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Motto M, Sahay S. Energy plants (crops): potential natural and future designer plants. HANDBOOK OF BIOFUELS 2022:73-114. [DOI: 10.1016/b978-0-12-822810-4.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Wu L, Zhang M, Zhang R, Yu H, Wang H, Li J, Wang Y, Hu Z, Wang Y, Luo Z, Li L, Wang L, Peng L, Xia T. Down-regulation of OsMYB103L distinctively alters beta-1,4-glucan polymerization and cellulose microfibers assembly for enhanced biomass enzymatic saccharification in rice. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:245. [PMID: 34961560 PMCID: PMC8713402 DOI: 10.1186/s13068-021-02093-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/13/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND As a major component of plant cell walls, cellulose provides the most abundant biomass resource convertible for biofuels. Since cellulose crystallinity and polymerization have been characterized as two major features accounting for lignocellulose recalcitrance against biomass enzymatic saccharification, genetic engineering of cellulose biosynthesis is increasingly considered as a promising solution in bioenergy crops. Although several transcription factors have been identified to regulate cellulose biosynthesis and plant cell wall formation, much remains unknown about its potential roles for genetic improvement of lignocellulose recalcitrance. RESULTS In this study, we identified a novel rice mutant (Osfc9/myb103) encoded a R2R3-MYB transcription factor, and meanwhile generated OsMYB103L-RNAi-silenced transgenic lines. We determined significantly reduced cellulose levels with other major wall polymers (hemicellulose, lignin) slightly altered in mature rice straws of the myb103 mutant and RNAi line, compared to their wild type (NPB). Notably, the rice mutant and RNAi line were of significantly reduced cellulose features (crystalline index/CrI, degree of polymerization/DP) and distinct cellulose nanofibers assembly. These alterations consequently improved lignocellulose recalcitrance for significantly enhanced biomass enzymatic saccharification by 10-28% at p < 0.01 levels (n = 3) after liquid hot water and chemical (1% H2SO4, 1% NaOH) pretreatments with mature rice straws. In addition, integrated RNA sequencing with DNA affinity purification sequencing (DAP-seq) analyses revealed that the OsMYB103L might specifically mediate cellulose biosynthesis and deposition by regulating OsCesAs and other genes associated with microfibril assembly. CONCLUSIONS This study has demonstrated that down-regulation of OsMYB103L could specifically improve cellulose features and cellulose nanofibers assembly to significantly enhance biomass enzymatic saccharification under green-like and mild chemical pretreatments in rice. It has not only indicated a powerful strategy for genetic modification of plant cell walls in bioenergy crops, but also provided insights into transcriptional regulation of cellulose biosynthesis in plants.
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Affiliation(s)
- Leiming Wu
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
- College of Life Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingliang Zhang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ran Zhang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Haizhong Yu
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Hailang Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Jingyang Li
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, China
| | - Youmei Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Zhen Hu
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Yanting Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lingqiang Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Liangcai Peng
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Tao Xia
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses. PLANTS 2021; 10:plants10102169. [PMID: 34685978 PMCID: PMC8538510 DOI: 10.3390/plants10102169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/01/2023]
Abstract
Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. β-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes.
