (TFs), long non-coding RNAs (lncRNAs), and alternative splicing (AS) events were identified, which might act as important contributors to control the stem elongation and development in the weak growth rootstocks. These findings might deepen the understanding of the complex mechanisms of the stem development responsible for citrus dwarfing and provide a series of candidate genes for the application in breeding new rootstocks with intensive dwarfing.
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Affiliation(s)
- Qingqing Gu
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qingjiang Wei
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yongwei Hu
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Mengru Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ziwen Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shuang Zheng
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qiaoli Ma
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
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Morphological, Transcriptome, and Hormone Analysis of Dwarfism in Tetraploids of Populus alba × P. glandulosa. Int J Mol Sci 2022; 23:ijms23179762. [PMID: 36077160 PMCID: PMC9456051 DOI: 10.3390/ijms23179762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 11/28/2022] Open
Abstract
Breeding for dwarfism is an important approach to improve lodging resistance. Here, we performed comparative analysis of the phenotype, transcriptome, and hormone contents between diploids and tetraploids of poplar 84K (Populus alba × P. glandulosa). Compared with diploids, the indole-3-acetic acid (IAA) and gibberellin (GA3) contents were increased, whereas the jasmonic acid (JA) and abscisic acid (ABA) contents were decreased in tetraploids. RNA-sequencing revealed that differentially expressed genes (DEGs) in leaves of tetraploids were mainly involved in plant hormone pathways. Most DEGs associated with IAA and GA promotion of plant growth and development were downregulated, whereas most DEGs associated with ABA and JA promotion of plant senescence were upregulated. Weighted gene co-expression network analysis indicated that certain transcription factors may be involved in the regulation of genes involved in plant hormone pathways. Thus, the altered expression of some genes in the plant hormone pathways may lead to a reduction in IAA and GA contents, as well as an elevation in ABA and JA contents, resulting in the dwarfing of tetraploids. The results show that polyploidization is a complex biological process affected by multiple plant hormone signals, and it provides a foundation for further exploration of the mechanism of tetraploids dwarfing in forest trees.
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Chen S, Zhang Y, Zhang T, Zhan D, Pang Z, Zhao J, Zhang J. Comparative Transcriptomic, Anatomical and Phytohormone Analyses Provide New Insights Into Hormone-Mediated Tetraploid Dwarfing in Hybrid Sweetgum ( Liquidambar styraciflua × L. formosana). FRONTIERS IN PLANT SCIENCE 2022; 13:924044. [PMID: 35832220 PMCID: PMC9271929 DOI: 10.3389/fpls.2022.924044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Polyploid breeding is an effective approach to improve plant biomass and quality. Both fast growth and dwarf types of in vitro or ex vitro plants are produced after polyploidization. However, little is known regarding the dwarf type mechanism in polyploids grown in vitro. In this study, the morphological and cytological characteristics were measured in tetraploid and diploid hybrid sweetgum (Liquidambar styraciflua × L. formosana) with the same genetic background. RNA sequencing (RNA-Seq) was used to analyse shoot and root variations between tetraploid and diploid plants; important metabolites were validated. The results showed that the shoot and root lengths were significantly shorter in tetraploids than in diploids after 25 d of culture. Most tetraploid root cells were wider and more irregular, and the length of the meristematic zone was shorter, while tetraploid cells were significantly larger than diploid cells. Differentially expressed genes (DEGs) were significantly enriched in the plant growth and organ elongation pathways, such as plant hormone biosynthesis and signal transduction, sugar and starch metabolism, and cell cycles. Hormone biosynthesis and signal transduction genes, such as YUCCA, TAA1, GH3, SAUR, CPS, KO, KAO, GA20ox, GA3ox, BAS1 and CYCD3, which help to regulate organ elongation, were generally downregulated. The auxin, gibberellin, and brassinolide (BL) contents in roots and stems were significantly lower in tetraploids than in diploids, which may greatly contribute to slow growth in the roots and stems of tetraploid regenerated plants. Exogenous gibberellic acid (GA3) and indole-3-acetic acid (IAA), which induced plant cell elongation, could significantly promote growth in the stems and roots of tetraploids. In summary, comparative transcriptomics and metabolite analysis showed that the slow growth of regenerated tetraploid hybrid sweetgum was strongly related to auxin and gibberellin deficiency. Our findings provide insights into the molecular mechanisms that underlie dwarfism in allopolyploid hybrid sweetgum.
