1
|
Pavlu S, Nikumbh S, Kovacik M, An T, Lenhard B, Simkova H, Navratilova P. Core promoterome of barley embryo. Comput Struct Biotechnol J 2024; 23:264-277. [PMID: 38173877 PMCID: PMC10762323 DOI: 10.1016/j.csbj.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024] Open
Abstract
Precise localization and dissection of gene promoters are key to understanding transcriptional gene regulation and to successful bioengineering applications. The core RNA polymerase II initiation machinery is highly conserved among eukaryotes, leading to a general expectation of equivalent underlying mechanisms. Still, less is known about promoters in the plant kingdom. In this study, we employed cap analysis of gene expression (CAGE) at three embryonic developmental stages in barley to accurately map, annotate, and quantify transcription initiation events. Unsupervised discovery of de novo sequence clusters grouped promoters based on characteristic initiator and position-specific core-promoter motifs. This grouping was complemented by the annotation of transcription factor binding site (TFBS) motifs. Integration with genome-wide epigenomic data sets and gene ontology (GO) enrichment analysis further delineated the chromatin environments and functional roles of genes associated with distinct promoter categories. The TATA-box presence governs all features explored, supporting the general model of two separate genomic regulatory environments. We describe the extent and implications of alternative transcription initiation events, including those that are specific to developmental stages, which can affect the protein sequence or the presence of regions that regulate translation. The generated promoterome dataset provides a valuable genomic resource for enhancing the functional annotation of the barley genome. It also offers insights into the transcriptional regulation of individual genes and presents opportunities for the informed manipulation of promoter architecture, with the aim of enhancing traits of agronomic importance.
Collapse
Affiliation(s)
- Simon Pavlu
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Sarvesh Nikumbh
- Merck Sharp & Dohme (UK) Limited, 120 Moorgate, London EC2M 6UR, UK
| | - Martin Kovacik
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Tadaichi An
- DNAFORM Precision Gene Technologies, 230–0046 Yokohama, Kanagawa, Japan
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Hana Simkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
| | - Pavla Navratilova
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
| |
Collapse
|
2
|
Campoli C, Eskan M, McAllister T, Liu L, Shoesmith J, Prescott A, Ramsay L, Waugh R, McKim SM. A GDSL-motif Esterase/Lipase Affects Wax and Cutin Deposition and Controls Hull-Caryopsis Attachment in Barley. PLANT & CELL PHYSIOLOGY 2024; 65:999-1013. [PMID: 38668634 PMCID: PMC11209556 DOI: 10.1093/pcp/pcae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/29/2024] [Accepted: 04/25/2024] [Indexed: 06/28/2024]
Abstract
The cuticle covering aerial organs of land plants is well known to protect against desiccation. Cuticles also play diverse and specialized functions, including organ separation, depending on plant and tissue. Barley shows a distinctive cuticular wax bloom enriched in β-diketones on leaf sheaths, stem nodes and internodes and inflorescences. Barley also develops a sticky surface on the outer pericarp layer of its grain fruit leading to strongly adhered hulls, 'covered grain', important for embryo protection and seed dispersal. While the transcription factor-encoding gene HvNUDUM (HvNUD) appears essential for adherent hulls, little is understood about how the pericarp cuticle changes during adhesion or whether changes in pericarp cuticles contribute to another phenotype where hulls partially shed, called 'skinning'. To that end, we screened barley lines for hull adhesion defects, focussing on the Eceriferum (= waxless, cer) mutants. Here, we show that the cer-xd allele causes defective wax blooms and compromised hull adhesion, and results from a mutation removing the last 10 amino acids of the GDS(L) [Gly, Asp, Ser, (Leu)]-motif esterase/lipase HvGDSL1. We used severe and moderate HvGDSL1 alleles to show that complete HvGDSL1 function is essential for leaf blade cuticular integrity, wax bloom deposition over inflorescences and leaf sheaths and pericarp cuticular ridge formation. Expression data suggest that HvGDSL1 may regulate hull adhesion independently of HvNUD. We found high conservation of HvGDSL1 among barley germplasm, so variation in HvGDSL1 unlikely leads to grain skinning in cultivated barley. Taken together, we reveal a single locus which controls adaptive cuticular properties across different organs in barley.