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Nguyen DT, Gomez LD, Harper A, Halpin C, Waugh R, Simister R, Whitehead C, Oakey H, Nguyen HT, Nguyen TV, Duong TX, McQueen-Mason SJ. Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:165. [PMID: 33062051 PMCID: PMC7545568 DOI: 10.1186/s13068-020-01807-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical production is limited by the cost-effectiveness of the production process due to its recalcitrance to enzymatic hydrolysis and fermentable sugar release (i.e., saccharification). Rice straw is a particularly attractive feedstock because millions of tons are currently burned in the field each year for disposal. The aim of this study was to explore the underlying natural genetic variation that impacts the recalcitrance of rice (Oryza sativa) straw to enzymatic saccharification. Ultimately, we wanted to investigate whether we could identify genetic markers that could be used in rice breeding to improve commercial cultivars for this trait. Here, we describe the development and characterization of a Vietnamese rice genome-wide association panel, high-throughput analysis of rice straw saccharification and lignin content, and the results from preliminary genome-wide association studies (GWAS) of the combined data sets. We identify both QTL and plausible candidate genes that may have an impact on the saccharification of rice straw. RESULTS We assembled a diversity panel comprising 151 rice genotypes (Indica and Japonica types) from commercial, historical elite cultivars, and traditional landraces grown in Vietnam. The diversity panel was genotyped using genotype by sequencing (GBS) methods yielding a total of 328,915 single nucleotide polymorphisms (SNPs). We collected phenotypic data from stems of these 151 genotypes for biomass saccharification and lignin content. Using GWAS on the indica genotypes over 2 years we identified ten significant QTL for saccharification (digestibility) and seven significant QTL for lignin. One QTL on chromosome 11 occurred in both GWAS for digestibility and for lignin. Seven QTL for digestibility, on CH2, CH6, CH7, CH8, and CH11, were observed in both years of the study. The QTL regions for saccharification include three potential candidate genes that have been previously reported to influence digestibility: OsAT10; OsIRX9; and OsMYB58/63-L. CONCLUSIONS Despite the difficulties associated with multi-phasic analysis of complex traits in novel germplasm, a moderate resolution GWAS successfully identified genetic associations encompassing both known and/or novel genes involved in determining the saccharification potential and lignin content of rice straw. Plausible candidates within QTL regions, in particular those with roles in cell wall biosynthesis, were identified but will require validation to confirm their value for application in rice breeding.
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Affiliation(s)
- Duong T. Nguyen
- Plant Biotechnology Division,, Field Crops Research Institute (FCRI), Hai Duong, Vietnam
- School of Agriculture and Environment, University of Western Australia (UWA), Crawley, WA Australia
| | - Leonardo D. Gomez
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Andrea Harper
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD), Dundee, UK
| | - Robbie Waugh
- Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD), Dundee, UK
- Cell, and Molecular Genetics, The James Hutton Institute (JHI), Invergowrie Dundee, UK
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Adelaide, SA Australia
| | - Rachael Simister
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Caragh Whitehead
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Helena Oakey
- Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD), Dundee, UK
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Adelaide, SA Australia
| | - Huong T. Nguyen
- Plant Biotechnology Division,, Field Crops Research Institute (FCRI), Hai Duong, Vietnam
| | - Tuat V. Nguyen
- Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Tu X. Duong
- Plant Biotechnology Division,, Field Crops Research Institute (FCRI), Hai Duong, Vietnam
| | - Simon J. McQueen-Mason
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
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Heidari P, Ahmadizadeh M, Izanlo F, Nussbaumer T. In silico study of the CESA and CSL gene family in Arabidopsis thaliana and Oryza sativa: Focus on post-translation modifications. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.plgene.2019.100189] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Hu H, Zhang R, Dong S, Li Y, Fan C, Wang Y, Xia T, Chen P, Wang L, Feng S, Persson S, Peng L. AtCSLD3 and GhCSLD3 mediate root growth and cell elongation downstream of the ethylene response pathway in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1065-1080. [PMID: 29253184 PMCID: PMC6018909 DOI: 10.1093/jxb/erx470] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 12/04/2017] [Indexed: 05/12/2023]
Abstract
CSLD3, a gene of the cellulose synthase-like D family, affects root hair elongation, but its interactions with ethylene signaling and phosphate-starvation are poorly understood. Here, we aim to understand the role of CSLD3 in the context of the ethylene signaling and phosphate starvation pathways in Arabidopsis plant growth. Therefore, we performed a comparative analysis of the csld3-1 mutant, CSLD3-overexpressing lines, and ethylene-response mutants, such as the constitutive ethylene-response mutant i-ctr1. We found that CSLD3 overexpression enhanced root and hypocotyl growth by increasing cell elongation, and that the root growth was highly sensitive to ethylene treatment (1 µM ACC), in particular under phosphate starvation. However, the CSLD3-mediated hypocotyl elongation occurred independently of the ethylene signaling pathway. Notably, the typical induction of root hair and root elongation by ethylene and phosphate-starvation was completely abolished in the csld3-1 mutant. Furthermore, i-ctr1 csld3-1 double-mutants were hairless like the csld3-1 parent, confirming that CSLD3 acts downstream of the ethylene signaling pathway during root growth. Moreover, the CSLD3 levels positively correlated with cellulose levels, indicating a role of CSLD3 in cellulose synthesis, which may explain the observed growth effects. Our results establish how CSLD3 works in the context of the ethylene signaling and phosphate-starvation pathways during root hair growth, cell elongation, and cell wall biosynthesis.
