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Vanhevel Y, De Moor A, Muylle H, Vanholme R, Boerjan W. Breeding for improved digestibility and processing of lignocellulosic biomass in Zea mays. FRONTIERS IN PLANT SCIENCE 2024; 15:1419796. [PMID: 39129761 PMCID: PMC11310149 DOI: 10.3389/fpls.2024.1419796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/10/2024] [Indexed: 08/13/2024]
Abstract
Forage maize is a versatile crop extensively utilized for animal nutrition in agriculture and holds promise as a valuable resource for the production of fermentable sugars in the biorefinery sector. Within this context, the carbohydrate fraction of the lignocellulosic biomass undergoes deconstruction during ruminal digestion and the saccharification process. However, the cell wall's natural resistance towards enzymatic degradation poses a significant challenge during both processes. This so-called biomass recalcitrance is primarily attributed to the presence of lignin and ferulates in the cell walls. Consequently, maize varieties with a reduced lignin or ferulate content or an altered lignin composition can have important beneficial effects on cell wall digestibility. Considerable efforts in genetic improvement have been dedicated towards enhancing cell wall digestibility, benefiting agriculture, the biorefinery sector and the environment. In part I of this paper, we review conventional and advanced breeding methods used in the genetic improvement of maize germplasm. In part II, we zoom in on maize mutants with altered lignin for improved digestibility and biomass processing.
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Affiliation(s)
- Yasmine Vanhevel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Astrid De Moor
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Hilde Muylle
- Plant Sciences Unit, Institute for Agricultural and Fisheries Research, Melle, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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Shi R, Cao Y, Yang T, Wang Y, Xiang Y, Chen F, Zhang W, Zhou X, Sun C, Fu S, Hu M, Zhang J, Wang X. Genome-Wide Association Study Reveals the Genetic Basis of Crude Fiber Components in Brassica napus L. Shoots at Stem Elongation Stage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16530-16540. [PMID: 39001851 DOI: 10.1021/acs.jafc.4c03032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Brassica napus is currently the principal field crop for producing materials for primary, secondary and tertiary industries. B. napus shoots at stem elongation stage are rich in anthocyanins, vitamin C and mineral elements such as selenium, calcium and zinc, and represent a new type of green vegetable. However, the high crude fiber (CF) content of B. napus shoots affects their taste, and few studies have focused on the quality traits of these vegetables. In this study, we investigated five traits related to the CF components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), hemicellulose (Hem) and cellulose (Cel), of B. napus shoots. Whole-genome resequencing at a depth of ∼20× was utilized to genotype an association panel of 202 diverse accessions, which resulted in the identification of 6,093,649 single nucleotide polymorphisms (SNPs) and 996,252 indels, respectively. A genome-wide association study (GWAS) was performed for the five CF-related traits based on the phenotypic data observed in four environments. A total of 1,285 significant SNPs were detected at the threshold of -log10 (p) = 5.16, and 97 significant association regions were obtained. In addition, seven candidate genes located on chromosomes A2 (one gene), A8 (three genes), A9 (two genes) and C9 (one gene) related to CF traits were identified, and ten lines containing low CF contents were selected as excellent germplasm resources for breeding. Our results contributed new insights into the genetic basis of CF traits and suggested germplasm resources for the quality improvement of B. napus shoots.
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Affiliation(s)
- Rui Shi
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yu Cao
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Tinghai Yang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Yaping Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Yanan Xiang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Feng Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Wei Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Xiaoying Zhou
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Chengming Sun
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Sanxiong Fu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Maolong Hu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Jiefu Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
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3
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Saberi Riseh R, Fathi F, Lagzian A, Vatankhah M, Kennedy JF. Modifying lignin: A promising strategy for plant disease control. Int J Biol Macromol 2024; 271:132696. [PMID: 38823737 DOI: 10.1016/j.ijbiomac.2024.132696] [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: 03/09/2024] [Revised: 05/02/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024]
Abstract
Lignin is a complex polymer found in the cell walls of plants, providing structural support and protection against pathogens. By modifying lignin composition and structure, scientists aim to optimize plant defense responses and increase resistance to pathogens. This can be achieved through various genetic engineering techniques which involve manipulating the genes responsible for lignin synthesis. By either up regulating or down regulating specific genes, researchers can alter the lignin content, composition, or distribution in plant tissues. Reducing lignin content in specific tissues like leaves can improve the effectiveness of defense mechanisms by allowing for better penetration of antimicrobial compounds. Overall, Lignin modification through techniques has shown promising results in enhancing various plants resistance against pathogens. Furthermore, lignin modification can have additional benefits beyond pathogen resistance. It can improve biomass processing for biofuel production by reducing lignin recalcitrance, making the extraction of sugars from cellulose more efficient. The complexity of lignin biosynthesis and its interactions with other plant components make it a challenging target for modification. Additionally, the potential environmental impact and regulatory considerations associated with genetically modified organisms (GMOs) require careful evaluation. Ongoing research aims to further optimize this approach and develop sustainable solutions for crop protection.
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Affiliation(s)
- Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran.
| | - Fariba Fathi
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran
| | - Arezoo Lagzian
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran
| | - Masoumeh Vatankhah
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran
| | - John F Kennedy
- Chembiotech Laboratories Ltd, WR15 8FF Tenbury Wells, United Kingdom.
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Yang J, Song J, Feng Y, Cao Y, Fu B, Zhang Z, Ma N, Li Q, Hu T, Wang Y, Yang P. Osmotic stress-induced lignin synthesis is regulated at multiple levels in alfalfa (Medicago sativa L.). Int J Biol Macromol 2023; 246:125501. [PMID: 37348591 DOI: 10.1016/j.ijbiomac.2023.125501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Alfalfa is an important forage crop. Yield and quality are frequently threatened by extreme environments such as drought and salt stress. As a component of the cell wall, lignin plays an important role in the abiotic stress response, the mechanisms of which have not been well clarified. In this study, we combined physiological, transcriptional, and metabolic analyses to reveal the changes in lignin content in alfalfa under mannitol-induced osmotic stress. Osmotic stress enhanced lignin accumulation by increasing G and S units, which was associated with increases in enzyme activities and decreases in 8 intermediate metabolites. Upon combined analysis of the transcriptome and metabolome, we identified five key structural genes and several coexpressed transcription factors, such as MYB and WRKY, which may play a core role in regulating lignin content and composition under osmotic stress. In addition, lignin synthesis was positively regulated by ABA but negatively regulated by ethylene under osmotic stress. These results provide new insight into the regulatory mechanism of lignin synthesis under abiotic stress.
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Affiliation(s)
- Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Jiaxing Song
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Yueyan Feng
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Yuman Cao
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Bingzhe Fu
- College of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Zhiqiang Zhang
- Key Laboratory of Grassland Resources of the Ministry of Education, Technology Engineering Center of Drought and Cold-Resistant Grass Breeding in the North of the National Forestry and Grassland Administration, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Qian Li
- Key Laboratory of Grassland Resources and Ecology of Western Arid Region, Ministry of Education, College of Grassland Science, Xinjiang Agricultural University, Urumqi 833400, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Yafang Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China.
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Assem SK, Basry MA, Taha TA, El-Aziz MHA, Alwa T, Fouad WM. Development of an in vitro regeneration system from immature inflorescences and CRISPR/Cas9-mediated gene editing in sudangrass. J Genet Eng Biotechnol 2023; 21:58. [PMID: 37184575 DOI: 10.1186/s43141-023-00517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/06/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND Sudangrass (Sorghum sudanense) is a major biomass producer for livestock feed and biofuel in many countries. It has a wide range of adaptations for growing on marginal lands under biotic and abiotic stresses. The immature inflorescence is an explant with high embryogenic competence and is frequently used to regenerate different sorghum cultivars. Caffeic acid O-methyl transferase (COMT) is a key enzyme in the lignin biosynthesis pathway, which limits ruminant digestion of forage cell walls and is a crucial barrier in the conversion of plant biomass to bioethanol. Genome editing by CRISPR/Cas9-mediated mutagenesis without a transgenic footprint will accelerate the improvement and facilitate regulatory approval and commercialization of biotech crops. METHODS AND RESULTS We report the overcome of the recalcitrance in sudangrass transformation and regeneration in order to use genome editing technique. Hence, an efficient regeneration system has been established to induce somatic embryogenesis from the immature inflorescence of two sudangrass cultivars on four MS-based media supplemented with different components. Our results indicate an interaction between genotype and medium composition. The combination of Giza-1 cultivar and M4 medium produces the maximum frequency of embryogenic calli of 80% and subsequent regeneration efficiency of 22.6%. Precise mutagenesis of the COMT gene is executed using the CRISPR/Cas9 system with the potential to reduce lignin content and enhance forage and biomass quality in sudangrass. CONCLUSION A reliable regeneration and transformation system has been established for sudangrass using immature inflorescence, and the CRISPR/Cas9 system has demonstrated a promising technology for genome editing. The outcomes of this research will pave the road for further improvement of various sorghum genotypes to meet the global demand for food, feed, and biofuels, achieving sustainable development goals (SDGs).
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Affiliation(s)
- Shireen K Assem
- Department of Plant Molecular Biology, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt.
| | - Mahmoud A Basry
- Department of Plant Molecular Biology, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Taha A Taha
- Department of Plant Molecular Biology, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - M H Abd El-Aziz
- Genetics Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Taher Alwa
- Department of Plant Molecular Biology, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Walid M Fouad
- Department of Biology, School of Science and Engineering, American University in Cairo, New Cairo, 11835, Cairo, Egypt
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Marinov O, Nomberg G, Sarkar S, Arya GC, Karavani E, Zelinger E, Manasherova E, Cohen H. Microscopic and metabolic investigations disclose the factors that lead to skin cracking in chili-type pepper fruit varieties. HORTICULTURE RESEARCH 2023; 10:uhad036. [PMID: 37799628 PMCID: PMC10548408 DOI: 10.1093/hr/uhad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 02/20/2023] [Indexed: 10/07/2023]
Abstract
The hydrophobic cuticle encasing the fruit skin surface plays critical roles during fruit development and post-harvest. Skin failure often results in the fruit surface cracking and forming a wound-periderm tissue made of suberin and lignin. The factors that make the fruit skin susceptible to cracking have yet to be fully understood. Herein, we investigated two varieties of chili peppers (Capsicum annuum L.), Numex Garnet, whose fruit has intact skin, and Vezena Slatka, whose fruit has cracked skin. Microscopical observations, gas chromatography-mass spectrometry, biochemical and gene expression assays revealed that Vezena Slatka fruit form a thicker cuticle with greater levels of cutin monomers and hydroxycinnamic acids, and highly express key cutin-related genes. The skin of these fruit also had a lower epidermal cell density due to cells with very large perimeters, and highly express genes involved in epidermal cell differentiation. We demonstrate that skin cracking in the Vezena Slatka fruit is accompanied by a spatial accumulation of lignin-like polyphenolic compounds, without the formation of a typical wound-periderm tissues made of suberized cells. Lastly, we establish that skin cracking in chili-type pepper significantly affects fruit quality during post-harvest storage in a temperature-dependent manner. In conclusion, our data highlight cuticle thickness and epidermal cell density as two critical factors determining fruit skin susceptibility to cracking in chili-type pepper fruit.
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Affiliation(s)
- Ofir Marinov
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Gal Nomberg
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Sutanni Sarkar
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Gulab Chand Arya
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
| | - Eldad Karavani
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
| | - Einat Zelinger
- Center for Scientific Imaging (CSI), The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ekaterina Manasherova
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
| | - Hagai Cohen
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
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Mierziak J, Wojtasik W, Kulma A, Żuk M, Grajzer M, Boba A, Dymińska L, Hanuza J, Szperlik J, Szopa J. Overexpression of Bacterial Beta-Ketothiolase Improves Flax (Linum usitatissimum L.) Retting and Changes the Fibre Properties. Metabolites 2023; 13:metabo13030437. [PMID: 36984877 PMCID: PMC10052753 DOI: 10.3390/metabo13030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Beta-ketothiolases are involved in the beta-oxidation of fatty acids and the metabolism of hormones, benzenoids, and hydroxybutyrate. The expression of bacterial beta-ketothiolase in flax (Linum usitatissimum L.) results in an increase in endogenous beta-ketothiolase mRNA levels and beta-hydroxybutyrate content. In the present work, the effect of overexpression of beta-ketothiolase on retting and stem and fibre composition of flax plants is presented. The content of the components was evaluated by high-performance liquid chromatography, gas chromatography–mass spectrometry, Fourier-transform infrared spectroscopy, and biochemical methods. Changes in the stem cell walls, especially in the lower lignin and pectin content, resulted in more efficient retting. The overexpression of beta-ketothiolase reduced the fatty acid and carotenoid contents in flax and affected the distribution of phenolic compounds between free and cell wall-bound components. The obtained fibres were characterized by a slightly lower content of phenolic compounds and changes in the composition of the cell wall. Based on the IR analysis, we concluded that the production of hydroxybutyrate reduced the cellulose crystallinity and led to the formation of shorter but more flexible cellulose chains, while not changing the content of the cell wall components. We speculate that the changes in chemical composition of the stems and fibres are the result of the regulatory properties of hydroxybutyrate. This provides us with a novel way to influence metabolic composition in agriculturally important crops.
