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Kovacik M, Nowicka A, Zwyrtková J, Strejčková B, Vardanega I, Esteban E, Pasha A, Kaduchová K, Krautsova M, Červenková M, Šafář J, Provart NJ, Simon R, Pecinka A. The transcriptome landscape of developing barley seeds. THE PLANT CELL 2024; 36:2512-2530. [PMID: 38635902 PMCID: PMC11218782 DOI: 10.1093/plcell/koae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.
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Affiliation(s)
- Martin Kovacik
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Anna Nowicka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30 239 Kraków, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Beáta Strejčková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Isaia Vardanega
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Kateřina Kaduchová
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Maryna Krautsova
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Marie Červenková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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Jørgensen ME, Houston K, Jørgensen HJL, Thomsen HC, Tekaat L, Krogh CT, Mellor SB, Braune KB, Damm ML, Pedas PR, Voss C, Rasmussen MW, Nielsen K, Skadhauge B, Motawia MS, Møller BL, Dockter C, Sørensen M. Disentangling hydroxynitrile glucoside biosynthesis in a barley (Hordeum vulgare) metabolon provides access to elite malting barleys for ethyl carbamate-free whisky production. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:364-382. [PMID: 38652034 DOI: 10.1111/tpj.16768] [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: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024]
Abstract
Barley produces several specialized metabolites, including five α-, β-, and γ-hydroxynitrile glucosides (HNGs). In malting barley, presence of the α-HNG epiheterodendrin gives rise to undesired formation of ethyl carbamate in the beverage production, especially after distilling. Metabolite-GWAS identified QTLs and underlying gene candidates possibly involved in the control of the relative and absolute content of HNGs, including an undescribed MATE transporter. By screening 325 genetically diverse barley accessions, we discovered three H. vulgare ssp. spontaneum (wild barley) lines with drastic changes in the relative ratios of the five HNGs. Knock-out (KO)-lines, isolated from the barley FIND-IT resource and each lacking one of the functional HNG biosynthetic genes (CYP79A12, CYP71C103, CYP71C113, CYP71U5, UGT85F22 and UGT85F23) showed unprecedented changes in HNG ratios enabling assignment of specific and mutually dependent catalytic functions to the biosynthetic enzymes involved. The highly similar relative ratios between the five HNGs found across wild and domesticated barley accessions indicate assembly of the HNG biosynthetic enzymes in a metabolon, the functional output of which was reconfigured in the absence of a single protein component. The absence or altered ratios of the five HNGs in the KO-lines did not change susceptibility to the fungal phytopathogen Pyrenophora teres causing net blotch. The study provides a deeper understanding of the organization of HNG biosynthesis in barley and identifies a novel, single gene HNG-0 line in an elite spring barley background for direct use in breeding of malting barley, eliminating HNGs as a source of ethyl carbamate formation in whisky production.
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Affiliation(s)
- Morten E Jørgensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Kelly Houston
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, Scotland
| | - Hans Jørgen L Jørgensen
- Section for Plant and Soil Sciences, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Hanne C Thomsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Linda Tekaat
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Camilla Timmermann Krogh
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Silas B Mellor
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | | | - Mette L Damm
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Cynthia Voss
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | | | - Kasper Nielsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Mohammed S Motawia
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Mette Sørensen
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Novo Nordisk Pharmatech, Københavnsvej 216, 4600, Køge, Denmark
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Zewodu A, Mohammed W, Shiferaw E. Analysis of genetic diversity and population structure of some Ethiopian barley (Hordeum vulgare L.) accessions using SSR markers. PLoS One 2024; 19:e0305945. [PMID: 38917122 PMCID: PMC11198791 DOI: 10.1371/journal.pone.0305945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/08/2024] [Indexed: 06/27/2024] Open
Abstract
Understanding the genetic diversity of existing genetic resources at the DNA level is an effective approach for germplasm conservation and utilization in breeding programs. However, the patterns of genetic diversity and population structure remain poorly characterized, making germplasm conservation and breeding efforts difficult to succeed. Thus, this study is aimed to evaluate the genetic diversity and population structure of 49 barley accessions collected from different geographic origins in Ethiopia. Twelve SSR markers were used to analyze all accessions and a total of 61 alleles were found, with a mean of 5.08 alleles per locus. The analysis pointed out the existence of moderate to high values of polymorphic information content ranging from 0.39 to 0.91 and the mean Shannon diversity index(I) was 1.25, indicating that they were highly informative markers. The highest Euclidean distance (1.32) was computed between accession 9950 and two accessions (247011 and 9949), while the lowest Euclidean distance (0.00) was estimated between accessions 243191 and 243192. The result of molecular variance analysis revealed that the highest variation was found among accessions (47) relative to within accessions (44) and among geographic origins (9). Cluster analysis grouped the 49 barley accessions into three major clusters regardless of their geographic origin which could be due to the presence of considerable gene flow (2.72). The result of the STRUCTURE analysis was consistent with neighbor-joining clustering and principal coordinate analysis. Generally, this study concluded that the variation among accessions was more important than the difference in geographical regions to develop an appropriate conservation strategy and for parental selection to use in breeding programs. This information will be helpful for barley conservation and breeding, and it may speed up the development of new competing barley varieties.
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Affiliation(s)
- Alemayehu Zewodu
- Department of Crop and Horticulture Biodiversity Research, Ethiopian Biodiversity Institute, Addis Ababa, Ethiopia
| | - Wassu Mohammed
- Department of Plant Science, Haramaya University, Haramaya, Ethiopia
| | - Eleni Shiferaw
- Department of Crop and Horticulture Biodiversity Research, Ethiopian Biodiversity Institute, Addis Ababa, Ethiopia
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Câmara AS, Kubalová I, Schubert V. Helical chromonema coiling is conserved in eukaryotes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1284-1300. [PMID: 37840457 DOI: 10.1111/tpj.16484] [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: 01/27/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023]
Abstract
Efficient chromatin condensation is required to transport chromosomes during mitosis and meiosis, forming daughter cells. While it is well accepted that these processes follow fundamental rules, there has been a controversial debate for more than 140 years on whether the higher-order chromatin organization in chromosomes is evolutionarily conserved. Here, we summarize historical and recent investigations based on classical and modern methods. In particular, classical light microscopy observations based on living, fixed, and treated chromosomes covering a wide range of plant and animal species, and even in single-cell eukaryotes suggest that the chromatids of large chromosomes are formed by a coiled chromatin thread, named the chromonema. More recently, these findings were confirmed by electron and super-resolution microscopy, oligo-FISH, molecular interaction data, and polymer simulation. Altogether, we describe common and divergent features of coiled chromonemata in different species. We hypothesize that chromonema coiling in large chromosomes is a fundamental feature established early during the evolution of eukaryotes to handle increasing genome sizes.
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Affiliation(s)
- Amanda Souza Câmara
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
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Hu Z, Chen J, Olatoye MO, Zhang H, Lin Z. Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum. THE PLANT GENOME 2024; 17:e20448. [PMID: 38602082 DOI: 10.1002/tpg2.20448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.
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Affiliation(s)
- Zhenbin Hu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Junhao Chen
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Marcus O Olatoye
- USDA-ARS, Forage Seed and Cereal Research Unit, Prosser, Washington, USA
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
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Siddiqui MN, Jahiu M, Kamruzzaman M, Sanchez-Garcia M, Mason AS, Léon J, Ballvora A. Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.). THE PLANT GENOME 2024; 17:e20463. [PMID: 38764204 DOI: 10.1002/tpg2.20463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024]
Abstract
Root architectural traits play pivotal roles in plant adaptation to drought stress, and hence they are considered promising targets in breeding programs. Here, we phenotyped eight root architecture traits in response to well-watered and drought stress conditions in 200 spring barley (Hordeum vulgare L.) inbred lines over two consecutive field seasons. Root architecture traits were less developed under drought in both seasons when compared with control treatments. Genetic variation in root architectural traits was dissected employing a genome-wide association study (GWAS) coupled with linkage disequilibrium mapping. GWAS uncovered a total of 186 significant single nucleotide polymorphism-trait associations for eight root traits under control, drought, and drought-related indices. Of these, a few loci for root traits were detected on chromosomes 3 and 5, which co-located with QTL identified in previous studies. Interestingly, 13 loci showed simultaneou associations with multiple root traits under drought and drought-related indices. These loci harbored candidate genes, which included a wide range of drought-responsive components such as transcription factors, binding proteins, protein kinases, nutrient and ion transporters, and stress signaling factors. For instance, two candidate genes, HORVU7Hr3G0713160 and HORVU6H r3G0626550, are orthologous to AtACX3 and AtVAMPs, which have reported functions in root length-mediated drought tolerance and as a key protein in abiotic stress tolerance, respectively. Interestingly, one of these loci underlying a high-confidence candidate gene NEW ENHANCER OF ROOT DWARFISM1 (NERD1) showed involvement with root development. An allelic variation of this locus in non-coding region was significantly associated with increased root length under drought. Collectively, these results offer promising multi-trait affecting loci and candidate genes underlying root phenotypic responses to drought stress, which may provide valuable resources for genetic improvement of drought tolerance in barley.
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Affiliation(s)
- Md Nurealam Siddiqui
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Melisa Jahiu
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Mohammad Kamruzzaman
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Miguel Sanchez-Garcia
- Department of Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Annaliese S Mason
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Jens Léon
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Agim Ballvora
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
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Nguyen DT, Zavadil Kokáš F, Gonin M, Lavarenne J, Colin M, Gantet P, Bergougnoux V. Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.). BMC PLANT BIOLOGY 2024; 24:438. [PMID: 38778283 PMCID: PMC11110440 DOI: 10.1186/s12870-024-05160-y] [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: 06/16/2023] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering. RESULTS Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process. CONCLUSIONS This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.
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Affiliation(s)
- Dieu Thu Nguyen
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- Department of Biochemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Filip Zavadil Kokáš
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- Present address: Masaryk Memorial Cancer Institute, Brno, Czechia
| | - Mathieu Gonin
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Jérémy Lavarenne
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Myriam Colin
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Pascal Gantet
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia.