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Affiliation(s)
- Huizhen Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
| | - Ran Zhang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
| | - Shuchao Dong
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
| | - Ying Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
| | - Chunfen Fan
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
| | - Tao Xia
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Life Science and Technology, Huazhong Agricultural University, China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
| | - Lingqiang Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
| | - Shengqiu Feng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
| | - Staffan Persson
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
- School of Biosciences, University of Melbourne, Australia
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, China
- College of Plant Science and Technology, Huazhong Agricultural University, China
- Correspondence:
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Li Y, Yang T, Dai D, Hu Y, Guo X, Guo H. Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton. BMC PLANT BIOLOGY 2017; 17:119. [PMID: 28693426 PMCID: PMC5504666 DOI: 10.1186/s12870-017-1063-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/25/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND Among CESA-like gene superfamily, the cellulose synthase-like D (CSLD) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, there has been no genome-wide characterization of this gene subfamily in cotton. We thus sought to analyze the evolution and functional characterization of CSLD proteins in cotton based on fully sequenced cotton genomes. RESULTS A total of 23 full-length CSLD proteins were identified in Gossypium raimondii, Gossypium arboreum and Gossypium hirsutum. The phylogenetic tree divided the CSLD proteins into five clades with strong support: CSLD1, CSLD2/3, CSLD4, CSLD5 and CSLD6. The total expression of GhCSLD genes was the highest in androecium & gynoecium (mostly contributed by CSLD1 and CSLD4) compared with other CSL genes. CSLD1 and CSLD4 were only highly expressed in androecium & gynoecium (A&G), and showed tissue-specific expression. The total expression of CSLD2/3, 5 and 6 was highest in the specific tissues. These results suggest that CSLD genes showed the different pattern of expression. Cotton CSLD proteins were subjected to different evolutionary pressures, and the CSLD1 and CSLD4 proteins exhibited episodic and long-term shift positive selection. The predicted three-dimensional structure of GrCSLD1 suggested that GrCSLD1 belongs to glycosyltransferase family 2. The amino acid residues under positive selection in the CSLD1 lineage are positioned in a region adjacent to the class-specific region (CSR), β1-strand and transmembrane helices (TMHs) in the GrCSLD1structure. CONCLUSION Our results characterized the CSLD proteins by an integrated approach containing phylogeny, transcriptional profiling and 3D modeling. The study added to the understanding about the importance of the CSLD family and provide a useful reference for selecting candidate genes and their associations with the biosynthesis of the cell wall in cotton.