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Affiliation(s)
- Justyna Mierziak
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
| | - Wioleta Wojtasik
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
- Correspondence:
| | - Anna Kulma
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
| | - Magdalena Żuk
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
| | - Magdalena Grajzer
- Department of Dietetics and Bromatology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Aleksandra Boba
- Department of Genetics, Plant Breeding and Seed Science, Wroclaw University of Environmental and Life Sciences, Grunwaldzki Sq. 24A, 50-363 Wroclaw, Poland
| | - Lucyna Dymińska
- Department of Bioorganic Chemistry, Wroclaw University of Economics and Business, Komandorska 118/120, 53-345 Wroclaw, Poland
| | - Jerzy Hanuza
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, 50-422 Wroclaw, Poland
| | - Jakub Szperlik
- Laboratory of Tissue Culture, Botanical Garden, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 23, 50-525 Wroclaw, Poland
| | - Jan Szopa
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
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Transcriptome analysis identifies differentially expressed genes involved in lignin biosynthesis in barley. Int J Biol Macromol 2023; 236:123940. [PMID: 36894063 DOI: 10.1016/j.ijbiomac.2023.123940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/18/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Lignin is an essential metabolite for plant growth but negatively affects the quality of forage barley. Genetic modification of quality traits to improve the forage digestibility requires an understanding of the molecular mechanism of lignin biosynthesis. RNA-Seq was used to quantify transcripts differentially expressed among leaf, stem and spike tissues from two barley genotypes. A total of 13,172 differentially expressed genes (DEGs) were identified, of which much more up-regulated DEGs were detected from the contrasting groups of leaf vs spike (L-S) and stem vs spike (S-S), and down-regulated DEGs were dominant in the group of stem vs leaf (S-L). 47 DEGs were successfully annotated to the monolignol pathway and six of them were candidate genes regulating the lignin biosynthesis. The qRT-PCR assay verified the expression profiles of the six candidate genes. Among them, four genes might positively regulate the lignin biosynthesis during forage barley development in terms of the consistency of their expression levels and changes of lignin content among the tissues, while the other two genes may have the reverse effects. These findings provide target genes for further investigations on molecular regulatory mechanisms of lignin biosynthesis and genetic resources for improvement of forage quality in barley molecular breeding programme.
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Choi SJ, Lee Z, Kim S, Jeong E, Shim JS. Modulation of lignin biosynthesis for drought tolerance in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1116426. [PMID: 37152118 PMCID: PMC10157170 DOI: 10.3389/fpls.2023.1116426] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/06/2023] [Indexed: 05/09/2023]
Abstract
Lignin is a complex polymer that is embedded in plant cell walls to provide physical support and water protection. For these reasons, the production of lignin is closely linked with plant adaptation to terrestrial regions. In response to developmental cues and external environmental conditions, plants use an elaborate regulatory network to determine the timing and location of lignin biosynthesis. In this review, we summarize the canonical lignin biosynthetic pathway and transcriptional regulatory network of lignin biosynthesis, consisting of NAC and MYB transcription factors, to explain how plants regulate lignin deposition under drought stress. Moreover, we discuss how the transcriptional network can be applied to the development of drought tolerant plants.
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10
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Song JL, Wang ZY, Wang YH, Du J, Wang CY, Zhang XQ, Chen S, Huang XL, Xie XM, Zhong TX. Overexpression of Pennisetum purpureum CCoAOMT Contributes to Lignin Deposition and Drought Tolerance by Promoting the Accumulation of Flavonoids in Transgenic Tobacco. FRONTIERS IN PLANT SCIENCE 2022; 13:884456. [PMID: 35620690 PMCID: PMC9129916 DOI: 10.3389/fpls.2022.884456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Elephant grass (Pennisetum purpureum) is a fast-growing and low-nutrient demand plant that is widely used as a forage grass and potential energy crop in tropical and subtropical regions of Asia, Africa, and the United States. Transgenic tobacco with the PpCCoAOMT gene from Pennisetum purpureum produces high lignin content that is associated with drought tolerance in relation to lower accumulation of reactive oxygen species (ROS), along with higher antioxidant enzyme activities and osmotic adjustment. In this study, transgenic tobacco plants revealed no obvious cost to plant growth when expressing the PpCCoAOMT gene. Metabolomic studies demonstrated that tobacco plants tolerant to drought stress accumulated flavonoids under normal and drought conditions, which likely explains the observed tolerance phenotype in wild-type tobacco. Our results suggest that plants overexpressing PpCCoAOMT were better able to cope with water deficit than were wild-type controls; metabolic flux was redirected within primary and specialized metabolism to induce metabolites related to defense to drought stress. These results could help to develop drought-resistant plants for agriculture in the future.
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Affiliation(s)
- Jian-Ling Song
- Office of Academic Research, Xingyi Normal University for Nationalities, Xingyi, China
| | - Ze-Yu Wang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Yin-Hua Wang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Juan Du
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, United States
| | - Chen-Yu Wang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xiang-Qian Zhang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Shu Chen
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Xiao-Ling Huang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xin-Ming Xie
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Tian-Xiu Zhong
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
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11
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Shrestha V, Chhetri HB, Kainer D, Xu Y, Hamilton L, Piasecki C, Wolfe B, Wang X, Saha M, Jacobson D, Millwood RJ, Mazarei M, Stewart CN. The Genetic Architecture of Nitrogen Use Efficiency in Switchgrass ( Panicum virgatum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:893610. [PMID: 35586220 PMCID: PMC9108870 DOI: 10.3389/fpls.2022.893610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Switchgrass (Panicum virgatum L.) has immense potential as a bioenergy crop with the aim of producing biofuel as an end goal. Nitrogen (N)-related sustainability traits, such as nitrogen use efficiency (NUE) and nitrogen remobilization efficiency (NRE), are important factors affecting switchgrass quality and productivity. Hence, it is imperative to develop nitrogen use-efficient switchgrass accessions by exploring the genetic basis of NUE in switchgrass. For that, we used 331 diverse field-grown switchgrass accessions planted under low and moderate N fertility treatments. We performed a genome wide association study (GWAS) in a holistic manner where we not only considered NUE as a single trait but also used its related phenotypic traits, such as total dry biomass at low N and moderate N, and nitrogen use index, such as NRE. We have evaluated the phenotypic characterization of the NUE and the related traits, highlighted their relationship using correlation analysis, and identified the top ten nitrogen use-efficient switchgrass accessions. Our GWAS analysis identified 19 unique single nucleotide polymorphisms (SNPs) and 32 candidate genes. Two promising GWAS candidate genes, caffeoyl-CoA O-methyltransferase (CCoAOMT) and alfin-like 6 (AL6), were further supported by linkage disequilibrium (LD) analysis. Finally, we discussed the potential role of nitrogen in modulating the expression of these two genes. Our findings have opened avenues for the development of improved nitrogen use-efficient switchgrass lines.
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Affiliation(s)
- Vivek Shrestha
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hari B. Chhetri
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David Kainer
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Yaping Xu
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Lance Hamilton
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Ben Wolfe
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xueyan Wang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Malay Saha
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Daniel Jacobson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Reginald J. Millwood
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Mitra Mazarei
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - C. Neal Stewart
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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12
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Capelari ÉF, Dos Anjos L, Rodrigues NF, Sousa RMDJ, Silvera JAG, Margis R. Transcriptional profiling and physiological responses reveal new insights into drought tolerance in a semiarid adapted species, Anacardium occidentale. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:1074-1085. [PMID: 34418258 DOI: 10.1111/plb.13312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/05/2021] [Indexed: 06/13/2023]
Abstract
Water stress affects plant performance at various organisational levels, from morphological to molecular, with a drastic drop in crop yield. Integrative studies involving transcriptomics and physiological data in recognized tolerant species are appropriate strategies to identify and understand molecular and functional processes related to water deficit tolerance. The cashew tree (Anacardium occidentale) is a species naturally adapted to environments with low water availability associated with adverse conditions such as heat, high radiation and salinity. We used an integrative strategy, combining classical physiological measurements with high throughput RNA-seq to understand the main adaptive mechanisms of cashew to water deficit followed by recovery. Physiological analyses indicate that young cashew plants display typical isohydric behaviour. They first exhibit rapid stomatal closure, followed by CO2 assimilation, thus preserving the relative water content, membrane integrity and photosystem II activity. Differential expression was observed in 1733 genes from plant leaves exposed to water deficit stress for 26 days. Among them, 705 were upregulated and 1028 were downregulated. After rewatering, 1330 (76.7%) genes returned to their basal expression level. Transcriptional, combined with physiological data, reveal that cashew plants display high phenotypic plasticity and resilience to acute water deficit, and do not activate senescence pathways. A series of genes/pathways and processes involved with drought tolerance in cashew are evidenced, particularly in carbon metabolism, photosynthesis and chloroplast homeostasis.
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Affiliation(s)
- É F Capelari
- Programa de Pós Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - L Dos Anjos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CEP, Brazil
| | - N F Rodrigues
- Programa de Pós Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - R M de J Sousa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CEP, Brazil
| | - J A G Silvera
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CEP, Brazil
| | - R Margis
- Programa de Pós Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas (LGPP), Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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13
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Liu D, Wu J, Lin L, Li P, Li S, Wang Y, Li J, Sun Q, Liang J, Wang Y. Overexpression of Cinnamoyl-CoA Reductase 2 in Brassica napus Increases Resistance to Sclerotinia sclerotiorum by Affecting Lignin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:732733. [PMID: 34630482 PMCID: PMC8494948 DOI: 10.3389/fpls.2021.732733] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/27/2021] [Indexed: 05/23/2023]
Abstract
Sclerotinia sclerotiorum causes severe yield and economic losses for many crop and vegetable species, especially Brassica napus. To date, no immune B. napus germplasm has been identified, giving rise to a major challenge in the breeding of Sclerotinia resistance. In the present study, we found that, compared with a Sclerotinia-susceptible line (J902), a Sclerotinia-resistant line (J964) exhibited better xylem development and a higher lignin content in the stems, which may limit the invasion and spread of S. sclerotiorum during the early infection period. In addition, genes involved in lignin biosynthesis were induced under S. sclerotiorum infection in both lines, indicating that lignin was deposited proactively in infected tissues. We then overexpressed BnaC.CCR2.b, which encodes the first rate-limiting enzyme (cinnamoyl-CoA reductase) that catalyzes the reaction of lignin-specific pathways, and found that overexpression of BnaC.CCR2.b increased the lignin content in the stems of B. napus by 2.28-2.76% under normal growth conditions. We further evaluated the Sclerotinia resistance of BnaC.CCR2.b overexpression lines at the flower-termination stage and found that the disease lesions on the stems of plants in the T2 and T3 generations decreased by 12.2-33.7% and 32.5-37.3% compared to non-transgenic control plants, respectively, at 7days post-inoculation (dpi). The above results indicate that overexpression of BnaC.CCR2.b leads to an increase in lignin content in the stems, which subsequently leads to increased resistance to S. sclerotiorum. Our findings demonstrate that increasing the lignin content in the stems of B. napus is an important strategy for controlling Sclerotinia.
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Affiliation(s)
- Dongxiao Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Jian Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Li Lin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Panpan Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Saifen Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yue Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Jian Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Qinfu Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Jiansheng Liang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
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14
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Li T, Mann R, Kaur J, Spangenberg G, Sawbridge T. Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant-Bacteria Interactions. PLANTS 2021; 10:plants10091802. [PMID: 34579335 PMCID: PMC8467301 DOI: 10.3390/plants10091802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022]
Abstract
Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant–bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two Paenibacillus sp. strains and one Erwinia gerundensis strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant–bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants.