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Affiliation(s)
- Siyuan Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yan Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Ting Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Dingju Zhan
- Guangxi Bagui Forest and Flowers Seedlings Co., Ltd., Nanning, China
| | - Zhenwu Pang
- Guangxi Bagui Forest and Flowers Seedlings Co., Ltd., Nanning, China
| | - Jian Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jinfeng Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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10
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Zhao X, Sun XF, Zhao LL, Huang LJ, Wang PC. Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height. BMC PLANT BIOLOGY 2022; 22:144. [PMID: 35337273 PMCID: PMC8951708 DOI: 10.1186/s12870-022-03503-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/02/2022] [Indexed: 05/28/2023]
Abstract
Sophora davidii is an important plant resource in the karst region of Southwest China, but S. davidii plant-height mutants are rarely reported. Therefore, we performed phenotypic, anatomic structural, transcriptomic and metabolomic analyses to study the mechanisms responsible for S. davidii plant-height mutants. Phenotypic and anatomical observations showed that compared to the wild type, the dwarf mutant displayed a significant decrease in plant height, while the tall mutant displayed a significant increase in plant height. The dwarf mutant cells were smaller and more densely arranged, while those of the wild type and the tall mutant were larger and loosely arranged. Transcriptomic analysis revealed that differentially expressed genes (DEGs) involved in cell wall biosynthesis, expansion, phytohormone biosynthesis, signal transduction pathways, flavonoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched in the S. davidii plant-height mutants. Metabolomic analysis revealed 57 significantly differential metabolites screened from both the dwarf and tall mutants. A total of 8 significantly different flavonoid compounds were annotated to LIPID MAPS, and three metabolites (chlorogenic acid, kaempferol and scopoletin) were involved in phenylpropanoid biosynthesis and flavonoid biosynthesis. These results shed light on the molecular mechanisms of plant height in S. davidii mutants and provide insight for further molecular breeding programs.
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Affiliation(s)
- Xin Zhao
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Xiao-Fu Sun
- Weining Plateau Grassland Test Station, Weining, 553100, China
| | - Li-Li Zhao
- College of Animal Science, Guizhou University, Guiyang, 550025, China.
| | - Li-Juan Huang
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Pu-Chang Wang
- Guizhou Institute of Prataculture, Guiyang, 550006, China.
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11
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Qian J, Wang N, Ren W, Zhang R, Hong X, Chen L, Zhang K, Shu Y, Hu N, Yang Y. Molecular Dissection Unveiling Dwarfing Effects of Plant Growth Retardants on Pomegranate. FRONTIERS IN PLANT SCIENCE 2022; 13:866193. [PMID: 35360308 PMCID: PMC8961278 DOI: 10.3389/fpls.2022.866193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 05/31/2023]
Abstract
Dwarfed stature is a desired trait for modern orchard production systems. One effective strategy for dwarfing cultivation is exogenously applying plant growth retardants (PGRs) to plants. However, for many economic fruit trees, the current knowledge on the regulatory mechanisms underlying the dwarfing effect of PGRs is limited, which largely restricts the agricultural application of PGRs. In this study, we exogenously applied three kinds of PGRs [paclobutrazol, daminozide (B9), and mannitol] to the seedlings of pomegranate (Punica granatum L.) and performed comparative transcriptome analysis to elucidate the molecular features of PGR-induced dwarfing in pomegranates. Our results showed that all the three PGRs could significantly suppress plant growth of pomegranate. The inhibition of auxin biosynthetic processes, as well as auxin-mediated shoot development, may be considered as the main reason for the dwarfing. Besides that, different PGRs were also found to induce dwarfing via specific mechanisms, for example, cellular response to strigolactone was particularly suppressed by the application of paclobutrazol, while the level of carbohydrate homeostasis and metabolism were downregulated in conditions of either B9 or mannitol treatments. Furthermore, exogenous PGR application was supposed to cause adverse impacts on the normal physiological process of pomegranate seedlings, which may bring extra burden to pomegranate plants. These novel findings unveiled the genetic basis underlying the dwarfing in pomegranates, which provides deeper insights into PGR-mediated dwarfing cultivation of pomegranates.