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Affiliation(s)
- Yanpeng Li
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Tiegang Yang
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Dandan Dai
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Ying Hu
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Xiaoyang Guo
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Hongxia Guo
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
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Zhu Y, Yu Y, Cheng K, Ouyang Y, Wang J, Gong L, Zhang Q, Li X, Xiao J, Zhang Q. Processes Underlying a Reproductive Barrier in indica- japonica Rice Hybrids Revealed by Transcriptome Analysis. PLANT PHYSIOLOGY 2017; 174:1683-1696. [PMID: 28483876 PMCID: PMC5490891 DOI: 10.1104/pp.17.00093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/04/2017] [Indexed: 05/13/2023]
Abstract
In rice (Oryza sativa), hybrids between indica and japonica subspecies are usually highly sterile, which provides a model system for studying postzygotic reproductive isolation. A killer-protector system, S5, composed of three adjacent genes (ORF3, ORF4, and ORF5), regulates female gamete fertility of indica-japonica hybrids. To characterize the processes underlying this system, we performed transcriptomic analyses of pistils from rice variety Balilla (BL), Balilla with transformed ORF5+ (BL5+) producing sterile female gametes, and Balilla with transformed ORF3+ and ORF5+ (BL3+5+) producing fertile gametes. RNA sequencing of tissues collected before (MMC), during (MEI), and after (AME) meiosis of the megaspore mother cell detected 19,269 to 20,928 genes as expressed. Comparison between BL5+ and BL showed that ORF5+ induced differential expression of 8,339, 6,278, and 530 genes at MMC, MEI, and AME, respectively. At MMC, large-scale differential expression of cell wall-modifying genes and biotic and abiotic response genes indicated that cell wall integrity damage induced severe biotic and abiotic stresses. The processes continued to MEI and induced endoplasmic reticulum (ER) stress as indicated by differential expression of ER stress-responsive genes, leading to programmed cell death at MEI and AME, resulting in abortive female gametes. In the BL3+5+/BL comparison, 3,986, 749, and 370 genes were differentially expressed at MMC, MEI, and AME, respectively. Large numbers of cell wall modification and biotic and abiotic response genes were also induced at MMC but largely suppressed at MEI without inducing ER stress and programed cell death , producing fertile gametes. These results have general implications for the understanding of biological processes underlying reproductive barriers.
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Affiliation(s)
- Yanfen Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Yu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Ke Cheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jia Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Gong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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CmMYB19 Over-Expression Improves Aphid Tolerance in Chrysanthemum by Promoting Lignin Synthesis. Int J Mol Sci 2017; 18:ijms18030619. [PMID: 28287502 PMCID: PMC5372634 DOI: 10.3390/ijms18030619] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/05/2017] [Accepted: 03/07/2017] [Indexed: 12/11/2022] Open
Abstract
The gene encoding the MYB (v-myb avian myeloblastosis vira l oncogene homolog) transcription factor CmMYB19 was isolated from chrysanthemum. It encodes a 200 amino acid protein and belongs to the R2R3-MYB subfamily. CmMYB19 was not transcriptionally activated in yeast, while a transient expression experiment conducted in onion epidermal cells suggested that the CmMYB19 product localized to the nucleus. CmMYB19 transcription was induced by aphid (Macrosiphoniella sanborni) infestation, and the abundance of transcript was higher in the leaf and stem than in the root. The over-expression of CmMYB19 restricted the multiplication of the aphids. A comparison of transcript abundance of the major genes involved in lignin synthesis showed that CmPAL1 (phenylalanine ammonia lyase 1), CmC4H (cinnamate4 hydroxylase), Cm4CL1 (4-hydroxy cinnamoyl CoA ligase 1), CmHCT (hydroxycinnamoyl CoA-shikimate/quinate hydroxycinnamoyl transferase), CmC3H1 (coumarate3 hydroxylase1), CmCCoAOMT1 (caffeoyl CoA O-methyltransferase 1) and CmCCR1 (cinnamyl CoA reductase1) were all upregulated, in agreement with an increase in lignin content in CmMYB19 over-expressing plants. Collectively, the over-expression of CmMYB19 restricted the multiplication of the aphids on the host, mediated by an enhanced accumulation of lignin.