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Affiliation(s)
- Tongda Li
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (R.M.); (J.K.); (G.S.); (T.S.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
- Correspondence: ; Tel.: +61-3-9032-7088
| | - Ross Mann
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (R.M.); (J.K.); (G.S.); (T.S.)
| | - Jatinder Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (R.M.); (J.K.); (G.S.); (T.S.)
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (R.M.); (J.K.); (G.S.); (T.S.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Timothy Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (R.M.); (J.K.); (G.S.); (T.S.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
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15
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Wang Q, Jin Q, Ma Y, Zhang S, Zhang L, Liu Z, Zhang Y. Iron toxicity-induced regulation of key secondary metabolic processes associated with the quality and resistance of Panax ginseng and Panax quinquefolius. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112648. [PMID: 34450425 DOI: 10.1016/j.ecoenv.2021.112648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/07/2021] [Accepted: 08/11/2021] [Indexed: 05/27/2023]
Abstract
Panax ginseng and Panax quinquefolius can survive for long periods of time in iron toxicity-stressed environments, which cause rusty roots and reduced productivity. To reveal the proteomic changes in these two Panax species in response to iron toxicity stress, plants of these two species were divided into a control group and an iron toxicity-stress group. An isobaric tags for relative and absolute quantitation (iTRAQ) proteomics approach was used to explore the changes in protein accumulation and the potential mechanisms underlying the response to iron toxicity stress in the two Panax species. Proteomic analyses revealed approximately 725 differentially expressed proteins (DEPs) in the iron toxicity-stress and control groups, including 233 and 492 proteins whose expression was upregulated and downregulated, respectively. The expression of DEPs related to photosynthesis was significantly downregulated, and DEPs whose expression was significantly upregulated were associated with redox reactions. Many upregulated DEPs were also involved in pathways such as those involving phenylpropanoid, flavonoid, isoflavone and ginsenoside synthesis. The abundance of some ginsenoside monomers (Rg1 and Rb3) also significantly increased in P. ginseng and P. quinquefolius. Moreover, P. quinquefolius contained 455 DEPs whose expression was higher than that in P. ginseng, including many proteins related to the regulation of ion homeostasis, indicating that P. quinquefolius is more resistant to iron toxicity stress than P. ginseng is.
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Affiliation(s)
- Qiuxia Wang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin 130112, China.
| | - Qiao Jin
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin 130112, China
| | - Yingying Ma
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin 130112, China
| | - Shuna Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin 130112, China
| | - Linlin Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin 130112, China
| | - Zhengbo Liu
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin 130112, China
| | - Yayu Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin 130112, China; College of Pharmacy and biological Engineering, Chengdu University, Chengdu 610106, China.
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16
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Genome Identification and Expression Profiles in Response to Nitrogen Treatment Analysis of the Class I CCoAOMT Gene Family in Populus. Biochem Genet 2021; 60:656-675. [PMID: 34410559 DOI: 10.1007/s10528-021-10112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
Lignin is essential for the characteristics and quality of timber. Nitrogen has significant effects on lignin contents in plants. Nitrogen has been found to affect wood quality in plantations and lignin content in plants. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is an important methyltransferase in lignin biosynthesis. However, the classification of woody plant CCoAOMT gene family members and the regulation mechanism of nitrogen are not clear. Bioinformatics methods were used to predict the members, classification, and transcriptional distribution of the CCoAOMT gene family in Populus trichocarpa. The results showed that there were five PtCCoAOMTs identified, and they could be divided into three sub-groups according to their structural and phylogenetic features. The results of tissue expression specificity analysis showed that: PtCCoAOMT1 was highly expressed in roots and internodes; PtCCoAOMT2 was highly expressed in roots, nodes, and internodes, PtCCoAOMT3 was highly expressed in stems; PtCCoAOMT4 was highly expressed in young leaves, and, PtCCoAOMT5 was highly expressed in roots. Different forms and concentrations of nitrogen had varying effects on the expression patterns of genes in different plant tissue types. The results of real-time PCR showed that the expression levels of PtCCoAOMT1 and PtCCoAOMT2 in stems increased significantly under different forms of nitrogen. PtCCoAOMT3 and PtCCoAOMT4 were induced by nitrate nitrogen in upper stems and lower leaves, respectively. PtCCoAOMT4 and PtCCoAOMT5 were induced by different concentrations of nitrate nitrogen in lower stems and roots, respectively. These results could provide valuable information for revealing the differences between functions and expression patterns of the various CCoAOMT gene family members under different forms and concentrations of exogenous nitrogen in poplar.
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17
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Yao T, Feng K, Xie M, Barros J, Tschaplinski TJ, Tuskan GA, Muchero W, Chen JG. Phylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:704697. [PMID: 34484267 PMCID: PMC8416159 DOI: 10.3389/fpls.2021.704697] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/19/2021] [Indexed: 05/19/2023]
Abstract
The phenylpropanoid pathway serves as a rich source of metabolites in plants and provides precursors for lignin biosynthesis. Lignin first appeared in tracheophytes and has been hypothesized to have played pivotal roles in land plant colonization. In this review, we summarize recent progress in defining the lignin biosynthetic pathway in lycophytes, monilophytes, gymnosperms, and angiosperms. In particular, we review the key structural genes involved in p-hydroxyphenyl-, guaiacyl-, and syringyl-lignin biosynthesis across plant taxa and consider and integrate new insights on major transcription factors, such as NACs and MYBs. We also review insight regarding a new transcriptional regulator, 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, canonically identified as a key enzyme in the shikimate pathway. We use several case studies, including EPSP synthase, to illustrate the evolution processes of gene duplication and neo-functionalization in lignin biosynthesis. This review provides new insights into the genetic engineering of the lignin biosynthetic pathway to overcome biomass recalcitrance in bioenergy crops.
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Affiliation(s)
- Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Jaime Barros
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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18
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Hodgson-Kratky K, Perlo V, Furtado A, Choudhary H, Gladden JM, Simmons BA, Botha F, Henry RJ. Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin. PLANT MOLECULAR BIOLOGY 2021; 106:173-192. [PMID: 33738678 DOI: 10.1007/s11103-021-01136-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/02/2021] [Indexed: 05/11/2023]
Abstract
A transcriptome analysis reveals the transcripts and alleles differentially expressed in sugarcane genotypes with contrasting lignin composition. Sugarcane bagasse is a highly abundant resource that may be used as a feedstock for the production of biofuels and bioproducts in order to meet increasing demands for renewable replacements for fossil carbon. However, lignin imparts rigidity to the cell wall that impedes the efficient breakdown of the biomass into fermentable sugars. Altering the ratio of the lignin units, syringyl (S) and guaiacyl (G), which comprise the native lignin polymer in sugarcane, may facilitate the processing of bagasse. This study aimed to identify genes and markers associated with S/G ratio in order to accelerate the development of sugarcane bioenergy varieties with modified lignin composition. The transcriptome sequences of 12 sugarcane genotypes that contrasted for S/G ratio were compared and there were 2019 transcripts identified as differentially expressed (DE) between the high and low S/G ratio groups. These included transcripts encoding possible monolignol biosynthetic pathway enzymes, transporters, dirigent proteins and transcriptional and post-translational regulators. Furthermore, the frequencies of single nucleotide polymorphisms (SNPs) were compared between the low and high S/G ratio groups to identify specific alleles expressed with the phenotype. There were 2063 SNP loci across 787 unique transcripts that showed group-specific expression. Overall, the DE transcripts and SNP alleles identified in this study may be valuable for breeding sugarcane varieties with altered S/G ratio that may provide desirable bioenergy traits.
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Affiliation(s)
- K Hodgson-Kratky
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - V Perlo
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - A Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - H Choudhary
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | - J M Gladden
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | - B A Simmons
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - F Botha
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - R J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.
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19
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Transcriptomic Analysis of Seasonal Gene Expression and Regulation during Xylem Development in “Shanxin” Hybrid Poplar (Populus davidiana × Populus bolleana). FORESTS 2021. [DOI: 10.3390/f12040451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Xylem development is a key process for wood formation in woody plants. To study the molecular regulatory mechanisms related to xylem development in hybrid poplar P. davidiana × P. bolleana, transcriptome analyses were conducted on developing xylem at six different growth stages within a single growing season. Xylem development and differentially expressed genes in the six time points were selected for a regulatory analysis. Xylem development was observed in stem sections at different growth stages, which showed that xylem development extended from the middle of April to early August and included cell expansion and secondary cell wall biosynthesis. An RNA-seq analysis of six samples with three replicates was performed. After transcriptome assembly and annotation, the differentially expressed genes (DEGs) were identified, and a Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and expression analysis of the DEGs were performed on each sample. On average, we obtained >20 million clean reads per sample, which were assembled into 84,733 nonredundant transcripts, of which there were 17,603 unigenes with lengths >1 kb. There were 14,890 genes that were differentially expressed among the six stages. The upregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S1 vs. S2 or S3 vs. S4 and, in GO terms, related to phytohormones in the S1 vs. S2 or S4 vs. S5 comparisons. The downregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S4 vs. S5 or S5 vs. S6 and, in GO terms, related to hormones between S1 vs. S2 or S2 vs. S3. The KEGG pathways in the DEGs related to “phenylpropanoid biosynthesis”, “plant hormone signal transduction” and “starch and sucrose metabolism” were significantly enriched among the different stages. The DEGs related to cell expansion, polysaccharide metabolism and synthesis, lignin synthesis, transcription factors and hormones were identified. The identification of genes involved in the regulation of xylem development will increase our understanding of the molecular regulation of wood formation in trees and, also, offers potential targets for genetic manipulation to improve the properties of wood.
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20
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Wang J, Ma Z, Tang B, Yu H, Tang Z, Bu T, Wu Q, Chen H. Tartary Buckwheat ( Fagopyrum tataricum) NAC Transcription Factors FtNAC16 Negatively Regulates of Pod Cracking and Salinity Tolerant in Arabidopsis. Int J Mol Sci 2021; 22:ijms22063197. [PMID: 33801146 PMCID: PMC8061773 DOI: 10.3390/ijms22063197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 11/27/2022] Open
Abstract
The thick and hard fruit shell of Fagopyrum tataricum (F. tataricum) represents a processing bottleneck. At the same time, soil salinization is one of the main problems faced by modern agricultural production. Bioinformatic analysis indicated that the F. tataricum transcription factor FtNAC16 could regulate the hull cracking of F. tataricum, and the function of this transcription factor was verified by genetic transformation of Arabidopsis thaliana (A. thaliana). Phenotypic observations of the wild-type (WT), OE-FtNAC16, nst1/3 and nst1/3-FtNAC16 plant lines confirmed that FtNAC16 negatively regulated pod cracking by downregulating lignin synthesis. Under salt stress, several physiological indicators (POD, GSH, Pro and MDA) were measured, A. thaliana leaves were stained with NBT (Nitroblue Tetrazolium) and DAB (3,3’-diaminobenzidine), and all genes encoding enzymes in the lignin synthesis pathway were analyzed. These experiments confirmed that FtNAC16 increased plant sensitivity by reducing the lignin content or changing the proportions of the lignin monomer. The results of this study may help to elucidate the possible association between changes in lignin monomer synthesis and salt stress and may also contribute to fully understanding the effects of FtNAC16 on plant growth and development, particularly regarding fruit pod cracking and environmental adaptability. In future studies, it may be useful to obtain suitable cracking varieties and salt-tolerant crops through molecular breeding.