Collapse
Affiliation(s)
- Chiara Campoli
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Errol road, Invergowrie, Dundee DD25DA, UK
- Cell and Molecular Sciences, James Hutton Institute, Errol road, Invergowrie, Dundee DD25DA, UK
| | - Mhmoud Eskan
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Errol road, Invergowrie, Dundee DD25DA, UK
| | - Trisha McAllister
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Errol road, Invergowrie, Dundee DD25DA, UK
| | - Linsan Liu
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Errol road, Invergowrie, Dundee DD25DA, UK
| | - Jennifer Shoesmith
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Errol road, Invergowrie, Dundee DD25DA, UK
| | - Alan Prescott
- DIF and Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Nethergate, Dundee DD14HN, UK
| | - Luke Ramsay
- Cell and Molecular Sciences, James Hutton Institute, Errol road, Invergowrie, Dundee DD25DA, UK
| | - Robbie Waugh
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Errol road, Invergowrie, Dundee DD25DA, UK
- Cell and Molecular Sciences, James Hutton Institute, Errol road, Invergowrie, Dundee DD25DA, UK
| | - Sarah M McKim
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Errol road, Invergowrie, Dundee DD25DA, UK
| |
Collapse
|
3
|
O’Lone C, Juhász A, Nye-Wood M, Moody D, Dunn H, Ral JP, Colgrave ML. Advancing Sustainable Malting Practices: Aquaporins as Potential Breeding Targets for Improved Water Uptake during Controlled Germination of Barley ( Hordeum vulgare L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10149-10161. [PMID: 38635353 PMCID: PMC11066872 DOI: 10.1021/acs.jafc.4c00884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
The conversion of raw barley (Hordeum vulgare L.) to malt requires a process of controlled germination, where the grain is submerged in water to raise the moisture content to >40%. The transmembrane proteins, aquaporins, influence water uptake during the initial stage of controlled germination, yet little is known of their involvement in malting. With the current focus on sustainability, understanding the mechanisms of water uptake and usage during the initial stages of malting has become vital in improving efficient malting practices. In this study, we used quantitative proteomics analysis of two malting barley genotypes demonstrating differing water-uptake phenotypes in the initial stages of malting. Our study quantified 19 transmembrane proteins from nine families, including seven distinct aquaporin isoforms, including the plasma intrinsic proteins (PIPs) PIP1;1, PIP2;1, and PIP2;4 and the tonoplast intrinsic proteins (TIPs) TIP1;1, TIP2;3, TIP3;1, and TIP3;2. Our findings suggest that the presence of TIP1;1, TIP3;1, and TIP3;2 in the mature barley grain proteome is essential for facilitating water uptake, influencing cell turgor and the formation of large central lytic vacuoles aiding storage reserve hydrolysis and endosperm modification efficiency. This study proposes that TIP3s mediate water uptake in malting barley grain, offering potential breeding targets for improving sustainable malting practices.