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Huang J, Li Y, Wang Y, Chen Y, Liu M, Wang Y, Zhang R, Zhou S, Li J, Tu Y, Hao B, Peng L, Xia T. A precise and consistent assay for major wall polymer features that distinctively determine biomass saccharification in transgenic rice by near-infrared spectroscopy. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:294. [PMID: 29234462 PMCID: PMC5719720 DOI: 10.1186/s13068-017-0983-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 11/26/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND The genetic modification of plant cell walls has been considered to reduce lignocellulose recalcitrance in bioenergy crops. As a result, it is important to develop a precise and rapid assay for the major wall polymer features that affect biomass saccharification in a large population of transgenic plants. In this study, we collected a total of 246 transgenic rice plants that, respectively, over-expressed and RNAi silenced 12 genes of the OsGH9 and OsGH10 family that are closely associated with cellulose and hemicellulose modification. We examined the wall polymer features and biomass saccharification among 246 transgenic plants and one wild-type plant. The samples presented a normal distribution applicable for statistical analysis and NIRS modeling. RESULTS Among the 246 transgenic rice plants, we determined largely varied wall polymer features and the biomass enzymatic saccharification after alkali pretreatment in rice straws, particularly for the fermentable hexoses, ranging from 52.8 to 95.9%. Correlation analysis indicated that crystalline cellulose and lignin levels negatively affected the hexose and total sugar yields released from pretreatment and enzymatic hydrolysis in the transgenic rice plants, whereas the arabinose levels and arabinose substitution degree (reverse xylose/arabinose ratio) exhibited positive impacts on the hexose and total sugars yields. Notably, near-infrared spectroscopy (NIRS) was applied to obtain ten equations for predicting biomass enzymatic saccharification and seven equations for distinguishing major wall polymer features. Most of the equations exhibited high R2/R2cv/R2ev and RPD values for a perfect prediction capacity. CONCLUSIONS Due to large generated populations of transgenic rice lines, this study has not only examined the key wall polymer features that distinctively affect biomass enzymatic saccharification in rice but has also established optimal NIRS models for a rapid and precise screening of major wall polymer features and lignocellulose saccharification in biomass samples. Importantly, this study has briefly explored the potential roles of a total of 12 OsGH9 and OsGH10 genes in cellulose and hemicellulose modification and cell wall remodeling in transgenic rice lines. Hence, it provides a strategy for genetic modification of plant cell walls by expressing the desired OsGH9 and OsGH10 genes that could greatly improve biomass enzymatic digestibility in rice.
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Affiliation(s)
- Jiangfeng Huang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ying Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuanyuan Chen
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Mingyong Liu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Youmei Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ran Zhang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shiguang Zhou
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jingyang Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102 China
| | - Yuanyuan Tu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bo Hao
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tao Xia
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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11
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Lin F, Manisseri C, Fagerström A, Peck ML, Vega-Sánchez ME, Williams B, Chiniquy DM, Saha P, Pattathil S, Conlin B, Zhu L, Hahn MG, Willats WGT, Scheller HV, Ronald PC, Bartley LE. Cell Wall Composition and Candidate Biosynthesis Gene Expression During Rice Development. PLANT & CELL PHYSIOLOGY 2016; 57:2058-2075. [PMID: 27481893 DOI: 10.1093/pcp/pcw125] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/09/2016] [Indexed: 05/02/2023]
Abstract
Cell walls of grasses, including cereal crops and biofuel grasses, comprise the majority of plant biomass and intimately influence plant growth, development and physiology. However, the functions of many cell wall synthesis genes, and the relationships among and the functions of cell wall components remain obscure. To better understand the patterns of cell wall accumulation and identify genes that act in grass cell wall biosynthesis, we characterized 30 samples from aerial organs of rice (Oryza sativa cv. Kitaake) at 10 developmental time points, 3-100 d post-germination. Within these samples, we measured 15 cell wall chemical components, enzymatic digestibility and 18 cell wall polysaccharide epitopes/ligands. We also used quantitative reverse transcription-PCR to measure expression of 50 glycosyltransferases, 15 acyltransferases and eight phenylpropanoid genes, many of which had previously been identified as being highly expressed in rice. Most cell wall components vary significantly during development, and correlations among them support current understanding of cell walls. We identified 92 significant correlations between cell wall components and gene expression and establish nine strong hypotheses for genes that synthesize xylans, mixed linkage glucan and pectin components. This work provides an extensive analysis of cell wall composition throughout rice development, identifies genes likely to synthesize grass cell walls, and provides a framework for development of genetically improved grasses for use in lignocellulosic biofuel production and agriculture.