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Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? NATURE PLANTS 2024; 10:719-731. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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Garza AB, Lerat E, Girgis HZ. Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats. Mob DNA 2024; 15:8. [PMID: 38627766 PMCID: PMC11020628 DOI: 10.1186/s13100-024-00317-w] [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: 07/29/2023] [Accepted: 03/08/2024] [Indexed: 04/20/2024] Open
Abstract
Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-retrotransposons; they are the most abundant type of transposons in plant genomes. They have many important functions involving gene regulation and the rise of new genes and pseudo genes in response to severe stress. Additionally, LTR-retrotransposons have several applications in biotechnology. Due to the abundance and the importance of LTR-retrotransposons, multiple computational tools have been developed for their detection. However, none of these tools take advantages of the availability of related genomes; they process one chromosome at a time. Further, recently nested LTR-retrotransposons (multiple elements of the same family are inserted into each other) cannot be annotated accurately - or cannot be annotated at all - by the currently available tools. Motivated to overcome these two limitations, we built Look4LTRs, which can annotate LTR-retrotransposons in multiple related genomes simultaneously and discover recently nested elements. The methodology of Look4LTRs depends on techniques imported from the signal-processing field, graph algorithms, and machine learning with a minimal use of alignment algorithms. Four plant genomes were used in developing Look4LTRs and eight plant genomes for evaluating it in contrast to three related tools. Look4LTRs is the fastest while maintaining better or comparable F1 scores (the harmonic average of recall and precision) to those obtained by the other tools. Our results demonstrate the added benefit of annotating LTR-retrotransposons in multiple related genomes simultaneously and the ability to discover recently nested elements. Expert human manual examination of six elements - not included in the ground truth - revealed that three elements belong to known families and two elements are likely from new families. With respect to examining recently nested LTR-retrotransposons, three out of five were confirmed to be valid elements. Look4LTRs - with its speed, accuracy, and novel features - represents a true advancement in the annotation of LTR-retrotransposons, opening the door to many studies focused on understanding their functions in plants.
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Affiliation(s)
- Anthony B Garza
- Bioinformatics Toolsmith Laboratory, Department of Electrical Engineering and Computer Science, Texas A &M University-Kingsville, Kingsville, Texas, USA
| | - Emmanuelle Lerat
- The Biometrics and Evolutionary Biology Laboratory, University Lyon 1, Lyon, France
| | - Hani Z Girgis
- Bioinformatics Toolsmith Laboratory, Department of Electrical Engineering and Computer Science, Texas A &M University-Kingsville, Kingsville, Texas, USA.
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Ahmed FF, Dola FS, Islam MSU, Zohra FT, Akter N, Rahman SM, Rauf Sarkar MA. Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley ( Hordeum vulgare L.). Genet Res (Camb) 2024; 2024:2924953. [PMID: 38444770 PMCID: PMC10914435 DOI: 10.1155/2024/2924953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/27/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Lectin receptor-like kinases (LecRLKs) are a significant subgroup of the receptor-like kinases (RLKs) protein family. They play crucial roles in plant growth, development, immune responses, signal transduction, and stress tolerance. However, the genome-wide identification and characterization of LecRLK genes and their regulatory elements have not been explored in a major cereal crop, barley (Hordeum vulgare L.). Therefore, in this study, integrated bioinformatics tools were used to identify and characterize the LecRLK gene family in barley. Based on the phylogenetic tree and domain organization, a total of 113 LecRLK genes were identified in the barley genome (referred to as HvlecRLK) corresponding to the LecRLK genes of Arabidopsis thaliana. These putative HvlecRLK genes were classified into three groups: 62 G-type LecRLKs, 1 C-type LecRLK, and 50 L-type LecRLKs. They were unevenly distributed across eight chromosomes, including one unknown chromosome, and were predominantly located in the plasma membrane (G-type HvlecRLK (96.8%), C-type HvlecRLK (100%), and L-type HvlecRLK (98%)). An analysis of motif composition and exon-intron configuration revealed remarkable homogeneity with the members of AtlecRLK. Notably, most of the HvlecRLKs (27 G-type, 43 L-type) have no intron, suggesting their rapid functionality. The Ka/Ks and syntenic analysis demonstrated that HvlecRLK gene pairs evolved through purifying selection and gene duplication was the major factor for the expansion of the HvlecRLK gene family. Exploration of gene ontology (GO) enrichment indicated that the identified HvlecRLK genes are associated with various cellular processes, metabolic pathways, defense mechanisms, kinase activity, catalytic activity, ion binding, and other essential pathways. The regulatory network analysis identified 29 transcription factor families (TFFs), with seven major TFFs including bZIP, C2H2, ERF, MIKC_MADS, MYB, NAC, and WRKY participating in the regulation of HvlecRLK gene functions. Most notably, eight TFFs were found to be linked to the promoter region of both L-type HvleckRLK64 and HvleckRLK86. The promoter cis-acting regulatory element (CARE) analysis of barley identified a total of 75 CARE motifs responsive to light responsiveness (LR), tissue-specific (TS), hormone responsiveness (HR), and stress responsiveness (SR). The maximum number of CAREs was identified in HvleckRLK11 (25 for LR), HvleckRLK69 (17 for TS), and HvleckRLK80 (12 for HR). Additionally, HvleckRLK14, HvleckRLK16, HvleckRLK33, HvleckRLK50, HvleckRLK52, HvleckRLK56, and HvleckRLK110 were predicted to exhibit higher responses in stress conditions. In addition, 46 putative miRNAs were predicted to target 81 HvlecRLK genes and HvlecRLK13 was the most targeted gene by 8 different miRNAs. Protein-protein interaction analysis demonstrated higher functional similarities of 63 HvlecRLKs with 7 Arabidopsis STRING proteins. Our overall findings provide valuable information on the LecRLK gene family which might pave the way to advanced research on the functional mechanism of the candidate genes as well as to develop new barley cultivars in breeding programs.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Farah Sumaiya Dola
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Shohel Ul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Nasrin Akter
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
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Pidon H, Ruge-Wehling B, Will T, Habekuß A, Wendler N, Oldach K, Maasberg-Prelle A, Korzun V, Stein N. High-resolution mapping of Ryd4 Hb, a major resistance gene to Barley yellow dwarf virus from Hordeum bulbosum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:60. [PMID: 38409375 PMCID: PMC10896957 DOI: 10.1007/s00122-024-04542-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024]
Abstract
KEY MESSAGE We mapped Ryd4Hb in a 66.5 kbp interval in barley and dissociated it from a sublethality factor. These results will enable a targeted selection of the resistance in barley breeding. Virus diseases are causing high yield losses in crops worldwide. The Barley yellow dwarf virus (BYDV) complex is responsible for one of the most widespread and economically important viral diseases of cereals. While no gene conferring complete resistance (immunity) has been uncovered in the primary gene pool of barley, sources of resistance were searched and identified in the wild relative Hordeum bulbosum, representing the secondary gene pool of barley. One such locus, Ryd4Hb, has been previously introgressed into barley, and was allocated to chromosome 3H, but is tightly linked to a sublethality factor that prevents the incorporation and utilization of Ryd4Hb in barley varieties. To solve this problem, we fine-mapped Ryd4Hb and separated it from this negative factor. We narrowed the Ryd4Hb locus to a corresponding 66.5 kbp physical interval in the barley 'Morex' reference genome. The region comprises a gene from the nucleotide-binding and leucine-rich repeat immune receptor family, typical of dominant virus resistance genes. The closest homolog to this Ryd4Hb candidate gene is the wheat Sr35 stem rust resistance gene. In addition to the fine mapping, we reduced the interval bearing the sublethality factor to 600 kbp in barley. Aphid feeding experiments demonstrated that Ryd4Hb provides a resistance to BYDV rather than to its vector. The presented results, including the high-throughput molecular markers, will permit a more targeted selection of the resistance in breeding, enabling the use of Ryd4Hb in barley varieties.
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Affiliation(s)
- Hélène Pidon
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.
| | - Brigitte Ruge-Wehling
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
| | - Torsten Will
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Antje Habekuß
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | | | | | | | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Göttingen, Germany.
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12
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [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: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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13
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Prazyan A, Podlutskii M, Volkova P, Kazakova E, Bitarishvili S, Shesterikova E, Saburov V, Makarenko E, Lychenkova M, Korol M, Kazakov E, Moiseev A, Geras’kin S, Bondarenko E. Comparative Analysis of the Effect of Gamma-, Electron, and Proton Irradiation on Transcriptomic Profile of Hordeum vulgare L. Seedlings: In Search for Molecular Contributors to Abiotic Stress Resilience. PLANTS (BASEL, SWITZERLAND) 2024; 13:342. [PMID: 38337875 PMCID: PMC10857502 DOI: 10.3390/plants13030342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024]
Abstract
The development of adaptation strategies for crops under ever-changing climate conditions is a critically important food security issue. Studies of barley responses to ionising radiation showed that this evolutionarily ancient stress factor can be successfully used to identify molecular pathways involved in adaptation to a range of abiotic stressors. In order to identify potential molecular contributors to abiotic stress resilience, we examined the transcriptomic profiles of barley seedlings after exposure to γ-rays, electrons, and protons. A total of 553 unique differentially expressed genes with increased expression and 124 with decreased expression were detected. Among all types of radiation, the highest number of differentially expressed genes was observed in electron-irradiated samples (428 upregulated and 56 downregulated genes). Significant upregulation after exposure to the three types of radiation was shown by a set of ROS-responsive genes, genes involved in DNA repair, cell wall metabolism, auxin biosynthesis and signalling, as well as photosynthesis-related genes. Most of these genes are known to be involved in plant ROS-mediated responses to other abiotic stressors, especially with genotoxic components, such as heavy metals and drought. Ultimately, the modulation of molecular pathways of plant responses to ionising radiation may be a prospective tool for stress tolerance programmes.
