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Meng G, Rasmussen SK, Christensen CSL, Fan W, Torp AM. Molecular breeding of barley for quality traits and resilience to climate change. Front Genet 2023; 13:1039996. [PMID: 36685930 PMCID: PMC9851277 DOI: 10.3389/fgene.2022.1039996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
Barley grains are a rich source of compounds, such as resistant starch, beta-glucans and anthocyanins, that can be explored in order to develop various products to support human health, while lignocellulose in straw can be optimised for feed in husbandry, bioconversion into bioethanol or as a starting material for new compounds. Existing natural variations of these compounds can be used to breed improved cultivars or integrated with a large number of mutant lines. The technical demands can be in opposition depending on barley's end use as feed or food or as a source of biofuel. For example beta-glucans are beneficial in human diets but can lead to issues in brewing and poultry feed. Barley breeders have taken action to integrate new technologies, such as induced mutations, transgenics, marker-assisted selection, genomic selection, site-directed mutagenesis and lastly machine learning, in order to improve quality traits. Although only a limited number of cultivars with new quality traits have so far reached the market, research has provided valuable knowledge and inspiration for future design and a combination of methodologies to achieve the desired traits. The changes in climate is expected to affect the quality of the harvested grain and it is already a challenge to mitigate the unpredictable seasonal and annual variations in temperature and precipitation under elevated [CO2] by breeding. This paper presents the mutants and encoded proteins, with a particular focus on anthocyanins and lignocellulose, that have been identified and characterised in detail and can provide inspiration for continued breeding to achieve desired grain and straw qualities.
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Affiliation(s)
- Geng Meng
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark,College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Søren K. Rasmussen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark,*Correspondence: Søren K. Rasmussen,
| | | | - Weiyao Fan
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Anna Maria Torp
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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4-Coumarate:coenzyme A ligase isoform 3 from Piper nigrum (Pn4CL3) catalyzes the CoA thioester formation of 3,4-methylenedioxycinnamic and piperic acids. Biochem J 2020; 477:61-74. [DOI: 10.1042/bcj20190527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022]
Abstract
Black pepper, dried green fruit of Piper nigrum L., is a household spice most popular in the world. Piperine, the pungency compound of black pepper, is proposed to partially arise from phenylpropanoid pathway. In the biosynthesis of piperine, 4-coumarate:CoA ligase (4CLs) must play a pivotal role in activating intermediate acids to corresponding CoA thioesters to serve as substrates. Based on transcriptome data, we isolated three P. nigrum 4CL isoforms (Pn4CL1, -2, and -3) from unripe peppercorn. These Pn4CLs were expressed in E. coli for in vitro enzyme assay with putative substrates, namely cinnamic, coumaric, ferulic, piperonylic, 3,4-methylenedioxycinnamic (3,4-MDCA), and piperic acids. Phylogenetic analysis and substrate usage study indicated that Pn4CL1, active towards coumaric and ferulic acids, belongs to class I 4CL for lignin synthesis. Pn4CL2 was a typical cinnamate-specific coumarate:CoA ligase-like (CLL) protein. The Pn4CL3, as class II enzyme, exhibited general 4CL activity towards coumaric and ferulic acids. However, Pn4CL3 was also active towards piperonylic acid, 3,4-MDCA, and piperic acid. Pn4CL3 possessed ∼2.6 times higher catalytic efficiency (kcat/KM) towards 3,4-MDCA and piperic acid than towards coumaric and ferulic acids, suggesting its specific role in piperine biosynthesis. Different substrate preference among the Pn4CL isoforms can be explained by 3-dimensional protein structure modeling, which demonstrated natural variants in amino acid residues of binding pocket to accommodate different substrates. Quantitative PCR analysis of these isoforms indicated that Pn4CL1 transcript level was highest in the roots whereas Pn4CL2 in the fruits and Pn4CL3 in the leaves.
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Chen X, Fang X, Zhang Y, Wang X, Zhang C, Yan X, Zhao Y, Wu J, Xu P, Zhang S. Overexpression of a soybean 4-coumaric acid: coenzyme A ligase (GmPI4L) enhances resistance to Phytophthora sojae in soybean. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:304-313. [PMID: 32172740 DOI: 10.1071/fp18111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/18/2018] [Indexed: 05/27/2023]
Abstract
Phytophthora root and stem rot of soybean (Glycine max (L.) Merr.) caused by Phytophthora sojae is a destructive disease worldwide. The enzyme 4-coumarate: CoA ligase (4CL) has been extensively studied with regard to plant responses to pathogens. However, the molecular mechanism of the response of soybean 4CL to P. sojae remains unclear. In a previous study, a highly upregulated 4CL homologue was characterised through suppressive subtractive hybridisation library and cDNA microarrays, in the resistant soybean cultivar 'Suinong 10' after infection with P. sojae race 1. Here, we isolated the full-length EST, and designated as GmPI4L (P. sojae-inducible 4CL gene) in this study, which is a novel member of the soybean 4CL gene family. GmPI4L has 34-43% over all amino acid sequence identity with other plant 4CLs. Overexpression of GmPI4L enhances resistance to P. sojae in transgenic soybean plants. The GmPI4L is located in the cell membrane when transiently expressed in Arabidopsis protoplasts. Further analyses showed that the contents of daidzein, genistein, and the relative content of glyceollins are significantly increased in overexpression GmPI4L soybeans. Taken together, these results suggested that GmPI4L plays an important role in response to P. sojae infection, possibly by enhancing the content of glyceollins, daidzein, and genistein in soybean.