Collapse
Affiliation(s)
- Clare
E. O’Lone
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
- Agriculture
and Food, Commonwealth Scientific and Industrial
Research Organization, Black
Mountain, Australian Capital Territory 2601, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
| | - Mitchell Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
| | - David Moody
- InterGrain
Pty Ltd, Bibra
Lake 6163, Western Australia, Australia
| | - Hugh Dunn
- Pilot
Malting Australia, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
| | - Jean-Philippe Ral
- Agriculture
and Food, Commonwealth Scientific and Industrial
Research Organization, Black
Mountain, Australian Capital Territory 2601, Australia
| | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
- Agriculture
and Food, Commonwealth Scientific and Industrial
Research Organization, St Lucia 4067, Queensland, Australia
| |
Collapse
|
4
|
Mir Drikvand R, Sohrabi SM, Sohrabi SS, Samiei K. Molecular Identification and Characterization of Hevein Antimicrobial Peptide Genes in Two-Row and Six-Row Cultivars of Barley (Hordeum vulgare L.). Biochem Genet 2024:10.1007/s10528-024-10695-8. [PMID: 38386212 DOI: 10.1007/s10528-024-10695-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/09/2024] [Indexed: 02/23/2024]
Abstract
Heveins are one of the most important groups of plant antimicrobial peptides. So far, various roles in plant growth and development and in response to biotic and abiotic stresses have reported for heveins. The present study aimed to identify and characterize the hevein genes in two-row and six-row cultivars of barley. In total, thirteen hevein genes were identified in the genome of two-row and six-row cultivars of barley. The identified heveins were identical in two-row and six-row cultivars of barley and showed a high similarity with heveins from other plant species. The hevein coding sequences produced open reading frames (ORFs) ranged from 342 to 1002 bp. Most of the identified hevein genes were intronless, and the others had only one intron. The hevein ORFs produced proteins ranged from 113 to 333 amino acids. Search for conserved functional domains showed CBD and LYZ domains in barley heveins. All barley heveins comprised extracellular signal peptides ranged from 19 to 35 amino acids. The phylogenetic analysis divided barley heveins into two groups. The promoter analysis showed regulatory elements with different frequencies between two-row and six-row cultivars. These cis-acting elements included elements related to growth and development, hormone response, and environmental stresses. The expression analysis showed high expression level of heveins in root and reproductive organs of both two-row and six-row cultivars. The expression analysis also showed that barley heveins is induced by both biotic and abiotic stresses. The results of antimicrobial activity prediction showed the highest antimicrobial activity in CBD domain of barley heveins. The findings of the current study can improve our knowledge about the role of hevein genes in plant and can be used for future studies.
Collapse
Affiliation(s)
- Reza Mir Drikvand
- Department of Plant Genetics and Breeding, Islamic Azad University, Khorramabad Branch, Khorramabad, Iran.
| | - Seyyed Mohsen Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University, Ahvaz, Iran
| | - Seyed Sajad Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Kamran Samiei
- Department of Plant Genetics and Breeding, Islamic Azad University, Khorramabad Branch, Khorramabad, Iran
| |
Collapse
|
5
|
Zeng Z, Jia Y, Huang X, Chen Z, Xiang T, Han N, Bian H, Li C. Transcriptional and protein structural characterization of homogentisate phytyltransferase genes in barley, wheat, and oat. BMC PLANT BIOLOGY 2023; 23:528. [PMID: 37904113 PMCID: PMC10617047 DOI: 10.1186/s12870-023-04535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Homogentisate phytyltransferase (HPT) is the critical enzyme for the biosynthesis of tocopherols (vitamin E), which are the major lipid-soluble antioxidants and help plants adapt to various stress conditions. HPT is generally strictly conserved in various plant genomes; however, a divergent lineage HPT2 was identified recently in some Triticeae species. The molecular function and transcriptional profiles of HPT2 remain to be characterized. RESULTS In this study, we performed comprehensive transcriptome data mining of HPT1 and HPT2 in different tissues and stages of barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa), followed by qRT-PCR experiments on HPT1 and HPT2 in different tissues of barley and wheat. We found that the common HPT1 genes (HvHPT1, TaHPT1s, and AsHPT1s) displayed a conserved transcriptional pattern in the three target species and were universally transcribed in various tissues, with a notable preference in leaf. In contrast, HPT2 genes (HvHPT2, TaHPT2, and AsHPT2) were specifically transcribed in spike (developmentally up-regulated) and shoot apex tissues, displaying a divergent tissue-specific pattern. Cis-regulatory elements prediction in the promoter region identified common factors related to light-, plant hormone-, low temperature-, drought- and defense- responses in both HPT1s and HPT2s. We observed the transcriptional up-regulation of HvHPT1 and HvHPT2 under various stress conditions, supporting their conserved function in environmental adaption. We detected a clear, relaxed selection pressure in the HPT2 lineage, consistent with the predicted evolution pattern following gene duplication. Protein structural modelling and substrate docking analyses identified putative catalytic amino acid residues for HvHPT1 and HvHPT2, which are strictly conserved and consistent with their function in vitamin E biosynthesis. CONCLUSIONS We confirmed the presence of two lineages of HPT in Triticeae and Aveninae, including hexaploid oat, and characterized their transcriptional profiles based on transcriptome and qRT-PCR data. HPT1s were ubiquitously transcribed in various tissues, whilst HPT2s were highly expressed in specific stages and tissue. The active transcription of HPT2s, together with its conserved cis-elements and protein structural features, support HPT2s' role in tocopherol production in Triticeae. This study is the first protein structural analysis on the membrane-bound plant HPTs and provides valuable insights into its catalytic mechanism.