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Affiliation(s)
- Fan Lin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Chithra Manisseri
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alexandra Fagerström
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Matthew L Peck
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Miguel E Vega-Sánchez
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
- Monsanto Company, Chesterfield Village Campus, Chesterfield, MO 63017, USA
| | - Brian Williams
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
| | - Dawn M Chiniquy
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
| | - Prasenjit Saha
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Sivakumar Pattathil
- Bioenergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Brian Conlin
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
| | - Lan Zhu
- Department of Statistics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Michael G Hahn
- Bioenergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - William G T Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Pamela C Ronald
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Laura E Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
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12
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Zhang M, Wei F, Guo K, Hu Z, Li Y, Xie G, Wang Y, Cai X, Peng L, Wang L. A Novel FC116/ BC10 Mutation Distinctively Causes Alteration in the Expression of the Genes for Cell Wall Polymer Synthesis in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1366. [PMID: 27708650 PMCID: PMC5030303 DOI: 10.3389/fpls.2016.01366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/29/2016] [Indexed: 05/11/2023]
Abstract
We report isolation and characterization of a fragile culm mutant fc116 that displays reduced mechanical strength caused by decreased cellulose content and altered cell wall structure in rice. Map-based cloning revealed that fc116 was a base substitution mutant (G to A) in a putative beta-1,6-N-acetylglucosaminyltransferase (C2GnT) gene (LOC_Os05g07790, allelic to BC10). This mutation resulted in one amino acid missing within a newly-identified protein motif "R, RXG, RA." The FC116/BC10 gene was lowly but ubiquitously expressed in the all tissues examined across the whole life cycle of rice, and slightly down-regulated during secondary growth. This mutant also exhibited a significant increase in the content of hemicelluloses and lignins, as well as the content of pentoses (xylose and arabinose). But the content of hexoses (glucose, mannose, and galactose) was decreased in both cellulosic and non-cellulosic (pectins and hemicelluloses) fractions of the mutant. Transcriptomic analysis indicated that the typical genes in the fc116 mutant were up-regulated corresponding to xylan biosynthesis, as well as lignin biosynthesis including p-hydroxyphenyl (H), syringyl (S), and guaiacyl (G). Our results indicate that FC116 has universal function in regulation of the cell wall polymers in rice.
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Affiliation(s)
- Mingliang Zhang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Feng Wei
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Kai Guo
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Zhen Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yuyang Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Guosheng Xie
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xiwen Cai
- Department of Plant Science, North Dakota State UniversityFargo, ND, USA
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Lingqiang Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
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13
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Wang Y, Fan C, Hu H, Li Y, Sun D, Wang Y, Peng L. Genetic modification of plant cell walls to enhance biomass yield and biofuel production in bioenergy crops. Biotechnol Adv 2016; 34:997-1017. [PMID: 27269671 DOI: 10.1016/j.biotechadv.2016.06.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 02/06/2023]
Abstract
Plant cell walls represent an enormous biomass resource for the generation of biofuels and chemicals. As lignocellulose property principally determines biomass recalcitrance, the genetic modification of plant cell walls has been posed as a powerful solution. Here, we review recent progress in understanding the effects of distinct cell wall polymers (cellulose, hemicelluloses, lignin, pectin, wall proteins) on the enzymatic digestibility of biomass under various physical and chemical pretreatments in herbaceous grasses, major agronomic crops and fast-growing trees. We also compare the main factors of wall polymer features, including cellulose crystallinity (CrI), hemicellulosic Xyl/Ara ratio, monolignol proportion and uronic acid level. Furthermore, the review presents the main gene candidates, such as CesA, GH9, GH10, GT61, GT43 etc., for potential genetic cell wall modification towards enhancing both biomass yield and enzymatic saccharification in genetic mutants and transgenic plants. Regarding cell wall modification, it proposes a novel groove-like cell wall model that highlights to increase amorphous regions (density and depth) of the native cellulose microfibrils, providing a general strategy for bioenergy crop breeding and biofuel processing technology.