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Affiliation(s)
- Xi Chen
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xin Fang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Youyi Zhang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xin Wang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Chuanzhong Zhang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiaofei Yan
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yuanling Zhao
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Junjiang Wu
- Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Soybean Cultivation of Ministry of Agriculture PR China, Harbin Heilongjiang, China
| | - Pengfei Xu
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Shuzhen Zhang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
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Daly P, McClellan C, Maluk M, Oakey H, Lapierre C, Waugh R, Stephens J, Marshall D, Barakate A, Tsuji Y, Goeminne G, Vanholme R, Boerjan W, Ralph J, Halpin C. RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:594-607. [PMID: 30133138 PMCID: PMC6381794 DOI: 10.1111/pbi.13001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 08/18/2018] [Indexed: 05/12/2023]
Abstract
Caffeic acid O-methyltransferase (COMT), the lignin biosynthesis gene modified in many brown-midrib high-digestibility mutants of maize and sorghum, was targeted for downregulation in the small grain temperate cereal, barley (Hordeum vulgare), to improve straw properties. Phylogenetic and expression analyses identified the barley COMT orthologue(s) expressed in stems, defining a larger gene family than in brachypodium or rice with three COMT genes expressed in lignifying tissues. RNAi significantly reduced stem COMT protein and enzyme activity, and modestly reduced stem lignin content while dramatically changing lignin structure. Lignin syringyl-to-guaiacyl ratio was reduced by ~50%, the 5-hydroxyguaiacyl (5-OH-G) unit incorporated into lignin at 10--15-fold higher levels than normal, and the amount of p-coumaric acid ester-linked to cell walls was reduced by ~50%. No brown-midrib phenotype was observed in any RNAi line despite significant COMT suppression and altered lignin. The novel COMT gene family structure in barley highlights the dynamic nature of grass genomes. Redundancy in barley COMTs may explain the absence of brown-midrib mutants in barley and wheat. The barley COMT RNAi lines nevertheless have the potential to be exploited for bioenergy applications and as animal feed.
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Affiliation(s)
- Paul Daly
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Present address:
Fungal PhysiologyWesterdijk Fungal Biodiversity Institute and Fungal Molecular PhysiologyUtrecht UniversityUtrechtThe Netherlands
| | - Christopher McClellan
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Marta Maluk
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Helena Oakey
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Faculty of SciencesSchool of Agriculture, Food and WineUniversity of AdelaideAdelaideAustralia
| | - Catherine Lapierre
- UMR1318 INRA‐AgroParistechIJPBUniversite Paris‐SaclayVersailles CedexFrance
| | - Robbie Waugh
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Cell and Molecular SciencesJames Hutton InstituteDundeeUK
| | | | - David Marshall
- Information and Computational SciencesJames Hutton InstituteDundeeUK
| | - Abdellah Barakate
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Yukiko Tsuji
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Energy's Great Lakes Bioenergy Research CenterThe Wisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Geert Goeminne
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Wout Boerjan
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - John Ralph
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Energy's Great Lakes Bioenergy Research CenterThe Wisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Claire Halpin
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
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Cheng X, Li M, Li D, Zhang J, Jin Q, Sheng L, Cai Y, Lin Y. Characterization and analysis of CCR and CAD gene families at the whole-genome level for lignin synthesis of stone cells in pear ( Pyrus bretschneideri) fruit. Biol Open 2017; 6:1602-1613. [PMID: 29141952 PMCID: PMC5703608 DOI: 10.1242/bio.026997] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/18/2017] [Indexed: 12/24/2022] Open
Abstract
The content of stone cells has significant effects on the flavour and quality of pear fruit. Previous research suggested that lignin deposition is closely related to stone cell formation. In the lignin biosynthetic pathway, cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD), dehydrogenase/reductase family members, catalyse the last two steps in monolignol synthesis. However, there is little knowledge of the characteristics of the CCR and CAD families in pear and their involvement in lignin synthesis of stone cells. In this study, 31 CCRs and 26 CADs were identified in the pear genome. Phylogenetic trees for CCRs and CADs were constructed; key amino acid residues were analysed, and three-dimensional structures were predicted. Using quantitative real-time polymerase chain reaction (qRT-PCR), PbCAD2, PbCCR1, -2 and -3 were identified as participating in lignin synthesis of stone cells in pear fruit. Subcellular localization analysis showed that the expressed proteins (PbCAD2, PbCCR1, -2 and -3) are found in the cytoplasm or at the cell membrane. These results reveal the evolutionary features of the CCR and CAD families in pear as well as the genes responsible for regulation of lignin synthesis and stone cell development in pear fruit.