Collapse
Affiliation(s)
- Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, 311121, China
| | - Yong Jia
- Western Crops Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia
| | - Xiaoping Huang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zhehao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Taihe Xiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Ning Han
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengdao Li
- Western Crops Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
- State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia.
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia.
| |
Collapse
|
6
|
Li T, Li Y, Shangguan H, Bian J, Luo R, Tian Y, Li Z, Nie X, Cui L. BarleyExpDB: an integrative gene expression database for barley. BMC PLANT BIOLOGY 2023; 23:170. [PMID: 37003963 PMCID: PMC10064564 DOI: 10.1186/s12870-023-04193-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND RNA-sequencing (RNA-seq) has been widely used to study the dynamic expression patterns of transcribed genes, which can lead to new biological insights. However, processing and analyzing these huge amounts of histological data remains a great challenge for wet labs and field researchers who lack bioinformatics experience and computational resources. RESULTS We present BarleyExpDB, an easy-to-operate, free, and web-accessible database that integrates transcriptional profiles of barley at different growth and developmental stages, tissues, and stress conditions, as well as differential expression of mutants and populations to build a platform for barley expression and visualization. The expression of a gene of interest can be easily queried by searching by known gene ID or sequence similarity. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Proteins Families Database, and Simple Modular Architecture Research Tool annotations. CONCLUSIONS BarleyExpDB will serve as a valuable resource for the barley research community to leverage the vast publicly available RNA-seq datasets for functional genomics research and crop molecular breeding.
Collapse
Affiliation(s)
- Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Hongbin Shangguan
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325 Shandong China
| | - Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yuan Tian
- Xintai Urban and Rural Development Group Co., Ltd, Taian, 271200 Shandong China
| | - Zhimin Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| |
Collapse
|
7
|
Jia Y, Xu M, Hu H, Chapman B, Watt C, Buerte B, Han N, Zhu M, Bian H, Li C, Zeng Z. Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication. BMC Biol 2023; 21:25. [PMID: 36747211 PMCID: PMC9903521 DOI: 10.1186/s12915-022-01503-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date. RESULTS Taking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint. CONCLUSIONS Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.
Collapse
Affiliation(s)
- Yong Jia
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Mingrui Xu
- grid.410595.c0000 0001 2230 9154College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Haifei Hu
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Brett Chapman
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Calum Watt
- grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.516230.30000 0005 0233 6218Intergrain Pty Ltd, Bibra Lake, WA 6163 Australia
| | - B. Buerte
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ning Han
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Muyuan Zhu
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chengdao Li
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Department of Primary Industries and Regional Development, 3-Baron-Hay Court, South Perth, WA, 6151, Australia.
| | - Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China. .,Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, 311121, China.