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Affiliation(s)
| | | | | | | | | | | | | | - Hui Chen
- Correspondence: ; Tel.: +86-18981604486
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21
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Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane. Funct Integr Genomics 2021; 21:73-99. [PMID: 33404914 DOI: 10.1007/s10142-020-00762-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 10/22/2022]
Abstract
Lignin is the main component of secondary cell walls and is essential for plant development and defense. However, lignin is recognized as a major recalcitrant factor for efficiency of industrial biomass processing. Genes involved in general phenylpropanoid and monolignol-specific metabolism in sugarcane have been previously analyzed at the transcriptomic level. Nevertheless, the number of genes identified in this species is still very low. The recently released sugarcane genome sequence has allowed the genome-wide characterization of the 11 gene families involved in the monolignol biosynthesis branch of the phenylpropanoid pathway. After an exhaustive analysis of sugarcane genomes, 438 haplotypes derived from 175 candidate genes from Saccharum spontaneum and 144 from Saccharum hybrid R570 were identified as associated with this biosynthetic route. The phylogenetic analyses, combined with the search for protein conserved residues involved in the catalytic activity of the encoded enzymes, were employed to identify the family members potentially involved in developmental lignification. Accordingly, 15 candidates were identified as bona fide lignin biosynthesis genes: PTAL1, PAL2, C4H4, 4CL1, HCT1, HCT2, C3'H1, C3'H2, CCoAOMT1, COMT1, F5H1, CCR1, CCR2, CAD2, and CAD7. For this core set of lignin biosynthetic genes, we searched for the chromosomal location, the gene expression pattern, the promoter cis-acting elements, and microRNA targets. Altogether, our results present a comprehensive characterization of sugarcane general phenylpropanoid and monolignol-specific genes, providing the basis for further functional studies focusing on lignin biosynthesis manipulation and biotechnological strategies to improve sugarcane biomass utilization.
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22
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Hegde N, Joshi S, Soni N, Kushalappa AC. The caffeoyl-CoA O-methyltransferase gene SNP replacement in Russet Burbank potato variety enhances late blight resistance through cell wall reinforcement. PLANT CELL REPORTS 2021; 40:237-254. [PMID: 33141312 DOI: 10.1007/s00299-020-02629-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/15/2020] [Indexed: 05/28/2023]
Abstract
Metabolic pathway gene editing in tetraploid potato enhanced resistance to late blight. Multiallelic mutation correction of a caffeoyl-CoA O-methyltransferase gene increased accumulation of resistance metabolites in Russet Burbank potato. Late blight of potato is a devastating disease worldwide and requires weekly applications of fungicides to manage. Genetic improvement is the best option, but the self-incompatibility and inter-specific incompatibility makes potato breeding very challenging. Immune receptor gene stacking has increased resistance, but its durability is limited. Quantitative resistance is durable, and it mainly involves secondary cell wall thickening due to several metabolites and their conjugates. Deleterious mutations in biosynthetic genes can hinder resistance metabolite biosynthesis. Here a probable resistance role of the StCCoAOMT gene was first confirmed by an in-planta transient overexpression of the functional StCCoAOMT allele in late blight susceptible Russet Burbank (RB) genotype. Following this, a precise single nucleotide polymorphism (SNP) mutation correction of the StCCoAOMT gene in RB potato was carried out using CRISPR-Cas9 mediated homology directed repair (HDR). The StCCoAOMT gene editing increased the transcript abundance of downstream biosynthetic resistance genes. Following pathogen inoculation, several phenylpropanoid pathway genes were highly expressed in the edited RB plants, as compared to the non-edited. The disease severity (fold change = 3.76) and pathogen biomass in inoculated stems of gene-edited RB significantly reduced (FC = 21.14), relative to non-edited control. The metabolic profiling revealed a significant increase in the accumulation of resistance-related metabolites in StCCoAOMT edited RB plants. Most of these metabolites are involved in suberization and lignification. The StCCoAOMT gene, if mutated, can be edited in other potato cultivars to enhance resistance to late blight, provided it is associated with other functional genes in the metabolic pathway network.
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Affiliation(s)
- Niranjan Hegde
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, QC, H9X3V9, Canada
| | - Sripad Joshi
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, QC, H9X3V9, Canada
| | - Nancy Soni
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, QC, H9X3V9, Canada
| | - Ajjamada C Kushalappa
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, QC, H9X3V9, Canada.
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23
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Fu Y, Zhu Y, Yang W, Xu W, Li Q, Chen M, Yang L. Isolation and functional identification of a Botrytis cinerea-responsive caffeoyl-CoA O-methyltransferase gene from Lilium regale wilson. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:379-389. [PMID: 33197727 DOI: 10.1016/j.plaphy.2020.10.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/27/2020] [Indexed: 05/28/2023]
Abstract
In plants, genes involved in the Phenylpropanoid/monolignol pathway play important roles in lignin biosynthesis and plant immunity. However, their biological function in Lilium remains poorly characterized. Comparative RNA sequencing of the expression profiles of the monolignol pathway genes from fungi-resistant species Lilium regale after inoculation with Botrytis cinerea was performed. One upregulated caffeoyl-CoA O-methyltransferase gene, LrCCoAOMT, was cloned for functional characterization by reverse genetic methods. LrCCoAOMT encodes a putative protein of 246 amino acids and is highly expressed in stem tissues and responsive to salicylic acid (SA) signaling and B. cinerea infection. LrCCoAOMT was largely directed to the cytoplasm. LrCCoAOMT overexpression in Arabidopsis resulted in an increased lignin deposition in vascular tissues and conferred resistance to B. cinerea infection in transgenic plants. Transient transformation of LrCCoAOMT in nonresistant Lilium sargentiae leaves also identified the defense function to B. cinerea. In addition, transcript levels of genes involved in the monolignol and SA-dependent signaling pathways were altered in transgenic Arabidopsis, suggesting that LrCCoAOMT might play vital roles in the resistance of L. regale to B. cinerea related to the levels of lignin and the regulation of SA signaling. This is the first report to functionally characterize a CCoAOMT gene in Lilium, a potential molecular target for lily molecular improvement.
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Affiliation(s)
- Yongyao Fu
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China
| | - Yiyong Zhu
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China
| | - Wei Yang
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China
| | - WenJi Xu
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China
| | - Qiang Li
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Mei Chen
- Clinical Laboratory, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, 610500, PR China.
| | - Liping Yang
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China.
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24
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Shi R, Panthee DR. Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot ( Xanthomonas perforans) Race T4. Int J Mol Sci 2020; 21:E4070. [PMID: 32517212 PMCID: PMC7313073 DOI: 10.3390/ijms21114070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/27/2020] [Accepted: 06/01/2020] [Indexed: 11/17/2022] Open
Abstract
Bacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato and is caused by multiple species of Xanthomonas. We performed the RNA sequencing (RNA-Seq) analysis of three tomato lines with different levels of resistance to Xanthomonas perforans race T4 to study the differentially expressed genes (DEGs) and transcript-based sequence variations. Analysis between inoculated and control samples revealed that resistant genotype Solanum pimpinellifolium accession PI 270443 had more DEGs (834), followed by susceptible genotype tomato (S. lycopersicum L) breeding line NC 714 (373), and intermediate genotype tomato breeding line NC 1CELBR (154). Gene ontology (GO) terms revealed that more GO terms (51) were enriched for upregulated DEGs in the resistant genotype PI 270443, and more downregulated DEGs (67) were enriched in the susceptible genotype NC 714. DEGs in the biotic stress pathway showed more upregulated biotic stress pathway DEGs (67) for PI 270443 compared to more downregulated DEGs (125) for the susceptible NC 714 genotype. Resistant genotype PI 270443 has three upregulated DEGs for pathogenesis-related (PR) proteins, and susceptible genotype NC 714 has one downregulated R gene. Sequence variations called from RNA-Seq reads against the reference genome of susceptible Heinz 1706 showed that chr11, which has multiple reported resistance quantitative trait loci (QTLs) to BS race T4, is identical between two resistant lines, PI 270443 and NC 1CELBR, suggesting that these two lines share the same resistance QTLs on this chromosome. Several loci for PR resistance proteins with sequence variation between the resistant and susceptible tomato lines were near the known Rx4 resistance gene on chr11, and additional biotic stress associated DEGs near to the known Rx4 resistance gene were also identified from the susceptible NC 714 line.
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Affiliation(s)
- Rui Shi
- Department of Horticultural Science, Mountain Horticultural Crops Research & Extension Center, North Carolina State University, Mills River, NC 28759, USA;
- Department of Crop and Soil Science, North Carolina State University, Raleigh, NC 27695-7620, USA
| | - Dilip R. Panthee
- Department of Horticultural Science, Mountain Horticultural Crops Research & Extension Center, North Carolina State University, Mills River, NC 28759, USA;
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25
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Parizotto AV, Ferro AP, Marchiosi R, Moreira-Vilar FC, Bevilaqua JM, Dos Santos WD, Seixas FAV, Ferrarese-Filho O. Entacapone improves saccharification without affecting lignin and maize growth: An in silico, in vitro, and in vivo approach. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:421-428. [PMID: 32289635 DOI: 10.1016/j.plaphy.2020.03.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/06/2020] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Caffeate 3-O-methyltransferase (COMT) catalyzes the methylation of the 3-hydroxyl group of caffeate to produce ferulate, an important precursor of the lignin biosynthesis. As a crucial drawback for biofuel production, lignin limits the enzymatic hydrolysis of polysaccharides to result in fermentable sugars. We hypothesized that a controlled inhibition of maize COMT can be an efficient approach to reduce ferulate and lignin, thus improving the saccharification process. First, we applied in silico techniques to prospect potential inhibitors of ZmaysCOMT, and the nitrocatechol entacapone was selected. Second, in vitro assays confirmed the inhibitory effect of entacapone on maize COMT. Finally, in vivo experiments revealed that entacapone reduced the contents of cell-wall-esterified hydroxycinnamates and increased saccharification of stems (18%) and leaves (70%), without negatively affecting maize growth and lignin biosynthesis. This non-genetically modified approach can be an alternative strategy to facilitate the enzymatic hydrolysis of biomass polysaccharides and increase saccharification for bioethanol production.
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Affiliation(s)
| | - Ana Paula Ferro
- Laboratory of Plant Biochemistry, Department of Biochemistry, University of Maringá, 87020-900, PR, Brazil
| | - Rogério Marchiosi
- Laboratory of Plant Biochemistry, Department of Biochemistry, University of Maringá, 87020-900, PR, Brazil
| | | | - Jennifer Munik Bevilaqua
- Laboratory of Plant Biochemistry, Department of Biochemistry, University of Maringá, 87020-900, PR, Brazil
| | | | - Flávio Augusto Vicente Seixas
- Laboratory of Structural Biochemistry, Department of Technology, University of Maringá, Umuarama, 87506-370, PR, Brazil
| | - Osvaldo Ferrarese-Filho
- Laboratory of Plant Biochemistry, Department of Biochemistry, University of Maringá, 87020-900, PR, Brazil.
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26
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Jardim-Messeder D, da Franca Silva T, Fonseca JP, Junior JN, Barzilai L, Felix-Cordeiro T, Pereira JC, Rodrigues-Ferreira C, Bastos I, da Silva TC, de Abreu Waldow V, Cassol D, Pereira W, Flausino B, Carniel A, Faria J, Moraes T, Cruz FP, Loh R, Van Montagu M, Loureiro ME, de Souza SR, Mangeon A, Sachetto-Martins G. Identification of genes from the general phenylpropanoid and monolignol-specific metabolism in two sugarcane lignin-contrasting genotypes. Mol Genet Genomics 2020; 295:717-739. [PMID: 32124034 DOI: 10.1007/s00438-020-01653-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/12/2020] [Indexed: 11/29/2022]
Abstract
The phenylpropanoid pathway is an important route of secondary metabolism involved in the synthesis of different phenolic compounds such as phenylpropenes, anthocyanins, stilbenoids, flavonoids, and monolignols. The flux toward monolignol biosynthesis through the phenylpropanoid pathway is controlled by specific genes from at least ten families. Lignin polymer is one of the major components of the plant cell wall and is mainly responsible for recalcitrance to saccharification in ethanol production from lignocellulosic biomass. Here, we identified and characterized sugarcane candidate genes from the general phenylpropanoid and monolignol-specific metabolism through a search of the sugarcane EST databases, phylogenetic analysis, a search for conserved amino acid residues important for enzymatic function, and analysis of expression patterns during culm development in two lignin-contrasting genotypes. Of these genes, 15 were cloned and, when available, their loci were identified using the recently released sugarcane genomes from Saccharum hybrid R570 and Saccharum spontaneum cultivars. Our analysis points out that ShPAL1, ShPAL2, ShC4H4, Sh4CL1, ShHCT1, ShC3H1, ShC3H2, ShCCoAOMT1, ShCOMT1, ShF5H1, ShCCR1, ShCAD2, and ShCAD7 are strong candidates to be bona fide lignin biosynthesis genes. Together, the results provide information about the candidate genes involved in monolignol biosynthesis in sugarcane and may provide useful information for further molecular genetic studies in sugarcane.