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Affiliation(s)
- Xi Cheng
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Manli Li
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Dahui Li
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Jinyun Zhang
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
- Horticultural Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Qing Jin
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Lingling Sheng
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
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Le Roy J, Blervacq AS, Créach A, Huss B, Hawkins S, Neutelings G. Spatial regulation of monolignol biosynthesis and laccase genes control developmental and stress-related lignin in flax. BMC PLANT BIOLOGY 2017; 17:124. [PMID: 28705193 PMCID: PMC5513022 DOI: 10.1186/s12870-017-1072-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/02/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Bast fibres are characterized by very thick secondary cell walls containing high amounts of cellulose and low lignin contents in contrast to the heavily lignified cell walls typically found in the xylem tissues. To improve the quality of the fiber-based products in the future, a thorough understanding of the main cell wall polymer biosynthetic pathways is required. In this study we have carried out a characterization of the genes involved in lignin biosynthesis in flax along with some of their regulation mechanisms. RESULTS We have first identified the members of the phenylpropanoid gene families through a combination of in silico approaches. The more specific lignin genes were further characterized by high throughput transcriptomic approaches in different organs and physiological conditions and their cell/tissue expression was localized in the stems, roots and leaves. Laccases play an important role in the polymerization of monolignols. This multigenic family was determined and a miRNA was identified to play a role in the posttranscriptional regulation by cleaving the transcripts of some specific genes shown to be expressed in lignified tissues. In situ hybridization also showed that the miRNA precursor was expressed in the young xylem cells located near the vascular cambium. The results obtained in this work also allowed us to determine that most of the genes involved in lignin biosynthesis are included in a unique co-expression cluster and that MYB transcription factors are potentially good candidates for regulating these genes. CONCLUSIONS Target engineering of cell walls to improve plant product quality requires good knowledge of the genes responsible for the production of the main polymers. For bast fiber plants such as flax, it is important to target the correct genes from the beginning since the difficulty to produce transgenic material does not make possible to test a large number of genes. Our work determined which of these genes could be potentially modified and showed that it was possible to target different regulatory pathways to modify lignification.
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Affiliation(s)
- Julien Le Roy
- University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Anne-Sophie Blervacq
- University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Anne Créach
- University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Brigitte Huss
- University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Simon Hawkins
- University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Godfrey Neutelings
- University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
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Muthamilarasan M, Khan Y, Jaishankar J, Shweta S, Lata C, Prasad M. Integrative analysis and expression profiling of secondary cell wall genes in C4 biofuel model Setaria italica reveals targets for lignocellulose bioengineering. FRONTIERS IN PLANT SCIENCE 2015; 6:965. [PMID: 26583030 PMCID: PMC4631826 DOI: 10.3389/fpls.2015.00965] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/22/2015] [Indexed: 05/08/2023]
Abstract
Several underutilized grasses have excellent potential for use as bioenergy feedstock due to their lignocellulosic biomass. Genomic tools have enabled identification of lignocellulose biosynthesis genes in several sequenced plants. However, the non-availability of whole genome sequence of bioenergy grasses hinders the study on bioenergy genomics and their genomics-assisted crop improvement. Foxtail millet (Setaria italica L.; Si) is a model crop for studying systems biology of bioenergy grasses. In the present study, a systematic approach has been used for identification of gene families involved in cellulose (CesA/Csl), callose (Gsl) and monolignol biosynthesis (PAL, C4H, 4CL, HCT, C3H, CCoAOMT, F5H, COMT, CCR, CAD) and construction of physical map of foxtail millet. Sequence alignment and phylogenetic analysis of identified proteins showed that monolignol biosynthesis proteins were highly diverse, whereas CesA/Csl and Gsl proteins were homologous to rice and Arabidopsis. Comparative mapping of foxtail millet lignocellulose biosynthesis genes with other C4 panicoid genomes revealed maximum homology with switchgrass, followed by sorghum and maize. Expression profiling of candidate lignocellulose genes in response to different abiotic stresses and hormone treatments showed their differential expression pattern, with significant higher expression of SiGsl12, SiPAL2, SiHCT1, SiF5H2, and SiCAD6 genes. Further, due to the evolutionary conservation of grass genomes, the insights gained from the present study could be extrapolated for identifying genes involved in lignocellulose biosynthesis in other biofuel species for further characterization.
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Affiliation(s)
| | - Yusuf Khan
- National Institute of Plant Genome ResearchNew Delhi, India
| | | | - Shweta Shweta
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Charu Lata
- Division of Plant-Microbe Interactions, CSIR-National Botanical Research InstituteLucknow, India
| | - Manoj Prasad
- National Institute of Plant Genome ResearchNew Delhi, India
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