| |
Collapse
|
8
|
Shafiei R, Hooper M, McClellan C, Oakey H, Stephens J, Lapierre C, Tsuji Y, Goeminne G, Vanholme R, Boerjan W, Ralph J, Halpin C. Downregulation of barley ferulate 5-hydroxylase dramatically alters straw lignin structure without impact on mechanical properties. FRONTIERS IN PLANT SCIENCE 2023; 13:1125003. [PMID: 36726680 PMCID: PMC9886061 DOI: 10.3389/fpls.2022.1125003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Barley is a major cereal crop for temperate climates, and a diploid genetic model for polyploid wheat. Cereal straw biomass is an attractive source of feedstock for green technologies but lignin, a key determinant of feedstock recalcitrance, complicates bio-conversion processes. However, manipulating lignin content to improve the conversion process could negatively affect agronomic traits. An alternative approach is to manipulate lignin composition which influences the physical and chemical properties of straw. This study validates the function of a barley ferulate 5-hydroxylase gene and demonstrates that its downregulation using the RNA-interference approach substantially impacts lignin composition. We identified five barley genes having putative ferulate 5-hydroxylase activity. Downregulation of HvF5H1 substantially reduced the lignin syringyl/guaiacyl (S/G) ratio in straw while the lignin content, straw mechanical properties, plant growth habit, and grain characteristics all remained unaffected. Metabolic profiling revealed significant changes in the abundance of 173 features in the HvF5H1-RNAi lines. The drastic changes in the lignin polymer of transgenic lines highlight the plasticity of barley lignification processes and the associated potential for manipulating and improving lignocellulosic biomass as a feedstock for green technologies. On the other hand, our results highlight some differences between the lignin biosynthetic pathway in barley, a temperate climate grass, and the warm climate grass, rice, and underscore potential diversity in the lignin biosynthetic pathways in grasses.
Collapse
Affiliation(s)
- Reza Shafiei
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Matthew Hooper
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Christopher McClellan
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Helena Oakey
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
- Faculty of Sciences, School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Jennifer Stephens
- Cell And Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
| | | | - Yukiko Tsuji
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
- Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent, Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent, Center for Plant Systems Biology, Ghent, Belgium
| | - John Ralph
- Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| |
Collapse
|
9
|
Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley. Nat Commun 2022; 13:6050. [PMID: 36229435 PMCID: PMC9561702 DOI: 10.1038/s41467-022-33300-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 09/12/2022] [Indexed: 12/24/2022] Open
Abstract
Faced with terrestrial threats, land plants seal their aerial surfaces with a lipid-rich cuticle. To breathe, plants interrupt their cuticles with adjustable epidermal pores, called stomata, that regulate gas exchange, and develop other specialised epidermal cells such as defensive hairs. Mechanisms coordinating epidermal features remain poorly understood. Addressing this, we studied two loci whose allelic variation causes both cuticular wax-deficiency and misarranged stomata in barley, identifying the underlying genes, Cer-g/ HvYDA1, encoding a YODA-like (YDA) MAPKKK, and Cer-s/ HvBRX-Solo, encoding a single BREVIS-RADIX (BRX) domain protein. Both genes control cuticular integrity, the spacing and identity of epidermal cells, and barley's distinctive epicuticular wax blooms, as well as stomatal patterning in elevated CO2 conditions. Genetic analyses revealed epistatic and modifying relationships between HvYDA1 and HvBRX-Solo, intimating that their products participate in interacting pathway(s) linking epidermal patterning with cuticular properties in barley. This may represent a mechanism for coordinating multiple adaptive features of the land plant epidermis in a cultivated cereal.
Collapse
|
10
|
Rajendran NR, Qureshi N, Pourkheirandish M. Genotyping by Sequencing Advancements in Barley. FRONTIERS IN PLANT SCIENCE 2022; 13:931423. [PMID: 36003814 PMCID: PMC9394214 DOI: 10.3389/fpls.2022.931423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Barley is considered an ideal crop to study cereal genetics due to its close relationship with wheat and diploid ancestral genome. It plays a crucial role in reducing risks to global food security posed by climate change. Genetic variations in the traits of interest in crops are vital for their improvement. DNA markers have been widely used to estimate these variations in populations. With the advancements in next-generation sequencing, breeders could access different types of genetic variations within different lines, with single-nucleotide polymorphisms (SNPs) being the most common type. However, genotyping barley with whole genome sequencing (WGS) is challenged by the higher cost and computational demand caused by the large genome size (5.5GB) and a high proportion of repetitive sequences (80%). Genotyping-by-sequencing (GBS) protocols based on restriction enzymes and target enrichment allow a cost-effective SNP discovery by reducing the genome complexity. In general, GBS has opened up new horizons for plant breeding and genetics. Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges. Moreover, a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium. The complete exploitation of GBS advancements will pave the way to a better understanding of crop genetics and offer opportunities for the successful improvement of barley and its close relatives.
