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Pavlu S, Nikumbh S, Kovacik M, An T, Lenhard B, Simkova H, Navratilova P. Core promoterome of barley embryo. Comput Struct Biotechnol J 2024; 23:264-277. [PMID: 38173877 PMCID: PMC10762323 DOI: 10.1016/j.csbj.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024] Open
Abstract
Precise localization and dissection of gene promoters are key to understanding transcriptional gene regulation and to successful bioengineering applications. The core RNA polymerase II initiation machinery is highly conserved among eukaryotes, leading to a general expectation of equivalent underlying mechanisms. Still, less is known about promoters in the plant kingdom. In this study, we employed cap analysis of gene expression (CAGE) at three embryonic developmental stages in barley to accurately map, annotate, and quantify transcription initiation events. Unsupervised discovery of de novo sequence clusters grouped promoters based on characteristic initiator and position-specific core-promoter motifs. This grouping was complemented by the annotation of transcription factor binding site (TFBS) motifs. Integration with genome-wide epigenomic data sets and gene ontology (GO) enrichment analysis further delineated the chromatin environments and functional roles of genes associated with distinct promoter categories. The TATA-box presence governs all features explored, supporting the general model of two separate genomic regulatory environments. We describe the extent and implications of alternative transcription initiation events, including those that are specific to developmental stages, which can affect the protein sequence or the presence of regions that regulate translation. The generated promoterome dataset provides a valuable genomic resource for enhancing the functional annotation of the barley genome. It also offers insights into the transcriptional regulation of individual genes and presents opportunities for the informed manipulation of promoter architecture, with the aim of enhancing traits of agronomic importance.
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Affiliation(s)
- Simon Pavlu
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Sarvesh Nikumbh
- Merck Sharp & Dohme (UK) Limited, 120 Moorgate, London EC2M 6UR, UK
| | - Martin Kovacik
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Tadaichi An
- DNAFORM Precision Gene Technologies, 230–0046 Yokohama, Kanagawa, Japan
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Hana Simkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
| | - Pavla Navratilova
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
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2
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Amouzoune M, Rehman S, Benkirane R, Udupa S, Mamidi S, Kehel Z, Al-Jaboobi M, Amri A. Genome wide association study of seedling and adult plant leaf rust resistance in two subsets of barley genetic resources. Sci Rep 2024; 14:15428. [PMID: 38965257 DOI: 10.1038/s41598-024-53149-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/29/2024] [Indexed: 07/06/2024] Open
Abstract
Leaf rust (LR) caused by Puccinia hordei is a serious disease of barley worldwide, causing significant yield losses and reduced grain quality. Discovery and incorporation of new sources of resistance from gene bank accessions into barley breeding programs is essential for the development of leaf rust resistant varieties. To identify Quantitative Trait Loci (QTL) conferring LR resistance in the two barley subsets, the Generation Challenge Program (GCP) reference set of 142 accessions and the leaf rust subset constructed using the Focused Identification of Germplasm Strategy (FIGS) of 76 barley accessions, were genotyped to conduct a genome-wide association study (GWAS). The results revealed a total of 59 QTL in the 218 accessions phenotyped against barley leaf rust at the seedling stage using two P. hordei isolates (ISO-SAT and ISO-MRC), and at the adult plant stage in four environments in Morocco. Out of these 59 QTL, 10 QTL were associated with the seedling resistance (SR) and 49 QTL were associated with the adult plant resistance (APR). Four QTL showed stable effects in at least two environments for APR, whereas two common QTL associated with SR and APR were detected on chromosomes 2H and 7H. Furthermore, 39 QTL identified in this study were potentially novel. Interestingly, the sequences of 27 SNP markers encoded the candidate genes (CGs) with predicted protein functions in plant disease resistance. These results will provide new perspectives on the diversity of leaf rust resistance loci for fine mapping, isolation of resistance genes, and for marker-assisted selection for the LR resistance in barley breeding programs worldwide.
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Affiliation(s)
- Mariam Amouzoune
- Faculty of Sciences, University Ibn Tofail, 14000, Kenitra, Morocco.