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Affiliation(s)
- Douglas Jardim-Messeder
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tatiane da Franca Silva
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, São Paulo, Brazil
| | - Jose Pedro Fonseca
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Nicomedes Junior
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Centro de Pesquisa e Desenvolvimento Leopoldo Américo Miguez de Mello, Gerência de Biotecnologia, CENPES, Petrobras, Rio de Janeiro, Brazil
| | - Lucia Barzilai
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thais Felix-Cordeiro
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joyce Carvalho Pereira
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clara Rodrigues-Ferreira
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabela Bastos
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tereza Cristina da Silva
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vinicius de Abreu Waldow
- Centro de Pesquisa e Desenvolvimento Leopoldo Américo Miguez de Mello, Gerência de Biotecnologia, CENPES, Petrobras, Rio de Janeiro, Brazil
| | - Daniela Cassol
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Willian Pereira
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Bruno Flausino
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adriano Carniel
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Centro de Pesquisa e Desenvolvimento Leopoldo Américo Miguez de Mello, Gerência de Biotecnologia, CENPES, Petrobras, Rio de Janeiro, Brazil
| | - Jessica Faria
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thamirys Moraes
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda P Cruz
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Roberta Loh
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marc Van Montagu
- Institute of Plant Biotechnology Outreach, Gent University, Technologiepark 3, Zwijnaarde, 9052, Gent, Belgium
| | - Marcelo Ehlers Loureiro
- Laboratório de Fisiologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Sonia Regina de Souza
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Amanda Mangeon
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Gilberto Sachetto-Martins
- Laboratório de Genômica Funcional e Transdução de Sinal, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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27
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Gomez-Cano L, Gomez-Cano F, Dillon FM, Alers-Velazquez R, Doseff AI, Grotewold E, Gray J. Discovery of modules involved in the biosynthesis and regulation of maize phenolic compounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110364. [PMID: 31928683 DOI: 10.1016/j.plantsci.2019.110364] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/25/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Phenolic compounds are among the most diverse and widespread of specialized plant compounds and underly many important agronomic traits. Our comprehensive analysis of the maize genome unraveled new aspects of the genes involved in phenylpropanoid, monolignol, and flavonoid production in this important crop. Remarkably, just 19 genes accounted for 70 % of the overall mRNA accumulation of these genes across 95 tissues, indicating that these are the main contributors to the flux of phenolic metabolites. Eighty genes with intermediate to low expression play minor and more specialized roles. Remaining genes are likely undergoing loss of function or are expressed in limited cell types. Phylogenetic and expression analyses revealed which members of gene families governing metabolic entry and branch points exhibit duplication, subfunctionalization, or loss of function. Co-expression analysis applied to genes in sequential biosynthetic steps revealed that certain isoforms are highly co-expressed and are candidates for metabolic complexes that ensure metabolite delivery to correct cellular compartments. Co-expression of biosynthesis genes with transcription factors discovered connections that provided candidate components for regulatory modules governing this pathway. Our study provides a comprehensive analysis of maize phenylpropanoid related genes, identifies major pathway contributors, and novel candidate enzymatic and regulatory modules of the metabolic network.
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Affiliation(s)
- Lina Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Francisco M Dillon
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Andrea I Doseff
- Department of Physiology, Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH, 43606, USA.
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28
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Wan Y, Zhang M, Hong A, Lan X, Yang H, Liu Y. Transcriptome and weighted correlation network analyses provide insights into inflorescence stem straightness in Paeonia lactiflora. PLANT MOLECULAR BIOLOGY 2020; 102:239-252. [PMID: 31832900 DOI: 10.1007/s11103-019-00945-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Lack of structural components results in inflorescence stem bending. Differentially expressed genes involved in lignin and hemicellulose biosynthesis are vital; genes involved in cellulose and glycan biosynthesis are also relevant. An erect inflorescence stem is essential for high-quality cut herbaceous peony flowers. To explore the factors underlying inflorescence stem bending, major cell walls contents were measured, and stem structure was observed in two herbaceous peony varieties with contrasting stem straightness traits ('Da Fugui', upright; 'Chui Touhong', bending). In addition, Illumina sequencing was performed and weighted correlation network analysis (WGCNA) was used to analyze the results. The results showed significant differences in lignin, hemicellulose and soluble sugar contents, sclerenchyma and xylem areas and thickening in cell walls in pith at stage S3, when bending begins. In addition, 44,182 significantly differentially expressed genes (DEGs) were found, and these DEGs were mainly enriched in 36 pathways. Among the DEGs, hub genes involved in lignin, cellulose, and xylan biosynthesis and transcription factors that regulated these process were identified by WGCNA. These results suggested that the contents of compounds that provided cell wall rigidity were vital factors affecting inflorescence stem straightness in herbaceous peony. Genes involved in or regulating the biosynthesis of these compounds are thus important; lignin and hemicellulose are of great interest, and cellulose and glycan should not be ignored. This paper lays a foundation for developing new herbaceous peony varieties suitable for cut flowers by molecular-assisted breeding.
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Affiliation(s)
- Yingling Wan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Min Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Aiying Hong
- Management Office of Caozhou Peony Garden, Heze, 274000, Shandong, People's Republic of China
| | - Xinyu Lan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Huiyan Yang
- Management Office of Caozhou Peony Garden, Heze, 274000, Shandong, People's Republic of China
| | - Yan Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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29
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Low Lignin Mutants and Reduction of Lignin Content in Grasses for Increased Utilisation of Lignocellulose. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9050256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biomass rich in lignocellulose from grasses is a major source for biofuel production and animal feed. However, the presence of lignin in cell walls limits its efficient utilisation such as in its bioconversion to biofuel. Reduction of the lignin content or alteration of its structure in crop plants have been pursued, either by regulating genes encoding enzymes in the lignin biosynthetic pathway using biotechnological techniques or by breeding naturally-occurring low lignin mutant lines. The aim of this review is to provide a summary of these studies, focusing on lignin (monolignol) biosynthesis and composition in grasses and, where possible, the impact on recalcitrance to bioconversion. An overview of transgenic crops of the grass family with regulated gene expression in lignin biosynthesis is presented, including the effect on lignin content and changes in the ratio of p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) units. Furthermore, a survey is provided of low-lignin mutants in grasses, including cereals in particular, summarising their origin and phenotypic traits together with genetics and the molecular function of the various genes identified.
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30
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Xie H, Engle NL, Venketachalam S, Yoo CG, Barros J, Lecoultre M, Howard N, Li G, Sun L, Srivastava AC, Pattathil S, Pu Y, Hahn MG, Ragauskas AJ, Nelson RS, Dixon RA, Tschaplinski TJ, Blancaflor EB, Tang Y. Combining loss of function of FOLYLPOLYGLUTAMATE SYNTHETASE1 and CAFFEOYL- COA 3- O- METHYLTRANSFERASE1 for lignin reduction and improved saccharification efficiency in Arabidopsis thaliana. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:108. [PMID: 31073332 PMCID: PMC6498598 DOI: 10.1186/s13068-019-1446-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/20/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Downregulation of genes involved in lignin biosynthesis and related biochemical pathways has been used as a strategy to improve biofuel production. Plant C1 metabolism provides the methyl units used for the methylation reactions carried out by two methyltransferases in the lignin biosynthetic pathway: caffeic acid 3-O-methyltransferase (COMT) and caffeoyl-CoA 3-O-methyltransferase (CCoAOMT). Mutations in these genes resulted in lower lignin levels and altered lignin compositions. Reduced lignin levels can also be achieved by mutations in the C1 pathway gene, folylpolyglutamate synthetase1 (FPGS1), in both monocotyledons and dicotyledons, indicating a link between the C1 and lignin biosynthetic pathways. To test if lignin content can be further reduced by combining genetic mutations in C1 metabolism and the lignin biosynthetic pathway, fpgs1ccoaomt1 double mutants were generated and functionally characterized. RESULTS Double fpgs1ccoaomt1 mutants had lower thioacidolysis lignin monomer yield and acetyl bromide lignin content than the ccoaomt1 or fpgs1 mutants and the plants themselves displayed no obvious long-term negative growth phenotypes. Moreover, extracts from the double mutants had dramatically improved enzymatic polysaccharide hydrolysis efficiencies than the single mutants: 15.1% and 20.7% higher than ccoaomt1 and fpgs1, respectively. The reduced lignin and improved sugar release of fpgs1ccoaomt1 was coupled with changes in cell-wall composition, metabolite profiles, and changes in expression of genes involved in cell-wall and lignin biosynthesis. CONCLUSION Our observations demonstrate that additional reduction in lignin content and improved sugar release can be achieved by simultaneous downregulation of a gene in the C1 (FPGS1) and lignin biosynthetic (CCOAOMT) pathways. These improvements in sugar accessibility were achieved without introducing unwanted long-term plant growth and developmental defects.
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Affiliation(s)
- Hongli Xie
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Sivasankari Venketachalam
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Jaime Barros
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Mitch Lecoultre
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Nikki Howard
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Guifen Li
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Liang Sun
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Avinash C. Srivastava
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Michael G. Hahn
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Richard S. Nelson
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- The Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Elison B. Blancaflor
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Yuhong Tang
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
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31
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Lignin engineering to improve saccharification and digestibility in grasses. Curr Opin Biotechnol 2019; 56:223-229. [DOI: 10.1016/j.copbio.2019.02.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 11/19/2022]
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Wu X, Yan Z, Dong X, Cao F, Peng J, Li M. Cloning and characterization of a CCoAOMT gene involved in rapid lignification of endocarp in dove tree (Davidia involucrata Baill.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2018.1525324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Xiaobo Wu
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
| | - Ziwei Yan
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
| | - Xujie Dong
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
| | - Fuxiang Cao
- Department of Horticulture, College of Horticulture and Landscape, Hunan Agricultural University, Changsha, PR China
| | - Jiqing Peng
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
| | - Meng Li
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
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Wang Z, Zhao Z, Fan G, Dong Y, Deng M, Xu E, Zhai X, Cao H. A comparison of the transcriptomes between diploid and autotetraploid Paulownia fortunei under salt stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:1-11. [PMID: 30804626 PMCID: PMC6352521 DOI: 10.1007/s12298-018-0578-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/08/2018] [Accepted: 06/29/2018] [Indexed: 05/06/2023]
Abstract
Paulownia is a tree species grown in many countries. Our previous study reveals that tetraploid Paulownia fortunei is more tolerant to salt stress than its corresponding diploid tree. To investigate the molecular mechanisms of salt stress tolerance in P. fortunei, the transcriptomes of normal and salt-stressed diploid and tetraploid were investigated. After assembling the clean reads, we obtained 130,842 unigenes. The unigenes were aligned against six public databases (Nr, Nt, Swiss-Prot, COG, KEGG, GO) to discover homologs and assign functional annotations. We retrieved 7983 and 15,503 differentially expressed unigenes (DEUs) between the normal and the salt-stressed diploid and tetraploid P. fortunei, respectively. We identified dozens of important DEUs including 3 related to photosynthesis, 10 related to plant growth and development and 11 related to osmolytes. Some of these DEUs were upregulated in tetraploid compared to diploid and others were upregulated under salt stress. Quantitative reverse transcriptase polymerase chain reaction verified the expression patterns of 15 unigenes. Our results provided insights into the molecular aspects why tetraploid is stronger and more energetic than diploid under saline environment. This study provides useful information for further studies on the molecular mechanisms of salt tolerance in other tree plants.