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Affiliation(s)
- Jingjing Qian
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Ning Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Wenxu Ren
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Rufan Zhang
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Xiyao Hong
- School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Lingyue Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Kaijing Zhang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yingjie Shu
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Nengbing Hu
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
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12
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Liu X, Liu L, Li L, Yue J. The complete chloroplast genome of Phyllostachys edulis f. tubiformis (Bambusoideae): a highly appreciated type of ornamental bamboo in China. Mitochondrial DNA B Resour 2022; 7:185-187. [PMID: 35028414 PMCID: PMC8751489 DOI: 10.1080/23802359.2021.2018945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Phyllostachys edulis (Carr.) H. de Lehaie f. tubiformis (S.Y.Wang) Ohrnberger (shengyin bamboo in Chinese) is a dwarf form of moso bamboo, which has important ornamental value. In this study, the complete chloroplast genome of P. edulis f. tubiformis was reported. The complete chloroplast genome of P. edulis f. tubiformis is a double-circular DNA of 139,678 bp in length with 38.89% G + C content, and contains 126 genes, including 84 protein-coding genes, eight ribosomal RNA (rRNA) genes, and 34 transfer RNA (tRNA) genes. Phylogenetic analysis results strongly supported that P. edulis f. tubiformis was clustered with the other infra-species of P. edulis, although its morphology is quite different from moso bamboo.
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Affiliation(s)
- Xinmiao Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lei Liu
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lubin Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jinjun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
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13
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Wang Y, Qiao G, Xu J, Jin K, Fan M, Ding Y, Wei Q, Zhuo R. Anatomical Characteristics and Variation Mechanisms on the Thick-Walled and Dwarfed Culm of Shidu Bamboo ( Phyllostachys nidularia f. farcta). FRONTIERS IN PLANT SCIENCE 2022; 13:876658. [PMID: 35685025 PMCID: PMC9171372 DOI: 10.3389/fpls.2022.876658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/28/2022] [Indexed: 05/13/2023]
Abstract
Stable culm variants are valuable and important material for the study of culm development in bamboo plants. However, to date, there are few reports on the mechanism of variation of these bamboo variants. Phyllostachys nidularia f. farcta (Shidu bamboo) is a bamboo variant with stable phenotypes such as a dwarf culm with a thickened wall. In this study, we systematically investigated the cytological characteristics and underlying mechanism of morphological variation in culms of this variant using anatomical, mathematical statistical, physiological, and genomic methods. The anatomical observation and statistical results showed that the lateral increase of ground tissue in the inner layer of culm wall and the enlargement of vascular bundles are the anatomical essence of the wall thickening of Shidu bamboo; the limited elongation of fiber cells and the decrease in the number of parenchyma cells longitudinally are probably the main causes of the shortening of its internodes. A number of genes involved in the gibberellin synthesis pathway and in the synthesis of cell wall components are differentially expressed between the variant and its prototype, Ph. nidularia, and may play an important role in determining the phenotype of internode shortening in Shidu bamboo. The decrease in gibberellin content and the content of the major chemical components of the cell wall of Shidu bamboo confirmed the results of the above transcriptome. In addition, the variation in culm morphology in Shidu bamboo had little effect on the volume of the culm wall of individual internodes, suggesting that the decrease in the total number of internodes and the decrease in dry matter content (lignin, cellulose, etc.) may be the main factor for the sharp decline in culm biomass of Shidu bamboo.