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Affiliation(s)
- Alexander Prazyan
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
| | - Mikhail Podlutskii
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
| | | | - Elizaveta Kazakova
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
| | - Sofia Bitarishvili
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
| | - Ekaterina Shesterikova
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
| | - Vyacheslav Saburov
- A. Tsyb Medical Radiological Research Centre—Branch of the National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249036 Obninsk, Russia
| | - Ekaterina Makarenko
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
| | - Maria Lychenkova
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
| | - Marina Korol
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
| | - Evgeniy Kazakov
- A. Tsyb Medical Radiological Research Centre—Branch of the National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249036 Obninsk, Russia
| | - Alexander Moiseev
- A. Tsyb Medical Radiological Research Centre—Branch of the National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249036 Obninsk, Russia
| | - Stanislav Geras’kin
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
| | - Ekaterina Bondarenko
- Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia
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14
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Fan C, Xu D, Wang C, Chen Z, Dou T, Qin D, Guo A, Zhao M, Pei H, Zhao M, Zhang R, Wang K, Zhang J, Ni Z, Guo G. Natural variations of HvSRN1 modulate the spike rachis node number in barley. PLANT COMMUNICATIONS 2024; 5:100670. [PMID: 37563835 PMCID: PMC10811343 DOI: 10.1016/j.xplc.2023.100670] [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: 02/17/2023] [Revised: 07/13/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Grain number, one of the major determinants of yield in Triticeae crops, is largely determined by spikelet number and spike rachis node number (SRN). Here, we identified three quantitative trait loci (QTLs) for SRN using 145 recombinant inbred lines derived from a barley R90/1815D cross. qSRN1, the major-effect QTL, was mapped to chromosome 2H and explained up to 38.77% of SRN variation. Map-based cloning revealed that qSRN1 encodes the RAWUL domain-containing protein HvSRN1. Further analysis revealed that two key SNPs in the HvSRN1 promoter region (∼2 kb upstream of the transcription start site) affect the transcript level of HvSRN1 and contribute to variation in SRN. Similar to its orthologous proteins OsLAX2 and ZmBA2, HvSRN1 showed protein-protein interactions with HvLAX1, suggesting that the LAX2-LAX1 model for spike morphology regulation may be conserved in Poaceae crops. CRISPR-Cas9-induced HvSRN1 mutants showed reduced SRN but increased grain size and weight, demonstrating a trade-off effect. Our results shed light on the role of HvSRN1 variation in regulating the balance between grain number and weight in barley.
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Affiliation(s)
- Chaofeng Fan
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Dongdong Xu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China; Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chunchao Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Zhaoyan Chen
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Tingyu Dou
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Dandan Qin
- Key Laboratory for Crop Molecular Breeding of Ministry of Agriculture and Rural Affairs, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Aikui Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Meng Zhao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Honghong Pei
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Mengwei Zhao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Renxu Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Ke Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Jing Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Zhongfu Ni
- Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| | - Ganggang Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China.
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15
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Qiu CW, Ma Y, Gao ZF, Sreesaeng J, Zhang S, Liu W, Ahmed IM, Cai S, Wang Y, Zhang G, Wu F. Genome-wide profiling of genetic variations reveals the molecular basis of aluminum stress adaptation in Tibetan wild barley. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132541. [PMID: 37716271 DOI: 10.1016/j.jhazmat.2023.132541] [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: 07/06/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Aluminum (Al) toxicity in acidic soil is a major factor affecting crop productivity. The extensive genetic diversity found in Tibetan wild barley germplasms offers a valuable reservoir of alleles associated with aluminum tolerance. Here, resequencing of two Al-tolerant barley genotypes (Tibetan wild barley accession XZ16 and cultivated barley Dayton) identified a total of 19,826,182 and 16,287,277 single nucleotide polymorphisms (SNPs), 1628,052 and 1386,973 insertions/deletions (InDels), 61,532 and 57,937 structural variations (SVs), 248,768 and 240,723 copy number variations (CNVs) in XZ16 and Dayton, respectively, and uncovered approximately 600 genes highly related to Al tolerance in barley. Comparative genomic analyses unveiled 71 key genes that contain unique genetic variants in XZ16 and are predominantly associated with organic acid exudation, Al sequestration, auxin response, and transcriptional regulation. Manipulation of these key genes at the genetic and transcriptional level is a promising strategy for developing optimal haplotype combinations and new barley cultivars with improved Al tolerance. This study represents the first comprehensive examination of genetic variation in Al-tolerant Tibetan wild barley through genome-wide profiling. The obtained results make the deep insight into the mechanisms underlying barley adaptation to Al toxicity, and identified the candidate genes useful for improvement of Al tolerance in barley.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Zi-Feng Gao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jakkrit Sreesaeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shuo Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Imrul Mosaddek Ahmed
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Plant Biotechnology Laboratory, Center for Viticulture & Small Fruit Research, Florida A&M University, FL 32317, USA
| | - Shengguan Cai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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16
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Walker PL, Belmonte MF, McCallum BD, McCartney CA, Randhawa HS, Henriquez MA. Dual RNA-sequencing of Fusarium head blight resistance in winter wheat. FRONTIERS IN PLANT SCIENCE 2024; 14:1299461. [PMID: 38239218 PMCID: PMC10794533 DOI: 10.3389/fpls.2023.1299461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/29/2023] [Indexed: 01/22/2024]
Abstract
Fusarium head blight (FHB) is a devastating fungal disease responsible for significant yield losses in wheat and other cereal crops across the globe. FHB infection of wheat spikes results in grain contamination with mycotoxins, reducing both grain quality and yield. Breeding strategies have resulted in the production of FHB-resistant cultivars, however, the underlying molecular mechanisms of resistance in the majority of these cultivars are still poorly understood. To improve our understanding of FHB-resistance, we performed a transcriptomic analysis of FHB-resistant AC Emerson, FHB-moderately resistant AC Morley, and FHB-susceptible CDC Falcon in response to Fusarium graminearum. Wheat spikelets located directly below the point of inoculation were collected at 7-days post inoculation (dpi), where dual RNA-sequencing was performed to explore differential expression patterns between wheat cultivars in addition to the challenging pathogen. Differential expression analysis revealed distinct defense responses within FHB-resistant cultivars including the enrichment of physical defense through the lignin biosynthesis pathway, and DON detoxification through the activity of UDP-glycosyltransferases. Nucleotide sequence variants were also identified broadly between these cultivars with several variants being identified within differentially expressed putative defense genes. Further, F. graminearum demonstrated differential expression of mycotoxin biosynthesis pathways during infection, leading to the identification of putative pathogenicity factors.
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Affiliation(s)
- Philip L. Walker
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Curt A. McCartney
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Harpinder S. Randhawa
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Maria A. Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB, Canada
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17
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Sato K, Nakamura S, Fujita M. Regulation of Seed Dormancy Genes in Triticeae Species. Methods Mol Biol 2024; 2830:13-23. [PMID: 38977564 DOI: 10.1007/978-1-0716-3965-8_2] [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] [Indexed: 07/10/2024]
Abstract
Wild progenitors of Triticeae crops generally have long dormancy periods. Domesticated crops inherited these longer dormancy alleles from their wild progenitors, which have since been modified and selected during cultivation and utilization by humans. Thus, allelic combinations at different seed dormancy loci are currently represented in Triticeae germplasm preserved in seed repositories and gene banks as accessions and materials of breeding programs. Methods to evaluate seed dormancy are key to explore, analyze, and exploit optimal alleles in dormancy genes. Recent developments in genomics have accelerated the identification and analysis of seed dormancy loci in Triticeae species. Transgenic experiments have been conducted to validate if candidate genes affect seed dormancy and more recently have yielded an array of mutations derived from genome editing for practical applications. The information gathered on these seed dormancy loci provides a deeper knowledge of germplasm diversity and offers strategies to control seed dormancy in breeding programs in Triticeae crops.
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Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science & Resources, Okayama University, Kurashiki, Japan.
- Faculty of Agriculture, Setsunan University, Hirakata, Japan.
- Kazusa DNA Research Institute, Kisarazu, Japan.
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18
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Zhang Z, Zhao P, Wang X, Wang H, Zhai Z, Zhao X, Xing L, Qi Z, Shang Y. Identification and map-based cloning of long glume mutant gene lgm1 in barley. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:3. [PMID: 38222975 PMCID: PMC10786806 DOI: 10.1007/s11032-024-01448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/03/2024] [Indexed: 01/16/2024]
Abstract
The spikes of gramineous plants are composed of specialized units called spikelets. Two bracts at the spikelet bases are known as glumes. The spikelet glumes in barley are degenerated into threadlike structures. Here, we report a long glume mutant, lgm1, similar in appearance to a lemma with a long awn at the apex. Map-based cloning showed that the mutant lgm1 allele has an approximate 1.27 Mb deletion of in chromosome 2H. The deleted segment contains five putative high-confidence genes, among which HORVU.MOREX.r3.2HG0170820 encodes a C2H2 zinc finger protein, an ortholog of rice NSG1/LRG1 and an important candidate for the Lgm1 allele. Line GA01 with a long glume and short awn was obtained in progenies of crosses involving the lgm1 mutant. Interestingly, lsg1, a mutant with long glumes on lateral spikelets, was obtained in the progenies of the lgm1 mutant. The long glume variant increased the weight of kernels in the lateral spikelets and increased kernel uniformity across the entire spike, greatly improving the potential of six-rowed barley for malting. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01448-x.
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Affiliation(s)
- Zhenlan Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Pengtao Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xiaoyun Wang
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004 Jiangxi China
| | - Haiyan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 Jiangsu China
| | - Zhouping Zhai
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xiaoguang Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 Jiangsu China
| | - Zengjun Qi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 Jiangsu China
| | - Yi Shang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
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19
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Varshney RK, Stein N, Reif J. Professor Andreas Graner: driven by the quest to unlock crop plant genomes for conservation and utilization of germplasm for breeding. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2426-2432. [PMID: 37549196 PMCID: PMC10651146 DOI: 10.1111/pbi.14143] [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: 06/22/2023] [Accepted: 07/23/2023] [Indexed: 08/09/2023]
Abstract
Professor Andreas Graner stands as a towering figure in international crop plant genomics research, leaving an indelible imprint on the field over the past four decades. As we commemorate the 80th anniversary of Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany and Professor Graner's retirement in September 2023, here we celebrate and acknowledge his profound impact on crop genome analyses and genebank genomics. His trailblazing work extends from developing the first integrated RFLP map of barley, establishing the foundation of barley genome sequencing, and advancing functional genomics of malting quality, to pioneering the use of high-throughput phenomics. As the dedicated custodian of Germany's largest ex situ genebank at IPK Gatersleben, Professor Graner has fortified the institution's collection management and crop research, thereby contributing significantly to global efforts on conservation and utilization of plant genetic resources through genomics approaches. Alongside his impressive array of scientific achievements, Professor Graner's inspiring mentorship has nurtured a new generation of scientists, including us, leaving a lasting legacy in the field. This tribute underscores his enduring influence and celebrates his unwavering dedication to the scientific community.