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Affiliation(s)
- Zhe Wang
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Yanpeng Dong
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Enkai Xu
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Xiaoqiao Zhai
- Henan Academy of Forestry, Zhengzhou, Henan People’s Republic of China
| | - Heping Cao
- Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, New Orleans, LA 70124 USA
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Tetreault HM, Scully ED, Gries T, Palmer NA, Funnell-Harris DL, Baird L, Seravalli J, Dien BS, Sarath G, Clemente TE, Sattler SE. Overexpression of the Sorghum bicolor SbCCoAOMT alters cell wall associated hydroxycinnamoyl groups. PLoS One 2018; 13:e0204153. [PMID: 30289910 PMCID: PMC6173380 DOI: 10.1371/journal.pone.0204153] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/04/2018] [Indexed: 11/25/2022] Open
Abstract
Sorghum (Sorghum bicolor) is a drought tolerant crop, which is being developed as a bioenergy feedstock. The monolignol biosynthesis pathway is a major focus for altering the abundance and composition of lignin. Caffeoyl coenzyme-A O-methyltransferase (CCoAOMT) is an S-adenosyl methionine (SAM)-dependent O-methyltransferase that methylates caffeoyl-CoA to generate feruloyl-CoA, an intermediate required for the biosynthesis of both G- and S-lignin. SbCCoAOMT was overexpressed to assess the impact of increasing the amount of this enzyme on biomass composition. SbCCoAOMT overexpression increased both soluble and cell wall-bound (esterified) ferulic and sinapic acids, however lignin concentration and its composition (S/G ratio) remained unaffected. This increased deposition of hydroxycinnamic acids in these lines led to an increase in total energy content of the stover. In stalk and leaf midribs, the increased histochemical staining and autofluorescence in the cell walls of the SbCCoAOMT overexpression lines also indicate increased phenolic deposition within cell walls, which is consistent with the chemical analyses of soluble and wall-bound hydroxycinnamic acids. The growth and development of overexpression lines were similar to wild-type plants. Likewise, RNA-seq and metabolite profiling showed that global gene expression and metabolite levels in overexpression lines were also relatively similar to wild-type plants. Our results demonstrate that SbCCoAOMT overexpression significantly altered cell wall composition through increases in cell wall associated hydroxycinnamic acids without altering lignin concentration or affecting plant growth and development.
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Affiliation(s)
- Hannah M. Tetreault
- Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United States of America
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Erin D. Scully
- Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United States of America
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Tammy Gries
- Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United States of America
| | - Nathan A. Palmer
- Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United States of America
| | - Deanna L. Funnell-Harris
- Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United States of America
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Lisa Baird
- Department of Biology, Shiley Center for Science and Technology, University of San Diego, San Diego, California, United States of America
| | - Javier Seravalli
- Redox Biology Center and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Bruce S. Dien
- National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, United States of America
| | - Gautam Sarath
- Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United States of America
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Thomas E. Clemente
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Scott E. Sattler
- Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United States of America
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
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35
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Rakoczy M, Femiak I, Alejska M, Figlerowicz M, Podkowinski J. Sorghum CCoAOMT and CCoAOMT-like gene evolution, structure, expression and the role of conserved amino acids in protein activity. Mol Genet Genomics 2018; 293:1077-1089. [PMID: 29721721 PMCID: PMC6153501 DOI: 10.1007/s00438-018-1441-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/24/2018] [Indexed: 11/28/2022]
Abstract
Sorghum is a crop plant that is grown for seeds, sucrose, forage and biofuel production. In all these applications, lignin is a superfluous component that decreases the efficiency of technological processes. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is an enzyme involved in monolignol synthesis that affects the efficiency of lignification and lignin composition. The sorghum genome harbors one CCoAOMT gene and six closely related CCoAOMT-like genes. The structures of four sorghum CCoAOMT-like enzymes suggest that these proteins might methylate caffeoyl coenzyme A and contribute to monolignol synthesis. In this study, two sorghum genes, CCoAOMT and one CCoAOMT-like, were found to be highly expressed in leaves, stems and immature seeds. The promoters of these genes possess clusters of transcription factor-binding sites specific for lignification, and this suggests that they are important for lignification. Phylogenetic analysis revealed that one sorghum CCoAOMT-like enzyme is closely related to ancestral cyanobacterial CCoAOMT-like proteins. The remaining CCoAOMT-like enzymes, including the one highly expressed in the leaves and stem, are closely related to CCoAOMT. Genes from these two groups possess different, evolutionarily conserved gene structures. The structure of the sorghum CCoAOMT-like protein from the ancestral clade was modeled and differences between enzymes from the two clades were analyzed. These results facilitate a better understanding of the evolution of genes involved in lignification, and provide valuable data for sorghum improvement through traditional breeding or molecular genetic techniques. The findings suggest that CCoAOMT-like genes might be recruited in lignification and raise questions of the frequency of such functional shifts.
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Affiliation(s)
- M Rakoczy
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - I Femiak
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - M Alejska
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - M Figlerowicz
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - J Podkowinski
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland.
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36
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Faria-Blanc N, Mortimer JC, Dupree P. A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:384. [PMID: 29636762 PMCID: PMC5881139 DOI: 10.3389/fpls.2018.00384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/08/2018] [Indexed: 05/21/2023]
Abstract
Yeast have long been known to possess a cell wall integrity (CWI) system, and recently an analogous system has been described for the primary walls of plants (PCWI) that leads to changes in plant growth and cell wall composition. A similar system has been proposed to exist for secondary cell walls (SCWI). However, there is little data to support this. Here, we analyzed the stem transcriptome of a set of cell wall biosynthetic mutants in order to investigate whether cell wall damage, in this case caused by aberrant xylan synthesis, activates a signaling cascade or changes in cell wall synthesis gene expression. Our data revealed remarkably few changes to the transcriptome. We hypothesize that this is because cells undergoing secondary cell wall thickening have entered a committed programme leading to cell death, and therefore a SCWI system would have limited impact. The absence of transcriptomic responses to secondary cell wall alterations may facilitate engineering of the secondary cell wall of plants.
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Affiliation(s)
- Nuno Faria-Blanc
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jenny C. Mortimer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Paul Dupree
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37
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Chen L, Guo X, Cui Y, Zheng X, Yang H. Comparative Transcriptome Analysis Reveals Hormone Signaling Genes Involved in the Launch of Culm-Shape Differentiation in Dendrocalamus sinicus. Genes (Basel) 2017; 9:E4. [PMID: 29271945 PMCID: PMC5793157 DOI: 10.3390/genes9010004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/09/2017] [Accepted: 12/20/2017] [Indexed: 12/23/2022] Open
Abstract
Dendrocalamus sinicus is a sympodial bamboo species endemic to Yunnan Province, China, and is the strongest bamboo species in the world. However, there is substantial variation in the basal culm shape, i.e., straight culm (SC) and bent culm (BC), among different D. sinicus as a result of genetic and growth factors. This study performed a comparative transcriptomic analysis of bamboo shoots of two variants at the early, mid-, and late shoot-development stages to examine the molecular basis of this variation. In total, 98,479 unigenes were annotated, of which 13,495 were differentially expressed in pairwise comparisons of the six libraries. More differentially expressed genes (DEGs) were involved in SC than in BC culm development. The DEGs between BC and SC were assigned to 108 metabolic pathways. The 1064 DEGs in early development might mainly control the launch of culm-shape differentiation. Sixty genes encoding components of hormone signaling pathways were differentially expressed between BC5 and SC5, indicating complex hormonal regulation of culm differentiation. The AUX/IAA, ARF, PP2C, SnRK2, and ABF genes involved in auxin and abscisic acid signaling played key roles. These results help us to understand the molecular mechanism of culm variation and other aspects of culm development in D. sinicus.
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Affiliation(s)
- Lingna Chen
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Panlong, Kunming 650233, China.
| | - Xiaojuan Guo
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Panlong, Kunming 650233, China.
| | - Yongzhong Cui
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Panlong, Kunming 650233, China.
| | - Xianggan Zheng
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Panlong, Kunming 650233, China.
| | - Hanqi Yang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Panlong, Kunming 650233, China.
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38
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Eloy NB, Voorend W, Lan W, Saleme MDLS, Cesarino I, Vanholme R, Smith RA, Goeminne G, Pallidis A, Morreel K, Nicomedes J, Ralph J, Boerjan W. Silencing CHALCONE SYNTHASE in Maize Impedes the Incorporation of Tricin into Lignin and Increases Lignin Content. PLANT PHYSIOLOGY 2017; 173:998-1016. [PMID: 27940492 PMCID: PMC5291018 DOI: 10.1104/pp.16.01108] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/06/2016] [Indexed: 05/18/2023]
Abstract
Lignin is a phenolic heteropolymer that is deposited in secondary-thickened cell walls, where it provides mechanical strength. A recent structural characterization of cell walls from monocot species showed that the flavone tricin is part of the native lignin polymer, where it is hypothesized to initiate lignin chains. In this study, we investigated the consequences of altered tricin levels on lignin structure and cell wall recalcitrance by phenolic profiling, nuclear magnetic resonance, and saccharification assays of the naturally silenced maize (Zea mays) C2-Idf (inhibitor diffuse) mutant, defective in the CHALCONE SYNTHASE Colorless2 (C2) gene. We show that the C2-Idf mutant produces highly reduced levels of apigenin- and tricin-related flavonoids, resulting in a strongly reduced incorporation of tricin into the lignin polymer. Moreover, the lignin was enriched in β-β and β-5 units, lending support to the contention that tricin acts to initiate lignin chains and that, in the absence of tricin, more monolignol dimerization reactions occur. In addition, the C2-Idf mutation resulted in strikingly higher Klason lignin levels in the leaves. As a consequence, the leaves of C2-Idf mutants had significantly reduced saccharification efficiencies compared with those of control plants. These findings are instructive for lignin engineering strategies to improve biomass processing and biochemical production.
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Affiliation(s)
- Nubia B Eloy
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Wannes Voorend
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Wu Lan
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Marina de Lyra Soriano Saleme
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Igor Cesarino
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Ruben Vanholme
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Rebecca A Smith
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Geert Goeminne
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Andreas Pallidis
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Kris Morreel
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - José Nicomedes
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - John Ralph
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.)
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.)
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
| | - Wout Boerjan
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.);
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (N.B.E., W.V., M.d.L.S.S., I.C., R.V., G.G., A.P., K.M., J.N., W.B.);
- Department of Botany, Institute of Biosciences, University of São Paulo, Butantã, Sao Paulo SP 05508-090, Brazil (I.C.);
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726 (W.L., R.A.S., J.R.); and
- Department of Biological System Engineering (W.L., J.R.) and Department of Biochemistry (R.A.S., J.R.), University of Wisconsin, Madison, Wisconsin 53706
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Wu L, Zhang W, Ding Y, Zhang J, Cambula ED, Weng F, Liu Z, Ding C, Tang S, Chen L, Wang S, Li G. Shading Contributes to the Reduction of Stem Mechanical Strength by Decreasing Cell Wall Synthesis in Japonica Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:881. [PMID: 28611803 PMCID: PMC5447739 DOI: 10.3389/fpls.2017.00881] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/10/2017] [Indexed: 05/08/2023]
Abstract
Low solar radiation caused by industrial development and solar dimming has become a limitation in crop production in China. It is widely accepted that low solar radiation influences many aspects of plant development, including slender, weak stems and susceptibility to lodging. However, the underlying mechanisms are not well understood. To clarify how low solar radiation affects stem mechanical strength formation and lodging resistance, the japonica rice cultivars Wuyunjing23 (lodging-resistant) and W3668 (lodging-susceptible) were grown under field conditions with normal light (Control) and shading (the incident light was reduced by 60%) with a black nylon net. The yield and yield components, plant morphological characteristics, the stem mechanical strength, cell wall components, culm microstructure, gene expression correlated with cellulose and lignin biosynthesis were measured. The results showed that shading significantly reduced grain yield attributed to reduction of spikelets per panicles and grain weight. The stem-breaking strength decreased significantly under shading treatment; consequently, resulting in higher lodging index in rice plant in both varieties, as revealed by decreased by culm diameter, culm wall thickness and increased plant height, gravity center height. Compared with control, cell wall components including non-structural carbohydrate, sucrose, cellulose, and lignin reduced quite higher. With histochemical straining, shading largely reduced lignin deposition in the sclerenchyma cells and vascular bundle cells compared with control, and decreased cellulose deposition in the parenchyma cells of culm tissue in both Wuyunjing23 and W3668. And under shading condition, gene expression involved in secondary cell wall synthesis, OsPAL, OsCOMT, OsCCoAOMT, OsCCR, and OsCAD2, and primary cell wall synthesis, OsCesA1, OsCesA3, and OsCesA8 were decreased significantly. These results suggest that gene expression involved in the reduction of lignin and cellulose in both sclerenchyma and parenchyma cells, which attribute to lignin and cellulose in culm tissue and weak mechanical tissue, consequently, result in poor stem strength and higher lodging risks. Highlights: (1) Shading decreases the stem mechanical strength of japonica rice by decreasing non-structural carbohydrate, sucrose, lignin, and cellulose accumulation in culms. (2) The decrease of carbon source under shading condition is the cause for the lower lignin and cellulose accumulation in culm. (3) The expression of genes involved in lignin and primarily cell wall cellulose biosynthesis (OsCesA1, OsCesA3, and OsCesA8) at the stem formation stage are down-regulated under shading condition, inducing defective cell wall development and poor lodging resistance.