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco.
| | - Sajid Rehman
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
- Field Crop Development Center, The Olds College, Lacombe, AB, T4L 1W8, Canada
| | - Rachid Benkirane
- Faculty of Sciences, University Ibn Tofail, 14000, Kenitra, Morocco
| | - Sripada Udupa
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
| | - Sujan Mamidi
- Hudson Alpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Zakaria Kehel
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
| | - Muamer Al-Jaboobi
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
| | - Ahmed Amri
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
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3
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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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She H, Liu Z, Xu Z, Zhang H, Wu J, Wang X, Cheng F, Charlesworth D, Qian W. Insights into spinach domestication from genome sequences of two wild spinach progenitors, Spinacia turkestanica and Spinacia tetrandra. THE NEW PHYTOLOGIST 2024; 243:477-494. [PMID: 38715078 DOI: 10.1111/nph.19799] [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: 02/12/2024] [Accepted: 04/18/2024] [Indexed: 06/07/2024]
Abstract
Cultivated spinach (Spinacia oleracea) is a dioecious species. We report high-quality genome sequences for its two closest wild relatives, Spinacia turkestanica and Spinacia tetrandra, which are also dioecious, and are used to study the genetics of spinach domestication. Using a combination of genomic approaches, we assembled genomes of both these species and analyzed them in comparison with the previously assembled S. oleracea genome. These species diverged c. 6.3 million years ago (Ma), while cultivated spinach split from S. turkestanica 0.8 Ma. In all three species, all six chromosomes include very large gene-poor, repeat-rich regions, which, in S. oleracea, are pericentromeric regions with very low recombination rates in both male and female genetic maps. We describe population genomic evidence that the similar regions in the wild species also recombine rarely. We characterized 282 structural variants (SVs) that have been selected during domestication. These regions include genes associated with leaf margin type and flowering time. We also describe evidence that the downy mildew resistance loci of cultivated spinach are derived from introgression from both wild spinach species. Collectively, this study reveals the genome architecture of spinach assemblies and highlights the importance of SVs during the domestication of cultivated spinach.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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5
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Clare SJ, Alhashel AF, Li M, Effertz KM, Poudel RS, Zhang J, Brueggeman RS. High resolution mapping of a novel non-transgressive hybrid susceptibility locus in barley exploited by P. teres f. maculata. BMC PLANT BIOLOGY 2024; 24:622. [PMID: 38951756 PMCID: PMC11218204 DOI: 10.1186/s12870-024-05303-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024]
Abstract
Hybrid genotypes can provide significant yield gains over conventional inbred varieties due to heterosis or hybrid vigor. However, hybrids can also display unintended negative attributes or phenotypes such as extreme pathogen susceptibility. The necrotrophic pathogen Pyrenophora teres f. maculata (Ptm) causes spot form net blotch, which has caused significant yield losses to barley worldwide. Here, we report on a non-transgressive hybrid susceptibility locus in barley identified between the three parental lines CI5791, Tifang and Golden Promise that are resistant to Ptm isolate 13IM.3. However, F2 progeny from CI5791 × Tifang and CI5791 × Golden Promise crosses exhibited extreme susceptibility. The susceptible phenotype segregated in a ratio of 1 resistant:1 susceptible representing a genetic segregation ratio of 1 parental (res):2 heterozygous (sus):1 parental (res) suggesting a single hybrid susceptibility locus. Genetic mapping using a total of 715 CI5791 × Tifang F2 individuals (1430 recombinant gametes) and 149 targeted SNPs delimited the hybrid susceptibility locus designated Susceptibility to Pyrenophora teres 2 (Spt2) to an ~ 198 kb region on chromosome 5H of the Morex V3 reference assembly. This single locus was independently mapped with 83 CI5791 × Golden Promise F2 individuals (166 recombinant gametes) and 180 genome wide SNPs that colocalized to the same Spt2 locus. The CI5791 genome was sequenced using PacBio Continuous Long Read technology and comparative analysis between CI5791 and the publicly available Golden Promise genome assembly determined that the delimited region contained a single high confidence Spt2 candidate gene predicted to encode a pentatricopeptide repeat-containing protein.