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Affiliation(s)
- Rajeev K. Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food InnovationMurdoch UniversityMurdochWAAustralia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Jochen Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
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20
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Shen L, Liu Y, Zhang L, Sun Z, Wang Z, Jiao Y, Shen K, Guo Z. A transcriptional atlas identifies key regulators and networks for the development of spike tissues in barley. Cell Rep 2023; 42:113441. [PMID: 37971941 DOI: 10.1016/j.celrep.2023.113441] [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: 01/10/2022] [Revised: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
Grain number and size determine grain yield in crops and are closely associated with spikelet fertility and grain filling in barley (Hordeum vulgare). Abortion of spikelet primordia within individual barley spikes causes a 30%-50% loss in the potential number of grains during development from the awn primordium stage to the tipping stage, after that grain filling is the primary factor regulating grain size. To identify transcriptional signatures associated with spike development, we use a six-rowed barley cultivar (Morex) to develop a spatiotemporal transcriptome atlas containing 255 samples covering 17 stages and 5 positions along the spike. We identify several fundamental regulatory networks, in addition to key regulators of spike development and morphology. Specifically, we show HvGELP96, encoding a GDSL domain-containing protein, as a regulator of spikelet fertility and grain number. Our transcriptional atlas offers a powerful resource to answer fundamental questions in spikelet development and degeneration in barley.
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Affiliation(s)
- Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuannian Jiao
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Botanical Garden, Beijing 100093, China.
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21
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Quan X, Meng C, Xie C, Sun H, Xu B, Santos Bermudez R, He W. Genome-Wide and Transcriptome Analysis of Jacalin-Related Lectin Genes in Barley and the Functional Characterization of HvHorcH in Low-Nitrogen Tolerance in Arabidopsis. Int J Mol Sci 2023; 24:16641. [PMID: 38068963 PMCID: PMC10706597 DOI: 10.3390/ijms242316641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The jacalin-related lectins (JRLs) are widely distributed in plants and are involved in plant development and multiple stress responses. However, the characteristics of the HvJRL gene family at the genome-wide level and the roles of JRLs in barley's response to low-nitrogen (LN) stress have been rarely reported. In this study, 32 HvJRL genes were identified and unevenly distributed at both ends of the seven chromosomes in barley. HvJRL proteins generally exhibited low sequence similarity but shared conserved jacalin domains by multiple sequence analysis. These proteins were classified into seven subfamilies based on phylogenetic analysis, with a similar gene structure and conserved motifs in the same subfamily. The HvJRL promoters contained a large number of diverse cis-elements associated with hormonal response and stress regulation. Based on the phylogenetic relationships and functionally known JRL homologs, it was predicted that some HvJRLs have the potential to serve functions in multiple stress responses but not nutrition deficiency stress. Subsequently, nine differentially expressed genes (DEGs) encoding eight HvJRL proteins were identified in two barley genotypes with different LN tolerance by transcriptome analysis. Furthermore, 35S:HvHorcH transgenic Arabidopsis seedlings did enhance LN tolerance, which indicated that HvHorcH may be an important regulator of LN stress response (LNSR). The HvJRL DEGs identified herein could provide new candidate genes for LN tolerance studies.
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Affiliation(s)
- Xiaoyan Quan
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | | | | | | | | | | | - Wenxing He
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
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22
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Bethke G, Huang Y, Hensel G, Heinen S, Liu C, Wyant SR, Li X, Quin MB, McCormick S, Morrell PL, Dong Y, Kumlehn J, Salvi S, Berthiller F, Muehlbauer GJ. UDP-glucosyltransferase HvUGT13248 confers type II resistance to Fusarium graminearum in barley. PLANT PHYSIOLOGY 2023; 193:2691-2710. [PMID: 37610244 DOI: 10.1093/plphys/kiad467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
Fusarium head blight (FHB) of barley (Hordeum vulgare) causes yield losses and accumulation of trichothecene mycotoxins (e.g. deoxynivalenol [DON]) in grains. Glucosylation of DON to the nontoxic DON-3-O-glucoside (D3G) is catalyzed by UDP-glucosyltransferases (UGTs), such as barley UGT13248. We explored the natural diversity of UGT13248 in 496 barley accessions and showed that all carried potential functional alleles of UGT13248, as no genotypes showed strongly increased seedling sensitivity to DON. From a TILLING population, we identified 2 mutant alleles (T368I and H369Y) that, based on protein modeling, likely affect the UDP-glucose binding of UGT13248. In DON feeding experiments, DON-to-D3G conversion was strongly reduced in spikes of these mutants compared to controls, and plants overexpressing UGT13248 showed increased resistance to DON and increased DON-to-D3G conversion. Moreover, field-grown plants carrying the T368I or H369Y mutations inoculated with Fusarium graminearum showed increased FHB disease severity and reduced D3G production. Barley is generally considered to have type II resistance that limits the spread of F. graminearum from the infected spikelet to adjacent spikelets. Point inoculation experiments with F. graminearum showed increased infection spread in T368I and H369Y across the spike compared to wild type, while overexpression plants showed decreased spread of FHB symptoms. Confocal microscopy revealed that F. graminearum spread to distant rachis nodes in T368I and H369Y mutants but was arrested at the rachis node of the inoculated spikelet in wild-type plants. Taken together, our data reveal that UGT13248 confers type II resistance to FHB in barley via conjugation of DON to D3G.
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Affiliation(s)
- Gerit Bethke
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yadong Huang
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Goetz Hensel
- Department of Physiology and Cell Biology, Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Shane Heinen
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Skylar R Wyant
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Maureen B Quin
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Susan McCormick
- Mycotoxin Prevention and Applied Microbiology Research, USDA-ARS NCAUR, Peoria, IL 61604, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jochen Kumlehn
- Department of Physiology and Cell Biology, Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Franz Berthiller
- Department of Agrobiotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln 3430, Austria
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
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23
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Zhang RG, Shang HY, Jia KH, Ma YP. Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations. Brief Bioinform 2023; 25:bbad513. [PMID: 38189536 PMCID: PMC10772947 DOI: 10.1093/bib/bbad513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.
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Affiliation(s)
- Ren-Gang Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
- University of Chinese Academy of Sciences, Beijing 101408 Beijing, China
| | - Hong-Yun Shang
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
| | - Kai-Hua Jia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100 Shandong, China
| | - Yong-Peng Ma
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
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24
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Farkas A, Gaál E, Ivanizs L, Blavet N, Said M, Holušová K, Szőke-Pázsi K, Spitkó T, Mikó P, Türkösi E, Kruppa K, Kovács P, Darkó É, Szakács É, Bartoš J, Doležel J, Molnár I. Chromosome genomics facilitates the marker development and selection of wheat-Aegilops biuncialis addition, substitution and translocation lines. Sci Rep 2023; 13:20499. [PMID: 37993509 PMCID: PMC10665447 DOI: 10.1038/s41598-023-47845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
The annual goatgrass, Aegilops biuncialis is a rich source of genes with considerable agronomic value. This genetic potential can be exploited for wheat improvement through interspecific hybridization to increase stress resistance, grain quality and adaptability. However, the low throughput of cytogenetic selection hampers the development of alien introgressions. Using the sequence of flow-sorted chromosomes of diploid progenitors, the present study enabled the development of chromosome-specific markers. In total, 482 PCR markers were validated on wheat (Mv9kr1) and Ae. biuncialis (MvGB642) crossing partners, and 126 on wheat-Aegilops additions. Thirty-two markers specific for U- or M-chromosomes were used in combination with GISH and FISH for the screening of 44 Mv9kr1 × Ae. biuncialis BC3F3 genotypes. The predominance of chromosomes 4M and 5M, as well as the presence of chromosomal aberrations, may indicate that these chromosomes have a gametocidal effect. A new wheat-Ae. biuncialis disomic 4U addition, 4M(4D) and 5M(5D) substitutions, as well as several introgression lines were selected. Spike morphology and fertility indicated that the Aegilops 4M or 5M compensated well for the loss of 4D and 5D, respectively. The new cytogenetic stocks represent valuable genetic resources for the introgression of key genes alleles into wheat.
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Affiliation(s)
- András Farkas
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Eszter Gaál
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary.
| | - László Ivanizs
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Nicolas Blavet
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Mahmoud Said
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Kateřina Holušová
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Kitti Szőke-Pázsi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Tamás Spitkó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Péter Mikó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Edina Türkösi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Klaudia Kruppa
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Péter Kovács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Éva Darkó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Éva Szakács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Jan Bartoš
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - István Molnár
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
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25
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Elakhdar A, El-Naggar AA, Kubo T, Kumamaru T. Genome-wide transcriptomic and functional analyses provide new insights into the response of spring barley to drought stress. PHYSIOLOGIA PLANTARUM 2023; 175:e14089. [PMID: 38148212 DOI: 10.1111/ppl.14089] [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: 08/08/2023] [Revised: 09/22/2023] [Accepted: 10/27/2023] [Indexed: 12/28/2023]
Abstract
Drought is a major abiotic stress that impairs the physiology and development of plants, ultimately leading to crop yield losses. Drought tolerance is a complex quantitative trait influenced by multiple genes and metabolic pathways. However, molecular intricacies and subsequent morphological and physiological changes in response to drought stress remain elusive. Herein, we combined morpho-physiological and comparative RNA-sequencing analyses to identify core drought-induced marker genes and regulatory networks in the barley cultivar 'Giza134'. Based on field trials, drought-induced declines occurred in crop growth rate, relative water content, leaf area duration, flag leaf area, concentration of chlorophyll (Chl) a, b and a + b, net photosynthesis, and yield components. In contrast, the Chl a/b ratio, stoma resistance, and proline concentration increased significantly. RNA-sequence analysis identified a total of 2462 differentially expressed genes (DEGs), of which 1555 were up-regulated and 907 were down-regulated in response to water-deficit stress (WD). Comparative transcriptomics analysis highlighted three unique metabolic pathways (carbohydrate metabolism, iron ion binding, and oxidoreductase activity) as containing genes differentially expressed that could mitigate water stress. Our results identified several drought-induced marker genes belonging to diverse physiochemical functions like chlorophyll concentration, photosynthesis, light harvesting, gibberellin biosynthetic, iron homeostasis as well as Cis-regulatory elements. These candidate genes can be utilized to identify gene-associated markers to develop drought-resilient barley cultivars over a short period of time. Our results provide new insights into the understanding of water stress response mechanisms in barley.