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Affiliation(s)
- Yujun Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Jing Xu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Kangming Jin
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Minyuan Fan
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Yulong Ding
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
| | - Qiang Wei
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- Qiang Wei
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- *Correspondence: Renying Zhuo
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Lan Y, Wu L, Wu M, Liu H, Gao Y, Zhang K, Xiang Y. Transcriptome analysis reveals key genes regulating signaling and metabolic pathways during the growth of moso bamboo (Phyllostachys edulis) shoots. PHYSIOLOGIA PLANTARUM 2021; 172:91-105. [PMID: 33280114 DOI: 10.1111/ppl.13296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Moso bamboo (Phyllostachys edulis), a high-value bamboo used to produce food (young shoots), building, and industrial goods. To explore key candidate genes regulating signal transduction and metabolic processes during the initiation of stem elongation in moso bamboo, a transcriptome analysis of the shoots during three successive early elongation stages was performed. From cluster and differential expression analyses, 2984 differentially expressed genes (DEGs) were selected for an enrichment analysis. The DEGs were significantly enriched in the plant hormone signal transduction, sugar and starch metabolism, and energy metabolism pathways. Consequently, the DEG expression patterns of these pathways were analyzed, and the plant endogenous hormone and carbon metabolite (including sucrose, total soluble sugar, and starch) contents for each growth stage, of the shoot, were determined. The cytokinin-signaling pathway was continuously active in the three successive elongation stages, in which several cytokinin-signaling genes played indispensable roles. Additionally, many key DEGs regulating sugar, starch metabolism, and energy conversion, which are actively involved in energy production and substrate synthesis during the continuous growth of the shoots, were found. In summary, our study lays a foundation for understanding the mechanisms of moso bamboo growth and provides useful gene resources for breeding through genetic engineering.
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Affiliation(s)
- Yangang Lan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Lin Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Huanlong Liu
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yameng Gao
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
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15
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Sun Z, Wang X, Liu R, Du W, Ma M, Han Y, Li H, Liu L, Hou S. Comparative transcriptomic analysis reveals the regulatory mechanism of the gibberellic acid pathway of Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) dwarf mutants. BMC PLANT BIOLOGY 2021; 21:206. [PMID: 33931042 PMCID: PMC8086092 DOI: 10.1186/s12870-021-02978-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Tartary buckwheat is an important minor crop species with high nutritional and medicinal value and is widely planted worldwide. Cultivated Tartary buckwheat plants are tall and have hollow stems that lodge easily, which severely affects their yield and hinders the development of the Tartary buckwheat industry. METHODS Heifeng No. 1 seeds were treated with ethylmethanesulfonate (EMS) to generate a mutant library. The dwarf mutant ftdm was selected from the mutagenized population, and the agronomic characteristics giving rise to the dwarf phenotype were evaluated. Ultra-fast liquid chromatography-electrospray ionization tandem mass spectrometry (UFLC-ESI-MS/MS) was performed to determine the factors underlying the different phenotypes between the wild-type (WT) and ftdm plants. In addition, RNA sequencing (RNA-seq) was performed via the HiSeq 2000 platform, and the resulting transcriptomic data were analysed to identify differentially expressed genes (DEGs). Single-nucleotide polymorphism (SNP) variant analysis revealed possible sites associated with dwarfism. The expression levels of the potential DEGs between the WT and ftdm mutant were then measured via qRT-PCR and fragments per kilobase of transcript per million mapped reads (FPKM). RESULT The plant height (PH) of the ftdm mutant decreased to 42% of that of the WT, and compared with the WT, the mutant and had a higher breaking force (BF) and lower lodging index (LI). Lower GA4 and GA7 contents and higher contents of jasmonic acid (JA), salicylic acid (SA) and brassinolactone (BR) were detected in the stems of the ftdm mutant compared with the WT. Exogenous application of GAs could not revert the dwarfism of the ftdm mutant. On the basis of the transcriptomic analysis, 146 homozygous SNP loci were identified. In total, 12 DEGs with nonsynonymous mutations were ultimately identified, which were considered potential candidate genes related to the dwarf trait. When the sequences of eight genes whose expression was downregulated and four genes whose expression was upregulated were compared, SKIP14, an F-box protein whose sequence is 85% homologous to that of SLY1 in Arabidopsis, presented an amino acid change (from Ser to Asn) and was expressed at a lower level in the stems of the ftdm mutant compared with the WT. Hence, we speculated that this amino acid change in SKIP14 resulted in a disruption in GA signal transduction, indirectly decreasing the GA content and downregulating the expression of genes involved in GA biosynthesis or the GA response. Further studies are needed to determine the molecular basis underlying the dwarf phenotype of the ftdm mutant. CONCLUSION We report a Tartary buckwheat EMS dwarf mutant, ftdm, suitable for high-density planting and commercial farming. A significant decrease in GA4 and GA7 levels was detected in the ftdm mutant, and 12 DEGs expressed in the stems of the ftdm mutant were selected as candidates of the dwarfing gene. One nonsynonymous mutation was detected in the SKIP14 gene in the ftdm mutant, and this gene had a lower transcript level compared with that in the WT.