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Affiliation(s)
- Longmei Wu
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Wujun Zhang
- Chongqing Ratooning Rice Research Center, Chongqing Academy of Agricultural SciencesChongqing, China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Jianwei Zhang
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Elidio D. Cambula
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Fei Weng
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Zhenghui Liu
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Chengqiang Ding
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - She Tang
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Lin Chen
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Ganghua Li
- College of Agronomy, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Ganghua Li,
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Zhang X, Liu Y, Fang Z, Li Z, Yang L, Zhuang M, Zhang Y, Lv H. Comparative Transcriptome Analysis between Broccoli ( Brassica oleracea var. italica) and Wild Cabbage ( Brassica macrocarpa Guss.) in Response to Plasmodiophora brassicae during Different Infection Stages. FRONTIERS IN PLANT SCIENCE 2016; 7:1929. [PMID: 28066482 PMCID: PMC5179516 DOI: 10.3389/fpls.2016.01929] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/05/2016] [Indexed: 05/02/2023]
Abstract
Clubroot, one of the most devastating diseases to the Brassicaceae family, is caused by the obligate biotrophic pathogen Plasmodiophora brassicae. However, studies of the molecular basis of disease resistance are still poor especially in quantitative resistance. In the present paper, two previously identified genotypes, a clubroot-resistant genotype (wild cabbage, B2013) and a clubroot-susceptible genotype (broccoli, 90196) were inoculated by P. brassicae for 0 (T0), 7 (T7), and 14 (T14) day after inoculation (DAI). Gene expression pattern analysis suggested that response changes in transcript level of two genotypes under P. brassicae infection were mainly activated at the primary stage (T7). Based on the results of DEGs functional enrichments from two infection stages, genes associated with cell wall biosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction showed down-regulated at T14 compared to T7, indicating that defense responses to P. brassicae were induced earlier, and related pathways were repressed at T14. In addition, the genes related to NBS-LRR proteins, SA signal transduction, cell wall and phytoalexins biosynthesis, chitinase, Ca2+ signals and RBOH proteins were mainly up-regulated in B2013 by comparing those of 90196, indicating the pathways of response defense to clubroot were activated in the resistant genotype. This is the first report about comparative transcriptome analysis for broccoli and its wild relative during the different stages of P. brassicae infection and the results should be useful for molecular assisted screening and breeding of clubroot-resistant genotypes.
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Affiliation(s)
| | - Yumei Liu
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers – Chinese Academy of Agricultural SciencesBeijing, China
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41
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Zhang X, Liu Y, Fang Z, Li Z, Yang L, Zhuang M, Zhang Y, Lv H. Comparative Transcriptome Analysis between Broccoli ( Brassica oleracea var. italica) and Wild Cabbage ( Brassica macrocarpa Guss.) in Response to Plasmodiophora brassicae during Different Infection Stages. FRONTIERS IN PLANT SCIENCE 2016; 7:1929. [PMID: 28066482 DOI: 10.1007/s11104-019-04196-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/05/2016] [Indexed: 05/27/2023]
Abstract
Clubroot, one of the most devastating diseases to the Brassicaceae family, is caused by the obligate biotrophic pathogen Plasmodiophora brassicae. However, studies of the molecular basis of disease resistance are still poor especially in quantitative resistance. In the present paper, two previously identified genotypes, a clubroot-resistant genotype (wild cabbage, B2013) and a clubroot-susceptible genotype (broccoli, 90196) were inoculated by P. brassicae for 0 (T0), 7 (T7), and 14 (T14) day after inoculation (DAI). Gene expression pattern analysis suggested that response changes in transcript level of two genotypes under P. brassicae infection were mainly activated at the primary stage (T7). Based on the results of DEGs functional enrichments from two infection stages, genes associated with cell wall biosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction showed down-regulated at T14 compared to T7, indicating that defense responses to P. brassicae were induced earlier, and related pathways were repressed at T14. In addition, the genes related to NBS-LRR proteins, SA signal transduction, cell wall and phytoalexins biosynthesis, chitinase, Ca2+ signals and RBOH proteins were mainly up-regulated in B2013 by comparing those of 90196, indicating the pathways of response defense to clubroot were activated in the resistant genotype. This is the first report about comparative transcriptome analysis for broccoli and its wild relative during the different stages of P. brassicae infection and the results should be useful for molecular assisted screening and breeding of clubroot-resistant genotypes.
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Affiliation(s)
- Xiaoli Zhang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Yumei Liu
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Zhiyuan Fang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Zhansheng Li
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Limei Yang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Mu Zhuang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Yangyong Zhang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Honghao Lv
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
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Li M, Pu Y, Ragauskas AJ. Current Understanding of the Correlation of Lignin Structure with Biomass Recalcitrance. Front Chem 2016; 4:45. [PMID: 27917379 PMCID: PMC5114238 DOI: 10.3389/fchem.2016.00045] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/02/2016] [Indexed: 12/22/2022] Open
Abstract
Lignin, a complex aromatic polymer in terrestrial plants, contributes significantly to biomass recalcitrance to microbial and/or enzymatic deconstruction. To reduce biomass recalcitrance, substantial endeavors have been exerted on pretreatment and lignin engineering in the past few decades. Lignin removal and/or alteration of lignin structure have been shown to result in reduced biomass recalcitrance with improved cell wall digestibility. While high lignin content is usually a barrier to a cost-efficient application of bioresources to biofuels, the direct correlation of lignin structure and its concomitant properties with biomass remains unclear due to the complexity of cell wall and lignin structure. Advancement in application of biorefinery to production of biofuels, chemicals, and bio-derived materials necessitates a fundamental understanding of the relationship of lignin structure and biomass recalcitrance. In this mini-review, we focus on recent investigations on the influence of lignin chemical properties on bioprocessability-pretreatment and enzymatic hydrolysis of biomass. Specifically, lignin-enzyme interactions and the effects of lignin compositional units, hydroxycinnamates, and lignin functional groups on biomass recalcitrance have been highlighted, which will be useful not only in addressing biomass recalcitrance but also in deploying renewable lignocelluloses efficiently.
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Affiliation(s)
- Mi Li
- BioEnergy Science Center, Biosciences Division, Joint Institute of Biological Science, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Yunqiao Pu
- BioEnergy Science Center, Biosciences Division, Joint Institute of Biological Science, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Arthur J Ragauskas
- BioEnergy Science Center, Biosciences Division, Joint Institute of Biological Science, Oak Ridge National LaboratoryOak Ridge, TN, USA; Department of Chemical and Bimolecular Engineering, University of Tennessee KnoxvilleKnoxville, TN, USA; Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University Tennessee Institute of AgricultureKnoxville, TN, USA
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Function Analysis of Caffeoyl-CoA O-Methyltransferase for Biosynthesis of Lignin and Phenolic Acid in Salvia miltiorrhiza. Appl Biochem Biotechnol 2016; 181:562-572. [PMID: 27613617 DOI: 10.1007/s12010-016-2231-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/29/2016] [Indexed: 10/21/2022]
Abstract
In this study, we cloned a full-length cDNA and the genomic DNA sequence of SmCCoAOMT (GenBank ID JQ007585) from Salvia miltiorrhiza. The 744-bp open-reading frame encodes a protein of 247 amino acids that shares 95 % similarity with one in Vitis vinifera. Real-time quantitative PCR analysis revealed that SmCCoAOMT is most highly expressed in the stems and can be induced by methyl jasmonate (MeJA) and XC-1 treatment. To evaluate its function in vivo, we generated RNA interference transgenic plants through Agrobacterium tumefaciens-mediated gene transfer. Compared with untransformed control plants, the transgenics had significantly less lignin and the expression of lignin-biosynthetic genes SmCCR and SmCOMT was depressed. In 90-day-old roots from plants of transgenic line M5, accumulations of rosmarinic acid and salvianolic acid B (Sal B) were greatly reduced by 0.89- and 0.69-fold, respectively. This low-Sal B phenotype was stable in the roots, with the level of accumulation being approximately 43.58 mg g-1 dry weight, which was 52 % of the amount measured in the untransformed control. Our results suggest that SmCCoAOMT is involved in lignin biosynthesis and affects the accumulation of phenolic acids. This study also provides potential guidance for using lignin-related genes to genetically engineer Salvia miltiorrhiza.
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Chateigner-Boutin AL, Ordaz-Ortiz JJ, Alvarado C, Bouchet B, Durand S, Verhertbruggen Y, Barrière Y, Saulnier L. Developing Pericarp of Maize: A Model to Study Arabinoxylan Synthesis and Feruloylation. FRONTIERS IN PLANT SCIENCE 2016; 7:1476. [PMID: 27746801 PMCID: PMC5043055 DOI: 10.3389/fpls.2016.01476] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/16/2016] [Indexed: 05/19/2023]
Abstract
Cell walls are comprised of networks of entangled polymers that differ considerably between species, tissues and developmental stages. The cell walls of grasses, a family that encompasses major crops, contain specific polysaccharide structures such as xylans substituted with feruloylated arabinose residues. Ferulic acid is involved in the grass cell wall assembly by mediating linkages between xylan chains and between xylans and lignins. Ferulic acid contributes to the physical properties of cell walls, it is a hindrance to cell wall degradability (thus biomass conversion and silage digestibility) and may contribute to pest resistance. Many steps leading to the formation of grass xylans and their cross-linkages remain elusive. One explanation might originate from the fact that many studies were performed on lignified stem tissues. Pathways leading to lignins and feruloylated xylans share several steps, and lignin may impede the release and thus the quantification of ferulic acid. To overcome these difficulties, we used the pericarp of the maize B73 line as a model to study feruloylated xylan synthesis and crosslinking. Using Fourier-transform infra-red spectroscopy and biochemical analyses, we show that this tissue has a low lignin content and is composed of approximately 50% heteroxylans and approximately 5% ferulic acid. Our study shows that, to date, maize pericarp contains the highest level of ferulic acid reported in plant tissue. The detection of feruloylated xylans with a polyclonal antibody shows that the occurrence of these polysaccharides is developmentally regulated in maize grain. We used the genomic tools publicly available for the B73 line to study the expression of genes within families involved or suggested to be involved in the phenylpropanoid pathway, xylan formation, feruloylation and their oxidative crosslinking. Our analysis supports the hypothesis that the feruloylated moiety of xylans originated from feruloylCoA and is transferred by a member of the BAHD acyltransferase family. We propose candidate genes for functional characterization that could subsequently be targeted for grass crop breeding.
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Affiliation(s)
| | - José J. Ordaz-Ortiz
- BIA, INRANantes, France
- National Laboratory of Genomics for Biodiversity (Langebio-CINVESTAV), Mass Spectrometry and Metabolomics LabIrapuato, Mexico
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Bewg WP, Poovaiah C, Lan W, Ralph J, Coleman HD. RNAi downregulation of three key lignin genes in sugarcane improves glucose release without reduction in sugar production. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:270. [PMID: 28031745 PMCID: PMC5168864 DOI: 10.1186/s13068-016-0683-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/06/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Sugarcane is a subtropical crop that produces large amounts of biomass annually. It is a key agricultural crop in many countries for the production of sugar and other products. Residual bagasse following sucrose extraction is currently underutilized and it has potential as a carbohydrate source for the production of biofuels. As with all lignocellulosic crops, lignin acts as a barrier to accessing the polysaccharides, and as such, is the focus of transgenic efforts. In this study, we used RNAi to individually reduce the expression of three key genes in the lignin biosynthetic pathway in sugarcane. These genes, caffeoyl-CoA O-methyltransferase (CCoAOMT), ferulate 5-hydroxylase (F5H) and caffeic acid O-methyltransferase (COMT), impact lignin content and/or composition. RESULTS For each RNAi construct, we selected three events for further analysis based on qRT-PCR results. For the CCoAOMT lines, there were no lines with a reduction in lignin content and only one line showed improved glucose release. For F5H, no lines had reduced lignin, but one line had a significant increase in glucose release. For COMT, one line had reduced lignin content, and this line and another released higher levels of glucose during enzymatic hydrolysis. Two of the lines with improved glucose release (F5H-2 and COMT-2) also had reduced S:G ratios. CONCLUSIONS Along with improvements in bagasse quality for the production of lignocellulosic-based fuels, there was only one line with reduction in juice sucrose extraction, and three lines with significantly improved sucrose production, providing evidence that the alteration of sugarcane for improved lignocellulosic ethanol production can be achieved without negatively impacting sugar production and perhaps even enhancing it.