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Affiliation(s)
- Ammar Elakhdar
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ahmed A El-Naggar
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | - Takahiko Kubo
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Toshihiro Kumamaru
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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26
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Chaudhary N, Salgotra RK, Chauhan BS. Genetic Enhancement of Cereals Using Genomic Resources for Nutritional Food Security. Genes (Basel) 2023; 14:1770. [PMID: 37761910 PMCID: PMC10530810 DOI: 10.3390/genes14091770] [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: 08/16/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Advances in genomics resources have facilitated the evolution of cereal crops with enhanced yield, improved nutritional values, and heightened resistance to various biotic and abiotic stresses. Genomic approaches present a promising avenue for the development of high-yielding varieties, thereby ensuring food and nutritional security. Significant improvements have been made within the omics domain, specifically in genomics, transcriptomics, and proteomics. The advent of Next-Generation Sequencing (NGS) techniques has yielded an immense volume of data, accompanied by substantial progress in bioinformatic tools for proficient analysis. The synergy between genomics and computational tools has been acknowledged as pivotal for unravelling the intricate mechanisms governing genome-wide gene regulation. Within this review, the essential genomic resources are delineated, and their harmonization in the enhancement of cereal crop varieties is expounded upon, with a paramount focus on fulfilling the nutritional requisites of humankind. Furthermore, an encompassing compendium of the available genomic resources for cereal crops is presented, accompanied by an elucidation of their judicious utilization in the advancement of crop attributes.
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Affiliation(s)
- Neeraj Chaudhary
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Romesh Kumar Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Bhagirath Singh Chauhan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Gatton, QLD 4343, Australia
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27
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Visioni A, Basile B, Amri A, Sanchez-Garcia M, Corrado G. Advancing the Conservation and Utilization of Barley Genetic Resources: Insights into Germplasm Management and Breeding for Sustainable Agriculture. PLANTS (BASEL, SWITZERLAND) 2023; 12:3186. [PMID: 37765350 PMCID: PMC10535687 DOI: 10.3390/plants12183186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
Barley is a very important crop particularly in marginal dry areas, where it often serves as the most viable option for farmers. Additionally, barley carries great significance in the Western world, serving not only as a fundamental crop for animal feed and malting but also as a nutritious food source. The broad adaptability of barley and its ability to withstand various biotic and abiotic stresses often make this species the sole cereal that can be cultivated in arid regions. The collection and utilization of barley genetic resources are crucial for identifying valuable traits to enhance productivity and mitigate the adverse effects of climate change. This review aims to provide an overview of the management and exploitation of barley genetic resources. Furthermore, the review explores the relationship between gene banks and participatory breeding, offering insights into the diversity and utilization of barley genetic resources through some examples such as the initiatives undertaken by ICARDA. Finally, this contribution highlights the importance of these resources for boosting barley productivity, addressing climate change impacts, and meeting the growing food demands in a rapidly changing agriculture. The understanding and utilizing the rich genetic diversity of barley can contribute to sustainable agriculture and ensure the success of this vital crop for future generations globally.
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Affiliation(s)
- Andrea Visioni
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10100, Morocco; (A.A.); (M.S.-G.)
| | - Boris Basile
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10100, Morocco; (A.A.); (M.S.-G.)
| | - Miguel Sanchez-Garcia
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10100, Morocco; (A.A.); (M.S.-G.)
| | - Giandomenico Corrado
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
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Pan R, Hu H, Xiao Y, Xu L, Xu Y, Ouyang K, Li C, He T, Zhang W. High-quality wild barley genome assemblies and annotation with Nanopore long reads and Hi-C sequencing data. Sci Data 2023; 10:535. [PMID: 37563167 PMCID: PMC10415357 DOI: 10.1038/s41597-023-02434-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Wild barley, from "Evolution Canyon (EC)" in Mount Carmel, Israel, are ideal models for cereal chromosome evolution studies. Here, the wild barley EC_S1 is from the south slope with higher daily temperatures and drought, while EC_N1 is from the north slope with a cooler climate and higher relative humidity, which results in a differentiated selection due to contrasting environments. We assembled a 5.03 Gb genome with contig N50 of 3.53 Mb for wild barley EC_S1 and a 5.05 Gb genome with contig N50 of 3.45 Mb for EC_N1 using 145 Gb and 160.0 Gb Illumina sequencing data, 295.6 Gb and 285.35 Gb Nanopore sequencing data and 555.1 Gb and 514.5 Gb Hi-C sequencing data, respectively. BUSCOs and CEGMA evaluation suggested highly complete assemblies. Using full-length transcriptome data, we predicted 39,179 and 38,373 high-confidence genes in EC_S1 and EC_N1, in which 93.6% and 95.2% were functionally annotated, respectively. We annotated repetitive elements and non-coding RNAs. These two wild barley genome assemblies will provide a rich gene pool for domesticated barley.
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Affiliation(s)
- Rui Pan
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025, China
| | - Haifei Hu
- Western Crop Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6155, Australia
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Yuhui Xiao
- Grandomics Biotechnology Co., Ltd, Wuhan, 430076, China
| | - Le Xu
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025, China
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025, China
| | - Yanhao Xu
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025, China
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025, China
| | - Kai Ouyang
- Grandomics Biotechnology Co., Ltd, Wuhan, 430076, China
| | - Chengdao Li
- Western Crop Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6155, Australia
- Department of Primary Industries and Regional Development, South Perth, WA, 6155, Australia
| | - Tianhua He
- Western Crop Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6155, Australia.
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025, China.
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Yangtze University, Jingzhou, 434025, China.
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Wonneberger R, Schreiber M, Haaning A, Muehlbauer GJ, Waugh R, Stein N. Major chromosome 5H haplotype switch structures the European two-rowed spring barley germplasm of the past 190 years. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:174. [PMID: 37477711 PMCID: PMC10361897 DOI: 10.1007/s00122-023-04418-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 07/22/2023]
Abstract
Selection over 70 years has led to almost complete fixation of a haplotype spanning ~ 250 Mbp of chomosome 5H in European two-rowed spring barleys, possibly originating from North Africa. Plant breeding and selection have shaped the genetic composition of modern crops over the past decades and centuries and have led to great improvements in agronomic and quality traits. Knowledge of the genetic composition of breeding germplasm is essential to make informed decisions in breeding programs. In this study, we characterized the structure and composition of 209 barley cultivars representative of the European two-rowed spring barley germplasm of the past 190 years. Utilizing high-density SNP marker data, we identified a distinct centromeric haplotype spanning a ~ 250 Mbp large region on chromosome 5H which likely was first introduced into the European breeding germplasm in the early to mid-twentieth century and has been non-recombining and under strong positive selection over the past 70 years. Almost all cultivars in our panel that were released after 2000 carry this new haplotype, suggesting that this region carries one or several genes conferring highly beneficial traits. Using the global barley collection of the German Federal ex situ gene bank at IPK Gatersleben, we found the new haplotype at high frequencies in six-rowed spring-type landraces from Northern Africa, from which it may have been introduced into modern European barley germplasm via southern European landraces. The presence of a 250 Mbp genomic region characterized by lack of recombination and high levels of fixation in modern barley germplasm has substantial implications for the genetic diversity of the modern barley germplasm and for barley breeding.
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Affiliation(s)
- Ronja Wonneberger
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Miriam Schreiber
- Division of Plant Sciences, University of Dundee, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Allison Haaning
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany.
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany.
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Gao Z, Bian J, Lu F, Jiao Y, He H. Triticeae crop genome biology: an endless frontier. FRONTIERS IN PLANT SCIENCE 2023; 14:1222681. [PMID: 37546276 PMCID: PMC10399237 DOI: 10.3389/fpls.2023.1222681] [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: 05/15/2023] [Accepted: 07/04/2023] [Indexed: 08/08/2023]
Abstract
Triticeae, the wheatgrass tribe, includes several major cereal crops and their wild relatives. Major crops within the Triticeae are wheat, barley, rye, and oat, which are important for human consumption, animal feed, and rangeland protection. Species within this tribe are known for their large genomes and complex genetic histories. Powered by recent advances in sequencing technology, researchers worldwide have made progress in elucidating the genomes of Triticeae crops. In addition to assemblies of high-quality reference genomes, pan-genome studies have just started to capture the genomic diversities of these species, shedding light on our understanding of the genetic basis of domestication and environmental adaptation of Triticeae crops. In this review, we focus on recent signs of progress in genome sequencing, pan-genome analyses, and resequencing analysis of Triticeae crops. We also propose future research avenues in Triticeae crop genomes, including identifying genome structure variations, the association of genomic regions with desired traits, mining functions of the non-coding area, introgression of high-quality genes from wild Triticeae resources, genome editing, and integration of genomic resources.