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Affiliation(s)
- Zhaoxia Sun
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan, 030031, Shanxi, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, 030031, Shanxi, China
| | - Xinfang Wang
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Ronghua Liu
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Wei Du
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Mingchuan Ma
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Yuanhuai Han
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan, 030031, Shanxi, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, 030031, Shanxi, China
| | - Hongying Li
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Longlong Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China.
| | - Siyu Hou
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan, 030031, Shanxi, China.
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, 030031, Shanxi, China.
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16
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Tao GY, Ramakrishnan M, Vinod KK, Yrjälä K, Satheesh V, Cho J, Fu Y, Zhou M. Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo. TREE PHYSIOLOGY 2020; 40:1487-1508. [PMID: 32705116 DOI: 10.1093/treephys/tpaa090] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/29/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely, starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8045 differentially expressed genes (DEGs) and 1053 differentially expressed proteins (DEPs) were identified in our analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs and 3 significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein-protein interaction network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription, and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway.
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Affiliation(s)
- Gui-Yun Tao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- The State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan, Haidian District, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan, Haidian District, Beijing, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | | | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Department of Forest Sciences, University of Helsinki, Helsinki P.O. Box 27 00014, Finland
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ying Fu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
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17
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Wang B, Zhang Y, Dong N, Chen Y, Zhang Y, Hao Y, Qi J. Comparative transcriptome analyses provide novel insights into etiolated shoot development of walnut (Juglans regia L.). PLANTA 2020; 252:74. [PMID: 33025156 DOI: 10.1007/s00425-020-03455-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
In general, genes promoting IAA, CTK GA and ethylene biosynthesis were upregulated, while genes participating in ABA, chlorophyll and starch biosynthesis pathways performed opposite tendency during etiolation. Etiolation as a method for rejuvenation plays an important role in the vegetative propagation of woody plants. However, the molecular mechanism of etiolated shoot development remains unclear. In this study, we investigated changes at different etiolation stages of Juglans regia. The histology and transcriptome of J. regia were analysed using etiolated stems, which were treated in darkness for 30, 60, 90 days. The results showed that the ratios of pith (Pi) diameter/stem diameter (D), cortex (Co) width/D, and phloem (Ph) width/D increased, while the ratio of xylem (Xy) width/D decreased after etiolation, and the difference in these ratios between etiolated stems and the control was more significant at 60 days than 90 days. Differentially expressed genes (DEGs) were significantly enriched in pathways such as plant hormone biosynthesis and signal transduction, chlorophyll biosynthesis and degradation, and starch and sucrose metabolism. The difference in the contents of indole-3-acetic acid (IAA), abscisic acid (ABA), sugar and chlorophyll between etiolated stems and the control increased with increasing treatment duration; in contrast, the concentrations of gibberellin (GA), zeatin (ZT), and starch, as well as the difference between the etiolated stems and control were lowest at 60 days among the three stages. On the whole, the positive effect of etiolation on the rejuvenation of walnut stems changed as the treatment period increased. The present investigation lays a foundation for future studies on the effect of etiolation on rejuvenation and for promoting the efficiency of vegetative propagation.
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Affiliation(s)
- Beibei Wang
- Beijing Academy of Forestry and Pomology Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Yan Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China
| | - Ningguang Dong
- Beijing Academy of Forestry and Pomology Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Yonghao Chen
- Beijing Academy of Forestry and Pomology Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Yunqi Zhang
- Beijing Academy of Forestry and Pomology Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Yanbin Hao
- Beijing Academy of Forestry and Pomology Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China.
| | - Jianxun Qi
- Beijing Academy of Forestry and Pomology Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China.