Collapse
Affiliation(s)
- Nirmal Raj Rajendran
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Naeela Qureshi
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico, Mexico
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
11
|
Cross A, Li JB, Waugh R, Golicz AA, Pourkheirandish M. Grain dispersal mechanism in cereals arose from a genome duplication followed by changes in spatial expression of genes involved in pollen development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1263-1277. [PMID: 35192007 PMCID: PMC9033732 DOI: 10.1007/s00122-022-04029-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/04/2022] [Indexed: 05/31/2023]
Abstract
Grain disarticulation in wild progenitor of wheat and barley evolved through a local duplication event followed by neo-functionalization resulting from changes in location of gene expression. One of the most critical events in the process of cereal domestication was the loss of the natural mode of grain dispersal. Grain dispersal in barley is controlled by two major genes, Btr1 and Btr2, which affect the thickness of cell walls around the disarticulation zone. The barley genome also encodes Btr1-like and Btr2-like genes, which have been shown to be the ancestral copies. While Btr and Btr-like genes are non-redundant, the biological function of Btr-like genes is unknown. We explored the potential biological role of the Btr-like genes by surveying their expression profile across 212 publicly available transcriptome datasets representing diverse organs, developmental stages and stress conditions. We found that Btr1-like and Btr2-like are expressed exclusively in immature anther samples throughout Prophase I of meiosis within the meiocyte. The similar and restricted expression profile of these two genes suggests they are involved in a common biological function. Further analysis revealed 141 genes co-expressed with Btr1-like and 122 genes co-expressed with Btr2-like, with 105 genes in common, supporting Btr-like genes involvement in a shared molecular pathway. We hypothesize that the Btr-like genes play a crucial role in pollen development by facilitating the formation of the callose wall around the meiocyte or in the secretion of callase by the tapetum. Our data suggest that Btr genes retained an ancestral function in cell wall modification and gained a new role in grain dispersal due to changes in their spatial expression becoming spike specific after gene duplication.
Collapse
Affiliation(s)
- Arthur Cross
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia
| | - John B Li
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia
| | - Robbie Waugh
- Division of Plant Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Agnieszka A Golicz
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia.
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Gießen, Gießen, Germany.
| | | |
Collapse
|
12
|
Barakate A, Arrieta M, Macaulay M, Vivera S, Davidson D, Stephens J, Orr J, Schreiber M, Ramsay L, Halpin C, Waugh R. Downregulation of Barley Regulator of Telomere Elongation Helicase 1 Alters the Distribution of Meiotic Crossovers. FRONTIERS IN PLANT SCIENCE 2021; 12:745070. [PMID: 34659314 PMCID: PMC8515186 DOI: 10.3389/fpls.2021.745070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Programmed meiotic DNA double-strand breaks (DSBs), necessary for proper chromosomal segregation and viable gamete formation, are repaired by homologous recombination (HR) as crossovers (COs) or non-crossovers (NCOs). The mechanisms regulating the number and distribution of COs are still poorly understood. The regulator of telomere elongation helicase 1 (RTEL1) DNA helicase was previously shown to enforce the number of meiotic COs in Caenorhabditis elegans but its function in plants has been studied only in the vegetative phase. Here, we characterised barley RTEL1 gene structure and expression using RNA-seq data previously obtained from vegetative and reproductive organs and tissues. Using RNAi, we downregulated RTEL1 expression specifically in reproductive tissues and analysed its impact on recombination using a barley 50k iSelect SNP Array. Unlike in C. elegans, in a population segregating for RTEL1 downregulated by RNAi, high resolution genome-wide genetic analysis revealed a significant increase of COs at distal chromosomal regions of barley without a change in their total number. Our data reveal the important role of RTEL1 helicase in plant meiosis and control of recombination.
Collapse
Affiliation(s)
- Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mikel Arrieta
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sebastian Vivera
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Diane Davidson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jennifer Stephens
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jamie Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Claire Halpin
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Waite Campus, Adelaide, SA, Australia
| |
Collapse
|