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Affiliation(s)
- Shaun J Clare
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Abdullah F Alhashel
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mengyuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Karl M Effertz
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Dewey Scientific, Pullman, WA, 99163, USA
| | - Roshan Sharma Poudel
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
- Syngenta Seed Inc, Durham, NC, 27709, USA
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Robert S Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
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6
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Liu Z, Yang F, Deng C, Wan H, Tang H, Feng J, Wang Q, Yang N, Li J, Yang W. Chromosome-level assembly of the synthetic hexaploid wheat-derived cultivar Chuanmai 104. Sci Data 2024; 11:670. [PMID: 38909086 PMCID: PMC11193762 DOI: 10.1038/s41597-024-03527-2] [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] [Received: 03/01/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024] Open
Abstract
Synthetic hexaploid wheats (SHWs) are effective genetic resources for transferring agronomically important genes from wild relatives to common wheat (Triticum aestivum L.). Dozens of reference-quality pseudomolecule assemblies of hexaploid wheat have been generated, but none is reported for SHW-derived cultivars. Here, we generated a chromosome-scale assembly for the SHW-derived cultivar 'Chuanmai 104' based on PacBio HiFi reads and chromosome conformation capture sequencing. The total assembly size was 14.81 Gb with a contig N50 length of 58.25 Mb. A BUSCO analysis yielded a completeness score of 99.30%. In total, repetitive elements comprised 81.36% of the genome and 122,554 high-confidence protein-coding gene models were predicted. In summary, the first chromosome-level assembly for a SHW-derived cultivar presents a promising outlook for the study and utilization of SHWs in wheat improvement, which is essential to meet the global food demand.
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Affiliation(s)
- Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Fan Yang
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Cao Deng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Departments of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Hao Tang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Junyan Feng
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qin Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Ning Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China.
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China.
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China.
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China.
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7
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Djari A, Madignier G, Di Valentin O, Gillet T, Frasse P, Djouhri A, Hu G, Julliard S, Liu M, Zhang Y, Regad F, Pirrello J, Maza E, Bouzayen M. Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine. Proc Natl Acad Sci U S A 2024; 121:e2403750121. [PMID: 38805269 PMCID: PMC11161759 DOI: 10.1073/pnas.2403750121] [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: 03/04/2024] [Accepted: 04/23/2024] [Indexed: 05/30/2024] Open
Abstract
Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous Vitis vinifera cultivars by combining high-fidelity long-read sequencing and high-throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar. The deletions/insertions, inversions, translocations, and duplications provide insight into the evolutionary history and parental relationship among grape varieties. Integration of de novo single long-read sequencing of full-length transcript isoforms (Iso-Seq) yielded a highly improved genome annotation. Given its higher contiguity, and the robustness of the IsoSeq-based annotation, the Chasselas assembly meets the standard to become the annotated reference genome for V. vinifera. Building on these resources, we developed VitExpress, an open interactive transcriptomic platform, that provides a genome browser and integrated web tools for expression profiling, and a set of statistical tools (StatTools) for the identification of highly correlated genes. Implementation of the correlation finder tool for MybA1, a major regulator of the anthocyanin pathway, identified candidate genes associated with anthocyanin metabolism, whose expression patterns were experimentally validated as discriminating between black and white grapes. These resources and innovative tools for mining genome-related data are anticipated to foster advances in several areas of grapevine research.
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Affiliation(s)
- Anis Djari
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
| | - Guillaume Madignier
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
- Fondation Jean Poupelain, Cognac, Javrezac16100, France
| | - Olivia Di Valentin
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
| | - Thibault Gillet
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
| | - Pierre Frasse
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
| | - Amel Djouhri
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
| | - Guojian Hu
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
- Fondation Jean Poupelain, Cognac, Javrezac16100, France
| | - Sebastien Julliard
- Conservatoire du vignoble charentais, Institut de Formation de Richemont, Cherves-Richemont16370, France
| | - Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Yang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Farid Regad
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
| | - Julien Pirrello
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
| | - Elie Maza
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
| | - Mondher Bouzayen
- Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan31326, France
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Mishina K, Kai H, Hamada M, Haraguchi Y, Oono Y, Ordon F, Komatsuda T. Series of Resistance Genes in Barley ( Hordeum vulgare) that Control Barley Yellow Mosaic Virus Multiplication and the Root-to-Leaf Systemic Movement. PLANT DISEASE 2024; 108:1719-1728. [PMID: 38173257 DOI: 10.1094/pdis-07-23-1451-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The infection of young winter barley (Hordeum vulgare L.) root system in winter by barley yellow mosaic virus (BaYMV) can lead to high yield losses. Resistance breeding is critical for managing this virus, but there are only a few reports on resistance genes that describe how the genes control BaYMV propagation and the systemic movement from the roots to the leaves. Here we report a real-time quantitative PCR analysis of the virus in barley roots and leaves carrying BaYMV resistance genes (rym1 to rym15 and an unknown gene) to elucidate the molecular mechanisms underlying the barley response to BaYMV. The resistance mechanism directly targets the virus. Moreover, the resistance genes/cultivars were classified into the following three groups according to their BaYMV titer: (i) immune (BaYMV was undetectable in the roots or leaves), (ii) partially immune (BaYMV was detected in the roots but not in the leaves), and (iii) susceptible (BaYMV was detected in the roots and leaves). Our results clarified the functions of the resistance genes in barley roots and leaves following a BaYMV infection. We anticipate our analysis to be a starting point for more understanding of the correspondence between resistance genes of Triticeae and the soil-borne viruses.