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Affiliation(s)
- William P Bewg
- Queensland University of Technology, Brisbane, QLD 4000 Australia
| | | | - Wu Lan
- Department of Biological Systems Engineering, University of Wisconsin, Madison, WI USA ; US Department of Energy, Great Lakes Bioenergy Research Center (GLBRC), Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726 USA
| | - John Ralph
- US Department of Energy, Great Lakes Bioenergy Research Center (GLBRC), Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726 USA ; Department of Biochemistry, University of Wisconsin, Madison, WI 53726 USA
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Kamei CLA, Severing EI, Dechesne A, Furrer H, Dolstra O, Trindade LM. Orphan Crops Browser: a bridge between model and orphan crops. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2016; 36:9. [PMID: 26798323 PMCID: PMC4710642 DOI: 10.1007/s11032-015-0430-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/23/2015] [Indexed: 05/20/2023]
Abstract
Many important crops have received little attention by the scientific community, either because they are not considered economically important or due to their large and complex genomes. De novo transcriptome assembly, using next-generation sequencing data, is an attractive option for the study of these orphan crops. In spite of the large amount of sequencing data that can be generated, there is currently a lack of tools which can effectively help molecular breeders and biologists to mine this type of information. Our goal was to develop a tool that enables molecular breeders, without extensive bioinformatics knowledge, to efficiently study de novo transcriptome data from any orphan crop (http://www.bioinformatics.nl/denovobrowser/db/species/index). The Orphan Crops Browser has been designed to facilitate the following tasks (1) search and identification of candidate transcripts based on phylogenetic relationships between orthologous sequence data from a set of related species and (2) design specific and degenerate primers for expression studies in the orphan crop of interest. To demonstrate the usability and reliability of the browser, it was used to identify the putative orthologues of 17 known lignin biosynthetic genes from maize and sugarcane in the orphan crop Miscanthus sinensis. Expression studies in miscanthus stem internode tissue differing in maturation were subsequently carried out, to follow the expression of these genes during lignification. Our results showed a negative correlation between lignin content and gene expression. The present data are in agreement with recent findings in maize and other crops, and it is further discussed in this paper.
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Affiliation(s)
- Claire Lessa Alvim Kamei
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- />Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Edouard I. Severing
- />Laboratory of Genetics, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- />Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Annemarie Dechesne
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Heleen Furrer
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Oene Dolstra
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Luisa M. Trindade
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Wan L, Li B, Pandey MK, Wu Y, Lei Y, Yan L, Dai X, Jiang H, Zhang J, Wei G, Varshney RK, Liao B. Transcriptome Analysis of a New Peanut Seed Coat Mutant for the Physiological Regulatory Mechanism Involved in Seed Coat Cracking and Pigmentation. FRONTIERS IN PLANT SCIENCE 2016; 7:1491. [PMID: 27790222 PMCID: PMC5063860 DOI: 10.3389/fpls.2016.01491] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/20/2016] [Indexed: 05/21/2023]
Abstract
Seed-coat cracking and undesirable color of seed coat highly affects external appearance and commercial value of peanuts (Arachis hypogaea L.). With an objective to find genetic solution to the above problems, a peanut mutant with cracking and brown colored seed coat (testa) was identified from an EMS treated mutant population and designated as "peanut seed coat crack and brown color mutant line (pscb)." The seed coat weight of the mutant was almost twice of the wild type, and the germination time was significantly shorter than wild type. Further, the mutant had lower level of lignin, anthocyanin, proanthocyanidin content, and highly increased level of melanin content as compared to wild type. Using RNA-Seq, we examined the seed coat transcriptome in three stages of seed development in the wild type and the pscb mutant. The RNA-Seq analysis revealed presence of highly differentially expressed phenylpropanoid and flavonoid pathway genes in all the three seed development stages, especially at 40 days after flowering (DAF40). Also, the expression of polyphenol oxidases and peroxidase were found to be activated significantly especially in the late seed developmental stage. The genome-wide comparative study of the expression profiles revealed 62 differentially expressed genes common across all the three stages. By analyzing the expression patterns and the sequences of the common differentially expressed genes of the three stages, three candidate genes namely c36498_g1 (CCoAOMT1), c40902_g2 (kinesin), and c33560_g1 (MYB3) were identified responsible for seed-coat cracking and brown color phenotype. Therefore, this study not only provided candidate genes but also provided greater insights and molecular genetic control of peanut seed-coat cracking and color variation. The information generated in this study will facilitate further identification of causal gene and diagnostic markers for breeding improved peanut varieties with smooth and desirable seed coat color.
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Affiliation(s)
- Liyun Wan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Bei Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Manish K. Pandey
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Yanshan Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Xiaofeng Dai
- Institute of Food Science and Technology of Chinese Academy of Agricultural SciencesBeijing, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Juncheng Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Guo Wei
- Institute of Food Science and Technology of Chinese Academy of Agricultural SciencesBeijing, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
- *Correspondence: Boshou Liao
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Dametto A, Sperotto RA, Adamski JM, Blasi ÉAR, Cargnelutti D, de Oliveira LFV, Ricachenevsky FK, Fregonezi JN, Mariath JEA, da Cruz RP, Margis R, Fett JP. Cold tolerance in rice germinating seeds revealed by deep RNAseq analysis of contrasting indica genotypes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:1-12. [PMID: 26259169 DOI: 10.1016/j.plantsci.2015.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 05/10/2023]
Abstract
Rice productivity is largely affected by low temperature, which can be harmful throughout plant development, from germination to grain filling. Germination of indica rice cultivars under cold is slow and not uniform, resulting in irregular emergence and small plant population. To identify and characterize novel genes involved in cold tolerance during the germination stage, two indica rice genotypes (sister lines previously identified as cold-tolerant and cold-sensitive) were used in parallel transcriptomic analysis (RNAseq) under cold treatment (seeds germinating at 13 °C for 7 days). We detected 1,361 differentially expressed transcripts. Differences in gene expression found by RNAseq were confirmed for 11 selected genes using RT-qPCR. Biological processes enhanced in the cold-tolerant seedlings include: cell division and expansion (confirmed by anatomical sections of germinating seeds), cell wall integrity and extensibility, water uptake and membrane transport capacity, sucrose synthesis, generation of simple sugars, unsaturation of membrane fatty acids, wax biosynthesis, antioxidant capacity (confirmed by histochemical staining of H2O2), and hormone and Ca(2+)-signaling. The cold-sensitive seedlings respond to low temperature stress increasing synthesis of HSPs and dehydrins, along with enhanced ubiquitin/proteasome protein degradation pathway and polyamine biosynthesis. Our findings can be useful in future biotechnological approaches aiming to cold tolerance in indica rice.
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Affiliation(s)
- Andressa Dametto
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro Universitário UNIVATES, Lajeado, RS, Brazil
| | - Raul A Sperotto
- Centro de Ciências Biológicas e da Saúde (CCBS), Centro Universitário UNIVATES, Lajeado, RS, Brazil; Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro Universitário UNIVATES, Lajeado, RS, Brazil.
| | - Janete M Adamski
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Édina A R Blasi
- Centro de Ciências Biológicas e da Saúde (CCBS), Centro Universitário UNIVATES, Lajeado, RS, Brazil
| | - Denise Cargnelutti
- Departamento de Agronomia, Universidade Federal da Fronteira Sul (UFFS), Erechim, RS, Brazil
| | - Luiz F V de Oliveira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Felipe K Ricachenevsky
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Jeferson N Fregonezi
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Jorge E A Mariath
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Renata P da Cruz
- Departamento de Plantas de Lavoura, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rogério Margis
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Janette P Fett
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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Shigeto J, Itoh Y, Hirao S, Ohira K, Fujita K, Tsutsumi Y. Simultaneously disrupting AtPrx2, AtPrx25 and AtPrx71 alters lignin content and structure in Arabidopsis stem. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:349-56. [PMID: 25644691 DOI: 10.1111/jipb.12334] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/20/2015] [Indexed: 05/23/2023]
Abstract
Plant class III heme peroxidases catalyze lignin polymerization. Previous reports have shown that at least three Arabidopsis thaliana peroxidases, AtPrx2, AtPrx25 and AtPrx71, are involved in stem lignification using T-DNA insertion mutants, atprx2, atprx25, and atprx71. Here, we generated three double mutants, atprx2/atprx25, atprx2/atprx71, and atprx25/atprx71, and investigated the impact of the simultaneous deficiency of these peroxidases on lignins and plant growth. Stem tissue analysis using the acetyl bromide method and derivatization followed by reductive cleavage revealed improved lignin characteristics, such as lowered lignin content and increased arylglycerol-β-aryl (β-O-4) linkage type, especially β-O-4 linked syringyl units, in lignin, supporting the roles of these genes in lignin polymerization. In addition, none of the double mutants exhibited severe growth defects, such as shorter plant stature, dwarfing, or sterility, and their stems had improved cell wall degradability. This study will contribute to progress in lignin bioengineering to improve lignocellulosic biomass.
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Affiliation(s)
- Jun Shigeto
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
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50
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Ricroch AE, Hénard-Damave MC. Next biotech plants: new traits, crops, developers and technologies for addressing global challenges. Crit Rev Biotechnol 2015; 36:675-90. [PMID: 25641327 DOI: 10.3109/07388551.2015.1004521] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Most of the genetically modified (GM) plants currently commercialized encompass a handful of crop species (soybean, corn, cotton and canola) with agronomic characters (traits) directed against some biotic stresses (pest resistance, herbicide tolerance or both) and created by multinational companies. The same crops with agronomic traits already on the market today will continue to be commercialized, but there will be also a wider range of species with combined traits. The timeframe anticipated for market release of the next biotech plants will not only depend on science progress in research and development (R&D) in laboratories and fields, but also primarily on how demanding regulatory requirements are in countries where marketing approvals are pending. Regulatory constraints, including environmental and health impact assessments, have increased significantly in the past decades, delaying approvals and increasing their costs. This has sometimes discouraged public research entities and small and medium size plant breeding companies from using biotechnology and given preference to other technologies, not as stringently regulated. Nevertheless, R&D programs are flourishing in developing countries, boosted by the necessity to meet the global challenges that are food security of a booming world population while mitigating climate change impacts. Biotechnology is an instrument at the service of these imperatives and a wide variety of plants are currently tested for their high yield despite biotic and abiotic stresses. Many plants with higher water or nitrogen use efficiency, tolerant to cold, salinity or water submergence are being developed. Food security is not only a question of quantity but also of quality of agricultural and food products, to be available and accessible for the ones who need it the most. Many biotech plants (especially staple food) are therefore being developed with nutritional traits, such as biofortification in vitamins and metals. The main international seed companies continue to be the largest investors in plant biotechnology R&D, and often collaborate in the developing world with public institutions, private entities and philanthropic organizations. These partnerships are particularly present in Africa. In developed countries, plant biotechnology is also used for non-food purposes, such as the pharmaceutical, biofuel, starch, paper and textile industries. For example, plants are modified to specifically produce molecules with therapeutic uses, or with an improved biomass conversion efficiency, or producing larger volumes of feedstocks for biofuels. Various plant breeding technologies are now used in the entire spectrum of plant biotechnology: transgenesis producing proteins or RNAi. Cisgenesis (transgenes isolated from a crossable donor plant) and intragenesis (transgenes originate from the same species or a crossable species), null segregants are also used. To date, the next generation precision gene editing tools are developed in basic research. They include: clustered regularly interspaced short palindromic repeats (CRISPR), oligonucleotide-directed mutagenesis (ODM), transcription activator-like effects nucleases (TALENs) and zinc-finger nuclease (ZFN).
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Affiliation(s)
- Agnès E Ricroch
- a Department of Life Sciences and Health , AgroParisTech , Génétique évolutive et amélioration des plantes , Paris Cedex , France and
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