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Affiliation(s)
- Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunfen Fan
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huizhen Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Sun
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; College of Chemistry and Chemical Engineering, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Youmei Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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14
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Zhang L, Wang SB, Li QG, Song J, Hao YQ, Zhou L, Zheng HQ, Dunwell JM, Zhang YM. An Integrated Bioinformatics Analysis Reveals Divergent Evolutionary Pattern of Oil Biosynthesis in High- and Low-Oil Plants. PLoS One 2016; 11:e0154882. [PMID: 27159078 PMCID: PMC4861283 DOI: 10.1371/journal.pone.0154882] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/20/2016] [Indexed: 11/19/2022] Open
Abstract
Seed oils provide a renewable source of food, biofuel and industrial raw materials that is important for humans. Although many genes and pathways for acyl-lipid metabolism have been identified, little is known about whether there is a specific mechanism for high-oil content in high-oil plants. Based on the distinct differences in seed oil content between four high-oil dicots (20~50%) and three low-oil grasses (<3%), comparative genome, transcriptome and differential expression analyses were used to investigate this mechanism. Among 4,051 dicot-specific soybean genes identified from 252,443 genes in the seven species, 54 genes were shown to directly participate in acyl-lipid metabolism, and 93 genes were found to be associated with acyl-lipid metabolism. Among the 93 dicot-specific genes, 42 and 27 genes, including CBM20-like SBDs and GPT2, participate in carbohydrate degradation and transport, respectively. 40 genes highly up-regulated during seed oil rapid accumulation period are mainly involved in initial fatty acid synthesis, triacylglyceride assembly and oil-body formation, for example, ACCase, PP, DGAT1, PDAT1, OLEs and STEROs, which were also found to be differentially expressed between high- and low-oil soybean accessions. Phylogenetic analysis revealed distinct differences of oleosin in patterns of gene duplication and loss between high-oil dicots and low-oil grasses. In addition, seed-specific GmGRF5, ABI5 and GmTZF4 were predicted to be candidate regulators in seed oil accumulation. This study facilitates future research on lipid biosynthesis and potential genetic improvement of seed oil content.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Shi-Bo Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Statistical Genomics Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Qi-Gang Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People’s Republic of China
| | - Jian Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Yu-Qi Hao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Ling Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Institute of Biotechnology, Jiangsu Academy of Agricultural Science, Nanjing 210014, People’s Republic of China
| | - Huan-Quan Zheng
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AS, United Kingdom
| | - Yuan-Ming Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Statistical Genomics Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
- * E-mail: ;
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15
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Zhang J, Zou W, Li Y, Feng Y, Zhang H, Wu Z, Tu Y, Wang Y, Cai X, Peng L. Silica distinctively affects cell wall features and lignocellulosic saccharification with large enhancement on biomass production in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 239:84-91. [PMID: 26398793 DOI: 10.1016/j.plantsci.2015.07.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/11/2015] [Accepted: 07/18/2015] [Indexed: 05/11/2023]
Abstract
Rice is a typical silicon-accumulating crop with enormous biomass residues for biofuels. Silica is a cell wall component, but its effect on the plant cell wall and biomass production remains largely unknown. In this study, a systems biology approach was performed using 42 distinct rice cell wall mutants. We found that silica levels are significantly positively correlated with three major wall polymers, indicating that silica is associated with the cell wall network. Silicon-supplied hydroculture analysis demonstrated that silica distinctively affects cell wall composition and major wall polymer features, including cellulose crystallinity (CrI), arabinose substitution degree (reverse Xyl/Ara) of xylans, and sinapyl alcohol (S) proportion in three typical rice mutants. Notably, the silicon supplement exhibited dual effects on biomass enzymatic digestibility in the mutant and wild type (NPB) after pre-treatments with 1% NaOH and 1% H2SO4. In addition, silicon supply largely enhanced plant height, mechanical strength and straw biomass production, suggesting that silica rescues mutant growth defects. Hence, this study provides potential approaches for silicon applications in biomass process and bioenergy rice breeding.