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Affiliation(s)
- Kohei Mishina
- National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroomi Kai
- Fukuoka Agricultural Research Center, Chikushino, Fukuoka 818-8577, Japan
| | - Michio Hamada
- Fukuoka Agricultural Research Center, Chikushino, Fukuoka 818-8577, Japan
| | - Yuhi Haraguchi
- Fukuoka Agricultural Research Center, Chikushino, Fukuoka 818-8577, Japan
| | - Youko Oono
- National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Quedlinburg, Germany
| | - Takao Komatsuda
- National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences (SAAS), Ji'nan, 250100 Shandong, China
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9
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Zhu H, Okiyama T, Mishina K, Kikuchi S, Sassa H, Komatsuda T, Kato T, Oono Y. Identification of Barley yellow mosaic virus Isolates Breaking rym3 Resistance in Japan. Genes (Basel) 2024; 15:697. [PMID: 38927633 PMCID: PMC11203024 DOI: 10.3390/genes15060697] [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: 04/14/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
In early spring 2018, significant mosaic disease symptoms were observed for the first time on barley leaves (Hordeum vulgare L., cv. New Sachiho Golden) in Takanezawa, Tochigi Prefecture, Japan. This cultivar carries the resistance gene rym3 (rym; resistance to yellow mosaic). Through RNA-seq analysis, Barley yellow mosaic virus (BaYMV-Takanezawa) was identified in the roots of all five plants (T01-T05) in the field. Phylogenetic analysis of RNA1, encompassing known BaYMV pathotypes I through V, revealed that it shares the same origin as isolate pathotype IV (BaYMV-Ohtawara pathotype). However, RNA2 analysis of isolates revealed the simultaneous presence of two distinct BaYMV isolates, BaYMV-Takanezawa-T01 (DRR552862, closely related to pathotype IV) and BaYMV-Takanezawa-T02 (DRR552863, closely related to pathotype III). The amino acid sequences of the BaYMV-Takanezawa isolates displayed variations, particularly in the VPg and N-terminal region of CP, containing mutations not found in other domains of the virus genome. Changes in the CI (RNA1 amino acid residue 459) and CP (RNA1 amino acid residue 2138) proteins correlated with pathogenicity. These findings underscore the importance of monitoring and understanding the genetic diversity of BaYMV for effective disease management strategies in crop breeding.
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Affiliation(s)
- Hongjing Zhu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan; (H.Z.); (K.M.)
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan; (S.K.); (H.S.)
| | - Takeshi Okiyama
- Tochigi Prefectural Agricultural Experiment Station, Kawaraya-cho 1080, Utsunomiya 320-0002, Japan; (T.O.); (T.K.)
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan; (H.Z.); (K.M.)
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan; (S.K.); (H.S.)
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan; (S.K.); (H.S.)
| | - Takao Komatsuda
- Shandong Academy of Agricultural Sciences (SAAS), Crop Research Institute, 202 Gongyebei Road, Licheng District, Jinan 250100, China;
| | - Tsuneo Kato
- Tochigi Prefectural Agricultural Experiment Station, Kawaraya-cho 1080, Utsunomiya 320-0002, Japan; (T.O.); (T.K.)
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan; (H.Z.); (K.M.)
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan; (S.K.); (H.S.)