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Affiliation(s)
- Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuling Jiao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
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Soleimani B, Lehnert H, Trebing S, Habekuß A, Ordon F, Stahl A, Will T. Identification of Markers Associated with Wheat Dwarf Virus (WDV) Tolerance/Resistance in Barley ( Hordeum vulgare ssp. vulgare) Using Genome-Wide Association Studies. Viruses 2023; 15:1568. [PMID: 37515254 PMCID: PMC10385604 DOI: 10.3390/v15071568] [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: 05/10/2023] [Revised: 07/05/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Wheat dwarf virus (WDV) causes an important vector transmitted virus disease, which leads to significant yield losses in barley production. Due to the fact that, at the moment, no plant protection products are approved to combat the vector Psammotettix alienus, and this disease cannot be controlled by chemical means, the use of WDV-resistant or -tolerant genotypes is the most efficient method to control and reduce the negative effects of WDV on barley growth and production. In this study, a set of 480 barley genotypes were screened to identify genotypic differences in response to WDV, and five traits were assessed under infected and noninfected conditions. In total, 32 genotypes showed resistance or tolerance to WDV. Subsequently, phenotypic data of 191 out of 480 genotypes combined with 34,408 single-nucleotide polymorphisms (SNPs) were used for a genome-wide association study to identify quantitative trait loci (QTLs) and markers linked to resistance/tolerance to WDV. Genomic regions significantly associated with WDV resistance/tolerance in barley were identified on chromosomes 3H, 4H, 5H, and 7H for traits such as relative virus titer, relative performance of total grain weight, plant height, number of ears per plant, and thousand grain weight.
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Affiliation(s)
- Behnaz Soleimani
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Heike Lehnert
- Institute for Biosafety in Plant Biotechnology, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Sarah Trebing
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Torsten Will
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
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32
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Guo J, Beemster GTS, Liu F, Wang Z, Li X. Abscisic Acid Regulates Carbohydrate Metabolism, Redox Homeostasis and Hormonal Regulation to Enhance Cold Tolerance in Spring Barley. Int J Mol Sci 2023; 24:11348. [PMID: 37511108 PMCID: PMC10379442 DOI: 10.3390/ijms241411348] [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: 06/11/2023] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Abscisic acid (ABA) plays a vital role in the induction of low temperature tolerance in plants. To understand the molecular basis of this phenomenon, we performed a proteomic analysis on an ABA-deficit mutant barley (Az34) and its wild type (cv Steptoe) under control conditions (25/18 °C) and after exposure to 0 °C for 24 h. Most of the differentially abundant proteins were involved in the processes of photosynthesis and metabolisms of starch, sucrose, carbon, and glutathione. The chloroplasts in Az34 leaves were more severely damaged, and the decrease in Fv/Fm was larger in Az34 plants compared with WT under low temperature. Under low temperature, Az34 plants possessed significantly higher activities of ADP-glucose pyrophosphorylase, fructokinase, monodehydroascorbate reductase, and three invertases, but lower UDP-glucose pyrophosphorylase activity than WT. In addition, concentrations of proline and soluble protein were lower, while concentration of H2O2 was higher in Az34 plants compared to WT under low temperature. Collectively, the results indicated that ABA deficiency induced modifications in starch and sucrose biosynthesis and sucrolytic pathway and overaccumulation of reactive oxygen species were the main reason for depressed low temperature tolerance in barley, which provide novel insights to the response of barley to low temperature under future climate change.
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Affiliation(s)
- Junhong Guo
- Key Laboratory of Black Soil Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Fulai Liu
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark
| | - Zongming Wang
- Key Laboratory of Black Soil Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiangnan Li
- Key Laboratory of Black Soil Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Zakhrabekova S, Chauhan P, Dockter C, Ealumalai P, Ivanova A, Jørgensen ME, Lu Q, Shoeva O, Werner K, Hansson M. Identification of a candidate dwarfing gene in Pallas, the first commercial barley cultivar generated through mutational breeding. Front Genet 2023; 14:1213815. [PMID: 37470037 PMCID: PMC10352844 DOI: 10.3389/fgene.2023.1213815] [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: 04/28/2023] [Accepted: 06/07/2023] [Indexed: 07/21/2023] Open
Abstract
Many induced mutants are available in barley (Hordeum vulgare L.). One of the largest groups of induced mutants is the Erectoides (ert) mutants, which is characterized by a compact and upright spike and a shortened culm. One isolated mutant, ert-k.32, generated by X-ray treatment and registered in 1958 under the named "Pallas", was the first ever induced barley mutant to be released on the market. Its value was improved culm strength and enhanced lodging resistance. In this study, we aimed to identify the casual gene of the ert-k.32 mutant by whole genome sequencing of allelic ert-k mutants. The suggested Ert-k candidate gene, HORVU.MOREX.r3.6HG0574880, is located in the centromeric region of chromosome 6H. The gene product is an alpha/beta hydrolase with a catalytic triad in the active site composed of Ser-167, His-261 and Asp-232. In comparison to proteins derived from the Arabidopsis genome, ErtK is most similar to a thioesterase with de-S-acylation activity. This suggests that ErtK catalyzes post-translational modifications by removing fatty acids that are covalently attached to cysteine residues of target proteins involved in regulation of plant architecture and important commercial traits such as culm stability and lodging resistance.
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Affiliation(s)
| | | | | | | | - Anastasiia Ivanova
- Department of Biology, Lund University, Lund, Sweden
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Qiongxian Lu
- Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Olesya Shoeva
- Department of Biology, Lund University, Lund, Sweden
- Department of Plant Genetics,Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Mats Hansson
- Department of Biology, Lund University, Lund, Sweden
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Karunarathne S, Walker E, Sharma D, Li C, Han Y. Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance. J Zhejiang Univ Sci B 2023; 24:1069-1092. [PMID: 38057266 PMCID: PMC10710907 DOI: 10.1631/jzus.b2200552] [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: 10/31/2022] [Accepted: 01/17/2023] [Indexed: 07/11/2023]
Abstract
Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern gene-editing platforms. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.
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Affiliation(s)
- Sakura Karunarathne
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Darshan Sharma
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
| | - Yong Han
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
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Qiu CW, Ma Y, Liu W, Zhang S, Wang Y, Cai S, Zhang G, Chater CCC, Chen ZH, Wu F. Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley. J Adv Res 2023; 49:31-45. [PMID: 36170948 PMCID: PMC10334146 DOI: 10.1016/j.jare.2022.09.008] [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: 05/26/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance. OBJECTIVES To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley. METHODS Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes. RESULTS Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley. CONCLUSION Our findings reveal functional genes that have been selected across barley's complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuo Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK; School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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Korotkov E, Suvorova Y, Kostenko D, Korotkova M. Search for Dispersed Repeats in Bacterial Genomes Using an Iterative Procedure. Int J Mol Sci 2023; 24:10964. [PMID: 37446142 DOI: 10.3390/ijms241310964] [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: 06/11/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
We have developed a de novo method for the identification of dispersed repeats based on the use of random position-weight matrices (PWMs) and an iterative procedure (IP). The created algorithm (IP method) allows detection of dispersed repeats for which the average number of substitutions between any two repeats per nucleotide (x) is less than or equal to 1.5. We have shown that all previously developed methods and algorithms (RED, RECON, and some others) can only find dispersed repeats for x ≤ 1.0. We applied the IP method to find dispersed repeats in the genomes of E. coli and nine other bacterial species. We identify three families of approximately 1.09 × 106, 0.64 × 106, and 0.58 × 106 DNA bases, respectively, constituting almost 50% of the complete E. coli genome. The length of the repeats is in the range of 400 to 600 bp. Other analyzed bacterial genomes contain one to three families of dispersed repeats with a total number of 103 to 6 × 103 copies. The existence of such highly divergent repeats could be associated with the presence of a single-type triplet periodicity in various genes or with the packing of bacterial DNA into a nucleoid.
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Affiliation(s)
- Eugene Korotkov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld. 2, 33 Leninsky Ave., 119071 Moscow, Russia
| | - Yulia Suvorova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld. 2, 33 Leninsky Ave., 119071 Moscow, Russia
| | - Dimitry Kostenko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld. 2, 33 Leninsky Ave., 119071 Moscow, Russia
| | - Maria Korotkova
- Moscow Engineering Physics Institute, National Research Nuclear University MEPhI, 31 Kashirskoye Shosse, 115409 Moscow, Russia
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Elakhdar A, Slaski JJ, Kubo T, Hamwieh A, Hernandez Ramirez G, Beattie AD, Capo-chichi LJ. Genome-wide association analysis provides insights into the genetic basis of photosynthetic responses to low-temperature stress in spring barley. FRONTIERS IN PLANT SCIENCE 2023; 14:1159016. [PMID: 37346141 PMCID: PMC10279893 DOI: 10.3389/fpls.2023.1159016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/04/2023] [Indexed: 06/23/2023]
Abstract
Low-temperature stress (LTS) is among the major abiotic stresses affecting the geographical distribution and productivity of the most important crops. Understanding the genetic basis of photosynthetic variation under cold stress is necessary for developing more climate-resilient barley cultivars. To that end, we investigated the ability of chlorophyll fluorescence parameters (FVFM, and FVF0) to respond to changes in the maximum quantum yield of Photosystem II photochemistry as an indicator of photosynthetic energy. A panel of 96 barley spring cultivars from different breeding zones of Canada was evaluated for chlorophyll fluorescence-related traits under cold acclimation and freeze shock stresses at different times. Genome-wide association studies (GWAS) were performed using a mixed linear model (MLM). We identified three major and putative genomic regions harboring 52 significant quantitative trait nucleotides (QTNs) on chromosomes 1H, 3H, and 6H for low-temperature tolerance. Functional annotation indicated several QTNs were either within the known or close to genes that play important roles in the photosynthetic metabolites such as abscisic acid (ABA) signaling, hydrolase activity, protein kinase, and transduction of environmental signal transduction at the posttranslational modification levels. These outcomes revealed that barley plants modified their gene expression profile in response to decreasing temperatures resulting in physiological and biochemical modifications. Cold tolerance could influence a long-term adaption of barley in many parts of the world. Since the degree and frequency of LTS vary considerably among production sites. Hence, these results could shed light on potential approaches for improving barley productivity under low-temperature stress.