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18
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Ramakrishnan M, Yrjälä K, Vinod KK, Sharma A, Cho J, Satheesh V, Zhou M. Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry. Food Energy Secur 2020. [DOI: 10.1002/fes3.229] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Department of Forest Sciences University of Helsinki Helsinki Finland
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS) Chinese Academy of Sciences Shanghai China
| | - Viswanathan Satheesh
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High‐efficiency Utilization Zhejiang A&F University Hangzhou China
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19
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Gebremeskel H, Dou J, Li B, Zhao S, Muhammad U, Lu X, He N, Liu W. Molecular Mapping and Candidate Gene Analysis for GA 3 Responsive Short Internode in Watermelon ( Citrullus lanatus). Int J Mol Sci 2019; 21:E290. [PMID: 31906246 PMCID: PMC6982186 DOI: 10.3390/ijms21010290] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/27/2019] [Accepted: 12/27/2019] [Indexed: 11/16/2022] Open
Abstract
Plants with shorter internodes are suitable for high-density planting, lodging resistance and the preservation of land resources by improving yield per unit area. In this study, we identified a locus controlling the short internode trait in watermelon using Zhengzhouzigua (long internode) and Duan125 (short internode) as mapping parents. Genetic analysis indicated that F1 plants were consistent with long internode plants, which indicates that the long internode was dominant over the short internode. The observed F2 and BC1 individuals fitted the expected phenotypic segregation ratios of 3:1 and 1:1, respectively. The locus was mapped on chromosome 9 using a bulked segregant analysis approach. The region was narrowed down to 8.525 kb having only one putative gene, Cla015407, flanking by CAPS90 and CAPS91 markers, which encodes gibberellin 3β-hydroxylase (GA 3β-hydroxylase). The sequence alignment of the candidate gene between both parents revealed a 13 bp deletion in the short internode parent, which resulted in a truncated protein. Before GA3 application, significantly lower GA3 content and shorter cell length were obtained in the short internode plants. However, the highest GA3 content and significant increase in cell length were observed in the short internode plants after exogenous GA3 application. In the short internode plants, the expression level of the Cla015407 was threefold lower than the long internode plants in the stem tissue. In general, our results suggested that Cla015407 might be the candidate gene responsible for the short internode phenotype in watermelon and the phenotype is responsive to exogenous GA3 application.
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Affiliation(s)
| | | | | | | | | | | | | | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (H.G.); (J.D.); (B.L.); (S.Z.); (U.M.); (X.L.); (N.H.)
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Ramakrishnan M, Zhou M, Pan C, Hänninen H, Yrjälä K, Vinod KK, Tang D. Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element. Int J Mol Sci 2019; 20:ijms20153692. [PMID: 31357686 PMCID: PMC6696609 DOI: 10.3390/ijms20153692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022] Open
Abstract
Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and gene therapy. Two active MLEs, Ppmar1 and Ppmar2, have previously been identified in moso bamboo (Phyllostachys edulis). Both of these have a preferential insertion affinity to AT-rich region and their insertion sites are close to random in the host genome. In Ppmar2 element, we studied the affinities of terminal inverted repeats (TIRs) to DNA binding domain (DBD) and their influence on the transposition activity. We could identify two putative boxes in the TIRs which play a significant role in defining the TIR's affinities to the DBD. Seven mutated TIRs were constructed, differing in affinities based on similarities with those of other plant MLEs. Gel mobility shift assays showed that the TIR mutants with mutation sites G669A-C671A had significantly higher affinities than the mutants with mutation sites C657T-A660T. The high-affinity TIRs indicated that their transposition frequency was 1.5-2.0 times higher than that of the wild type TIRs in yeast transposition assays. The MLE mutants with low-affinity TIRs had relatively lower transposition frequency from that of wild types. We conclude that TIR affinity to DBD significantly affects the transposition activity of Ppmar2. The mutant MLEs highly active TIRs constructed in this study can be used as a tool for bamboo genetic studies.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
| | - Chunfang Pan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Heikki Hänninen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Kunnummal Kurungara Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, Tamil Nadu 612101, India
| | - Dingqin Tang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
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