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Affiliation(s)
- Jing Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China; Biomass and Bioenergy Research Centre, Huazhong Agriculture University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
| | - Weihua Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China; Biomass and Bioenergy Research Centre, Huazhong Agriculture University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
| | - Ying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China; Biomass and Bioenergy Research Centre, Huazhong Agriculture University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
| | - Yongqing Feng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China; Biomass and Bioenergy Research Centre, Huazhong Agriculture University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
| | - Hui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China; Biomass and Bioenergy Research Centre, Huazhong Agriculture University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
| | - Zhiliang Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China; Biomass and Bioenergy Research Centre, Huazhong Agriculture University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
| | - Yuanyuan Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China; Biomass and Bioenergy Research Centre, Huazhong Agriculture University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
| | - Yanting Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China; Biomass and Bioenergy Research Centre, Huazhong Agriculture University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiwen Cai
- Department of Plant Science, North Dakota State University, Loftsgard Hall, P.O. Box 6050, Fargo, ND 58108, USA
| | - Liangcai Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China; Biomass and Bioenergy Research Centre, Huazhong Agriculture University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agriculture University, Wuhan 430070, China.
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16
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Li F, Zhang M, Guo K, Hu Z, Zhang R, Feng Y, Yi X, Zou W, Wang L, Wu C, Tian J, Lu T, Xie G, Peng L. High-level hemicellulosic arabinose predominately affects lignocellulose crystallinity for genetically enhancing both plant lodging resistance and biomass enzymatic digestibility in rice mutants. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:514-25. [PMID: 25418842 DOI: 10.1111/pbi.12276] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/07/2014] [Accepted: 09/10/2014] [Indexed: 05/03/2023]
Abstract
Rice is a major food crop with enormous biomass residue for biofuels. As plant cell wall recalcitrance basically decides a costly biomass process, genetic modification of plant cell walls has been regarded as a promising solution. However, due to structural complexity and functional diversity of plant cell walls, it becomes essential to identify the key factors of cell wall modifications that could not much alter plant growth, but cause an enhancement in biomass enzymatic digestibility. To address this issue, we performed systems biology analyses of a total of 36 distinct cell wall mutants of rice. As a result, cellulose crystallinity (CrI) was examined to be the key factor that negatively determines either the biomass enzymatic saccharification upon various chemical pretreatments or the plant lodging resistance, an integrated agronomic trait in plant growth and grain production. Notably, hemicellulosic arabinose (Ara) was detected to be the major factor that negatively affects cellulose CrI probably through its interlinking with β-1,4-glucans. In addition, lignin and G monomer also exhibited the positive impact on biomass digestion and lodging resistance. Further characterization of two elite mutants, Osfc17 and Osfc30, showing normal plant growth and high biomass enzymatic digestion in situ and in vitro, revealed the multiple GH9B candidate genes for reducing cellulose CrI and XAT genes for increasing hemicellulosic Ara level. Hence, the results have suggested the potential cell wall modifications for enhancing both biomass enzymatic digestibility and plant lodging resistance by synchronically overexpressing GH9B and XAT genes in rice.
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Affiliation(s)
- Fengcheng Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China; Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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