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Affiliation(s)
- Ammar Elakhdar
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Jan J. Slaski
- Bio Industrial Services Division, InnoTech Alberta Inc., Vegreville, AB, Canada
| | - Takahiko Kubo
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Aladdin Hamwieh
- International Center for Agriculture Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Guillermo Hernandez Ramirez
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Aaron D. Beattie
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ludovic J.A. Capo-chichi
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
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Quan X, Meng C, Zhang N, Liang X, Li J, Li H, He W. Genome-Wide Analysis of Barley bHLH Transcription Factors and the Functional Characterization of HvbHLH56 in Low Nitrogen Tolerance in Arabidopsis. Int J Mol Sci 2023; 24:ijms24119740. [PMID: 37298691 DOI: 10.3390/ijms24119740] [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: 03/31/2023] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Improvement of low nitrogen (LN) tolerance or nitrogen use efficiency (NUE) in crops is imperative for environment-friendly agriculture development. The basic helix-loop-helix (bHLH) transcription factors are involved in multiple abiotic stresses and are suitable as candidate genes for improving LN tolerance. Few studies were performed on the characterization of the HvbHLH gene family and their function in response to LN stress in barley. In this study, 103 HvbHLH genes were identified through genome-wide analysis. HvbHLH proteins were classified into 20 subfamilies based on phylogenetic analysis in barley, which was supported by conserved motifs and gene structure analysis. The stress-related cis-element analysis in the promoters showed that HvbHLHs are probably involved in multiple stress responses. By phylogenetic analysis of HvbHLHs and bHLHs in other plants, some HvbHLHs were predicted to play roles in response to nutrition deficiency stress. Furthermore, at least 16 HvbHLHs were differentially expressed in two barley genotypes differing in LN tolerance under LN stress. Finally, overexpression of HvbHLH56 enhanced LN stress tolerance in transgenic Arabidopsis, suggesting it is an important regulator in LN stress response. The differentially expressed HvbHLHs identified herein may be valuable for the breeding of barley cultivars with LN tolerance.
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Affiliation(s)
- Xiaoyan Quan
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Chen Meng
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Ning Zhang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xiaoli Liang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Hongmei Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
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Siddiqui MN, Pandey K, Bhadhury SK, Sadeqi B, Schneider M, Sanchez-Garcia M, Stich B, Schaaf G, Léon J, Ballvora A. Convergently selected NPF2.12 coordinates root growth and nitrogen use efficiency in wheat and barley. THE NEW PHYTOLOGIST 2023; 238:2175-2193. [PMID: 36808608 DOI: 10.1111/nph.18820] [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: 10/31/2022] [Accepted: 02/13/2023] [Indexed: 05/04/2023]
Abstract
Understanding the genetic and molecular function of nitrate sensing and acquisition across crop species will accelerate breeding of cultivars with improved nitrogen use efficiency (NUE). Here, we performed a genome-wide scan using wheat and barley accessions characterized under low and high N inputs that uncovered the NPF2.12 gene, encoding a homolog of the Arabidopsis nitrate transceptor NRT1.6 and other low-affinity nitrate transporters that belong to the MAJOR FACILITATOR SUPERFAMILY. Next, it is shown that variations in the NPF2.12 promoter correlated with altered NPF2.12 transcript levels where decreased gene expression was measured under low nitrate availability. Multiple field trials revealed a significantly enhanced N content in leaves and grains and NUE in the presence of the elite allele TaNPF2.12TT grown under low N conditions. Furthermore, the nitrate reductase encoding gene NIA1 was up-regulated in npf2.12 mutant upon low nitrate concentrations, thereby resulting in elevated levels of nitric oxide (NO) production. This increase in NO correlated with the higher root growth, nitrate uptake, and N translocation observed in the mutant when compared to wild-type. The presented data indicate that the elite haplotype alleles of NPF2.12 are convergently selected in wheat and barley that by inactivation indirectly contribute to root growth and NUE by activating NO signaling under low nitrate conditions.
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Affiliation(s)
- Md Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Kailash Pandey
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
| | - Suzan Kumer Bhadhury
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
| | - Bahman Sadeqi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
| | - Michael Schneider
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Miguel Sanchez-Garcia
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, 10101, Morocco
| | - Benjamin Stich
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Gabriel Schaaf
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, D-53115, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Klein-Altendorf 2, Rheinbach, 53359, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
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Rozanova IV, Grigoriev YN, Efimov VM, Igoshin AV, Khlestkina EK. Genetic Dissection of Spike Productivity Traits in the Siberian Collection of Spring Barley. Biomolecules 2023; 13:909. [PMID: 37371489 DOI: 10.3390/biom13060909] [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: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Barley (Hordeum vulgare L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity traits in Siberian spring barley and to develop diagnostic DNA markers for marker-assisted breeding programs. For this purpose we conducted a genome-wide association study using a panel of 94 barley varieties. In total, 64 SNPs significantly associated with productivity traits were revealed. Twenty-three SNP markers were validated by genotyping in an independent sample set using competitive allele-specific PCR (KASP). Finally, fourteen markers associated with spike productivity traits on chromosomes 2H, 4H and 5H can be suggested for use in breeding programs.
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Affiliation(s)
- Irina V Rozanova
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Yuriy N Grigoriev
- Siberian Research Institute of Plant Cultivation and Breeding-Branch of Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Krasnoobsk, 630501 Novosibirsk, Russia
| | - Vadim M Efimov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Alexander V Igoshin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Elena K Khlestkina
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
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Chaudhry A, Hassan AU, Khan SH, Abbasi A, Hina A, Khan MT, Abdelsalam NR. The changing landscape of agriculture: role of precision breeding in developing smart crops. Funct Integr Genomics 2023; 23:167. [PMID: 37204621 DOI: 10.1007/s10142-023-01093-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Food plants play a crucial role in human survival, providing them essential nutrients. However, traditional breeding methods have not been able to keep up with the demands of the growing population. The improvement of food plants aims to increase yield, quality, and resistance to biotic and abiotic stresses. With CRISPR/Cas9, researchers can identify and edit key genes conferring desirable qualities in agricultural plants, including increased yield, enhanced product quality attributes, and increased tolerance to biotic and abiotic challenges. These modifications have enabled the creation of "smart crops" that exhibit rapid climatic adaptation, resistance to extreme weather conditions and high yield and quality. The use of CRISPR/Cas9 combined with viral vectors or growth regulators has made it possible to produce more efficient modified plants with certain conventional breeding methods. However, ethical and regulatory aspects of this technology must be carefully considered. Proper regulation and application of genome editing technology can bring immense benefits to agriculture and food security. This article provides an overview of genetically modified genes and conventional as well as emerging tools, including CRISPR/Cas9, that have been utilized to enhance the quality of plants/fruits and their products. The review also discusses the challenges and prospects associated with these techniques.
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Affiliation(s)
- Amna Chaudhry
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, 38040, Pakistan
| | - Ahtsham Ul Hassan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, 38040, Pakistan
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University, Murree, 47150, Pakistan.
| | - Aiman Hina
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Muhammad Tajammal Khan
- Institute of Botany, University of the Punjab, Lahore, 54590, Pakistan
- Division of Science and Technology, Department of Botany, University of Education, Lahore, Pakistan
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
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Houston K, Learmonth A, Hassan AS, Lahnstein J, Looseley M, Little A, Waugh R, Burton RA, Halpin C. Natural variation in HvAT10 underlies grain cell wall-esterified phenolic acid content in cultivated barley. FRONTIERS IN PLANT SCIENCE 2023; 14:1095862. [PMID: 37235033 PMCID: PMC10206312 DOI: 10.3389/fpls.2023.1095862] [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: 11/11/2022] [Accepted: 04/06/2023] [Indexed: 05/28/2023]
Abstract
The phenolic acids, ferulic acid and p-coumaric acid, are components of plant cell walls in grasses, including many of our major food crops. They have important health-promoting properties in grain, and influence the digestibility of biomass for industrial processing and livestock feed. Both phenolic acids are assumed to be critical to cell wall integrity and ferulic acid, at least, is important for cross-linking cell wall components, but the role of p-coumaric acid is unclear. Here we identify alleles of a BAHD p-coumaroyl arabinoxylan transferase, HvAT10, as responsible for the natural variation in cell wall-esterified phenolic acids in whole grain within a cultivated two-row spring barley panel. We show that HvAT10 is rendered non-functional by a premature stop codon mutation in half of the genotypes in our mapping panel. This results in a dramatic reduction in grain cell wall-esterifed p-coumaric acid, a moderate rise in ferulic acid, and a clear increase in the ferulic acid to p-coumaric acid ratio. The mutation is virtually absent in wild and landrace germplasm suggesting an important function for grain arabinoxylan p-coumaroylation pre-domestication that is dispensable in modern agriculture. Intriguingly, we detected detrimental impacts of the mutated locus on grain quality traits where it was associated with smaller grain and poorer malting properties. HvAT10 could be a focus for improving grain quality for malting or phenolic acid content in wholegrain foods.
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Affiliation(s)
- Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Scotland, United Kingdom
| | - Amy Learmonth
- Division of Plant Sciences, School of Life Sciences, University of Dundee at The James Hutton Institute, Scotland, United Kingdom
| | - Ali Saleh Hassan
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Jelle Lahnstein
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Mark Looseley
- Cell and Molecular Sciences, The James Hutton Institute, Scotland, United Kingdom
| | - Alan Little
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Scotland, United Kingdom
- Division of Plant Sciences, School of Life Sciences, University of Dundee at The James Hutton Institute, Scotland, United Kingdom
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Rachel A. Burton
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee at The James Hutton Institute, Scotland, United Kingdom
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Schmidt SB, Brown LK, Booth A, Wishart J, Hedley PE, Martin P, Husted S, George TS, Russell J. Heritage genetics for adaptation to marginal soils in barley. TRENDS IN PLANT SCIENCE 2023; 28:544-551. [PMID: 36858842 DOI: 10.1016/j.tplants.2023.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 05/22/2023]
Abstract
Future crops need to be sustainable in the face of climate change. Modern barley varieties have been bred for high productivity and quality; however, they have suffered considerable genetic erosion, losing crucial genetic diversity. This renders modern cultivars vulnerable to climate change and stressful environments. We highlight the potential to tailor crops to a specific environment by utilising diversity inherent in an adapted landrace population. Tapping into natural biodiversity, while incorporating information about local environmental and climatic conditions, allows targeting of key traits and genotypes, enabling crop production in marginal soils. We outline future directions for the utilisation of genetic resources maintained in landrace collections to support sustainable agriculture through germplasm development via the use of genomics technologies and big data.
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Affiliation(s)
- Sidsel Birkelund Schmidt
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; Innovation Centre for Organic Farming, Agro Food Park 26, 8200 Aarhus N., Denmark
| | - Lawrie K Brown
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Allan Booth
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - John Wishart
- Agronomy Institute, Orkney College, University of the Highlands and Islands, Orkney, UK
| | - Pete E Hedley
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter Martin
- Agronomy Institute, Orkney College, University of the Highlands and Islands, Orkney, UK
| | - Søren Husted
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1879 Frederiksberg C., Denmark
| | | | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
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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.
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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
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Ventimiglia M, Castellacci M, Usai G, Vangelisti A, Simoni S, Natali L, Cavallini A, Mascagni F, Giordani T. Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study. PLANTS (BASEL, SWITZERLAND) 2023; 12:1405. [PMID: 36987093 PMCID: PMC10058865 DOI: 10.3390/plants12061405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/08/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Genome divergence by repeat proliferation and/or loss is a process that plays a crucial role in species evolution. Nevertheless, knowledge of the variability related to repeat proliferation among species of the same family is still limited. Considering the importance of the Asteraceae family, here we present a first contribution towards the metarepeatome of five Asteraceae species. A comprehensive picture of the repetitive components of all genomes was obtained by genome skimming with Illumina sequence reads and by analyzing a pool of full-length long terminal repeat retrotransposons (LTR-REs). Genome skimming allowed us to estimate the abundance and variability of repetitive components. The structure of the metagenome of the selected species was composed of 67% repetitive sequences, of which LTR-REs represented the bulk of annotated clusters. The species essentially shared ribosomal DNA sequences, whereas the other classes of repetitive DNA were highly variable among species. The pool of full-length LTR-REs was retrieved from all the species and their age of insertion was established, showing several lineage-specific proliferation peaks over the last 15-million years. Overall, a large variability of repeat abundance at superfamily, lineage, and sublineage levels was observed, indicating that repeats within individual genomes followed different evolutionary and temporal dynamics, and that different events of amplification or loss of these sequences may have occurred after species differentiation.
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Guan X, Cheng Z, Li Y, Wang J, Zhao R, Guo Z, Zhao T, Huang L, Qiu C, Shi W, Jin S. Mixed organic and inorganic amendments enhance soil microbial interactions and environmental stress resistance of Tibetan barley on plateau farmland. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 330:117137. [PMID: 36584462 DOI: 10.1016/j.jenvman.2022.117137] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Sufficient crop yield while maintaining soil health and sustainable agricultural development is a global objective, serving a special challenge to certain climate-sensitive plateau areas. Despite conducting trails on a variety of soil amendments in plateau areas, systematic research is lacking regarding the influences of organic and inorganic amendments on soil quality, particularly soil microbiome. To our knowledge, this was the first study that compared the effects of inorganic, organic, and mixed amendments on typical plateau crop hulless barley (Hordeum vulgare L. var. Nudum, also known as "Qingke" in Chinese) over the course of tillering, jointing, and ripening. Microbial communities and their responses to amendments, soil properties and Tibetan hulless barley growth, yield were investigated. Results indicated that mixed organic and inorganic amendments promoted the abundance of rhizosphere microorganisms, enhancing the rhizosphere root-microbes interactions and resistance to pathogenic bacteria and environmental stresses. The rhizosphere abundant and significantly different genera Arthrobacter, Rhodanobacter, Sphingomona, Nocardioides and so on demonstrated their unique adaptation to the plateau environment based on the results of metagenomic binning. The abundance of 23 genes about plant growth and environmental adaptations in the mixed amendment soil were significantly higher than other treatments. Findings from this study suggest that the mixed organic/inorganic amendments can help establish a healthy microbiome and increase soil quality while achieving sufficient hulless barley yields in Tibet and presumably other similar geographic areas of high altitude.
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Affiliation(s)
- Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Zhen Cheng
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Yiqiang Li
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, No. 17 Qinghuadong Road, Haidian District, Beijing, 100083, China.
| | - Ruoyu Zhao
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Zining Guo
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Tingting Zhao
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Liying Huang
- Institute of Agricultural Quality Standards and Testing, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, 850031, China
| | - Cheng Qiu
- Institute of Agricultural Quality Standards and Testing, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, 850031, China
| | - Wenyu Shi
- College of Food Science & Nutritional Engineering, China Agricultural University, No. 17 Qinghuadong Road, Haidian District, Beijing, 100083, China
| | - Song Jin
- Department of Civil and Architectural Engineering, University of Wyoming, Laramie, WY, 82071, USA.
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Yang X, Wilkinson LG, Aubert MK, Houston K, Shirley NJ, Tucker MR. Ovule cell wall composition is a maternal determinant of grain size in barley. THE NEW PHYTOLOGIST 2023; 237:2136-2147. [PMID: 36600397 DOI: 10.1111/nph.18714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In cereal species, grain size is influenced by growth of the ovule integuments (seed coat), the spikelet hull (lemma and palea) and the filial endosperm. Whether a highly conserved ovule tissue, the nucellus, has any impact on grain size has remained unclear. Immunolabelling revealed that the barley nucellus comprises two distinct cell types that differ in terms of cell wall homogalacturonan (HG) accumulation. Transcriptional profiling of the nucellus identified two pectin methylesterase (PME) genes, OVULE PECTIN MODIFIER 1 (OPM1) and OPM2, which are expressed in the unfertilized ovule but absent from the seed. Ovules from an opm1 opm2 mutant and plants expressing an ovule-specific pectin methylesterase inhibitor (PMEI), exhibit reduced HG accumulation. This results in changes to ovule cell size and shape and ovules that are longer than wild-type (WT) controls. At grain maturity, this is manifested as significantly longer grain. These findings indicate that cell wall composition during ovule development acts to limit ovule and seed growth. The investigation of ovule PME and PMEI activity reveals an unexpected role of maternal tissues in controlling grain growth before fertilization, one that has been lacking from models exploring improvements in grain size.
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Affiliation(s)
- Xiujuan Yang
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Laura G Wilkinson
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Matthew K Aubert
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- Australian Grain Technologies, 100 Byfield Street, Northam, WA, 6401, Australia
| | - Kelly Houston
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Neil J Shirley
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Matthew R Tucker
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
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Steckenborn S, Cuacos M, Ayoub MA, Feng C, Schubert V, Hoffie I, Hensel G, Kumlehn J, Heckmann S. The meiotic topoisomerase VI B subunit (MTOPVIB) is essential for meiotic DNA double-strand break formation in barley (Hordeum vulgare L.). PLANT REPRODUCTION 2023; 36:1-15. [PMID: 35767067 PMCID: PMC9957907 DOI: 10.1007/s00497-022-00444-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/31/2022] [Indexed: 06/01/2023]
Abstract
In barley (Hordeum vulgare), MTOPVIB is critical for meiotic DSB and accompanied SC and CO formation while dispensable for meiotic bipolar spindle formation. Homologous recombination during meiosis assures genetic variation in offspring. Programmed meiotic DNA double-strand breaks (DSBs) are repaired as crossover (CO) or non-crossover (NCO) during meiotic recombination. The meiotic topoisomerase VI (TopoVI) B subunit (MTOPVIB) plays an essential role in meiotic DSB formation critical for CO-recombination. More recently MTOPVIB has been also shown to play a role in meiotic bipolar spindle formation in rice and maize. Here, we describe a meiotic DSB-defective mutant in barley (Hordeum vulgare L.). CRISPR-associated 9 (Cas9) endonuclease-generated mtopVIB plants show complete sterility due to the absence of meiotic DSB, synaptonemal complex (SC), and CO formation leading to the occurrence of univalents and their unbalanced segregation into aneuploid gametes. In HvmtopVIB plants, we also frequently found the bi-orientation of sister kinetochores in univalents during metaphase I and the precocious separation of sister chromatids during anaphase I. Moreover, the near absence of polyads after meiosis II, suggests that despite being critical for meiotic DSB formation in barley, MTOPVIB seems not to be strictly required for meiotic bipolar spindle formation.
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Affiliation(s)
- Stefan Steckenborn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Maria Cuacos
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Mohammad A Ayoub
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Chao Feng
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Iris Hoffie
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany.
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49
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Abstract
KEY MESSAGE Chromatin state, and dynamic loading of pro-crossover protein HEI10 at recombination intermediates shape meiotic chromosome patterning in plants. Meiosis is the basis of sexual reproduction, and its basic progression is conserved across eukaryote kingdoms. A key feature of meiosis is the formation of crossovers which result in the reciprocal exchange of segments of maternal and paternal chromosomes. This exchange generates chromosomes with new combinations of alleles, increasing the efficiency of both natural and artificial selection. Crossovers also form a physical link between homologous chromosomes at metaphase I which is critical for accurate chromosome segregation and fertility. The patterning of crossovers along the length of chromosomes is a highly regulated process, and our current understanding of its regulation forms the focus of this review. At the global scale, crossover patterning in plants is largely governed by the classically observed phenomena of crossover interference, crossover homeostasis and the obligatory crossover which regulate the total number of crossovers and their relative spacing. The molecular actors behind these phenomena have long remained obscure, but recent studies in plants implicate HEI10 and ZYP1 as key players in their coordination. In addition to these broad forces, a wealth of recent studies has highlighted how genomic and epigenomic features shape crossover formation at both chromosomal and local scales, revealing that crossovers are primarily located in open chromatin associated with gene promoters and terminators with low nucleosome occupancy.
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Affiliation(s)
- Andrew Lloyd
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, Ceredigion, UK.
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The biological functions of nonsense-mediated mRNA decay in plants: RNA quality control and beyond. Biochem Soc Trans 2023; 51:31-39. [PMID: 36695509 DOI: 10.1042/bst20211231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved quality control pathway that inhibits the expression of transcripts containing premature termination codon. Transcriptome and phenotypic studies across a range of organisms indicate roles of NMD beyond RNA quality control and imply its involvement in regulating gene expression in a wide range of physiological processes. Studies in moss Physcomitrella patens and Arabidopsis thaliana have shown that NMD is also important in plants where it contributes to the regulation of pathogen defence, hormonal signalling, circadian clock, reproduction and gene evolution. Here, we provide up to date overview of the biological functions of NMD in plants. In addition, we discuss several biological processes where NMD factors implement their function through NMD-independent mechanisms.
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