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10
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Mahmood K, Sarup P, Oertelt L, Jahoor A, Orabi J. Assessing myBaits Target Capture Sequencing Methodology Using Short-Read Sequencing for Variant Detection in Oat Genomics and Breeding. Genes (Basel) 2024; 15:700. [PMID: 38927635 PMCID: PMC11203172 DOI: 10.3390/genes15060700] [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: 04/29/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The integration of target capture systems with next-generation sequencing has emerged as an efficient tool for exploring specific genetic regions with a high resolution and facilitating the rapid discovery of novel alleles. Despite these advancements, the application of targeted sequencing methodologies, such as the myBaits technology, in polyploid oat species remains relatively unexplored. In this study, we utilized the myBaits target capture method offered by Daicel Arbor Biosciences to detect variants and assess their reliability for variant detection in oat genomics and breeding. Ten oat genotypes were carefully chosen for targeted sequencing, focusing on specific regions on chromosome 2A to detect variants. The selected region harbors 98 genes. Precisely designed baits targeting the genes within these regions were employed for the target capture sequencing. We employed various mappers and variant callers to identify variants. After the identification of variants, we focused on the variants identified via all variants callers to assess the applicability of the myBaits sequencing methodology in oat breeding. In our efforts to validate the identified variants, we focused on two SNPs, one deletion and one insertion identified via all variant callers in the genotypes KF-318 and NOS 819111-70 but absent in the remaining eight genotypes. The Sanger sequencing of targeted SNPs failed to reproduce target capture data obtained through the myBaits technology. Similarly, the validation of deletion and insertion variants via high-resolution melting (HRM) curve analysis also failed to reproduce target capture data, again suggesting limitations in the reliability of the myBaits target capture sequencing using short-read sequencing for variant detection in the oat genome. This study shed light on the importance of exercising caution when employing the myBaits target capture strategy for variant detection in oats. This study provides valuable insights for breeders seeking to advance oat breeding efforts and marker development using myBaits target capture sequencing, emphasizing the significance of methodological sequencing considerations in oat genomics research.
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Affiliation(s)
- Khalid Mahmood
- Nordic Seed, Grindsnabevej 25, 8300 Odder, Denmark; (P.S.); (A.J.); (J.O.)
| | - Pernille Sarup
- Nordic Seed, Grindsnabevej 25, 8300 Odder, Denmark; (P.S.); (A.J.); (J.O.)
| | - Lukas Oertelt
- Nordic Seed Germany, Kirchhorster Str. 16, 31688 Nienstädt, Germany;
| | - Ahmed Jahoor
- Nordic Seed, Grindsnabevej 25, 8300 Odder, Denmark; (P.S.); (A.J.); (J.O.)
- Nordic Seed Germany, Kirchhorster Str. 16, 31688 Nienstädt, Germany;
| | - Jihad Orabi
- Nordic Seed, Grindsnabevej 25, 8300 Odder, Denmark; (P.S.); (A.J.); (J.O.)
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11
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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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12
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Du B, Wu J, Wang Q, Sun C, Sun G, Zhou J, Zhang L, Xiong Q, Ren X, Lu B. Genome-wide screening of meta-QTL and candidate genes controlling yield and yield-related traits in barley (Hordeum vulgare L.). PLoS One 2024; 19:e0303751. [PMID: 38768114 PMCID: PMC11104655 DOI: 10.1371/journal.pone.0303751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/30/2024] [Indexed: 05/22/2024] Open
Abstract
Increasing yield is an important goal of barley breeding. In this study, 54 papers published from 2001-2022 on QTL mapping for yield and yield-related traits in barley were collected, which contained 1080 QTLs mapped to the barley high-density consensus map for QTL meta-analysis. These initial QTLs were integrated into 85 meta-QTLs (MQTL) with a mean confidence interval (CI) of 2.76 cM, which was 7.86-fold narrower than the CI of the initial QTL. Among these 85 MQTLs, 68 MQTLs were validated in GWAS studies, and 25 breeder's MQTLs were screened from them. Seventeen barley orthologs of yield-related genes in rice and maize were identified within the hcMQTL region based on comparative genomics strategy and were presumed to be reliable candidates for controlling yield-related traits. The results of this study provide useful information for molecular marker-assisted breeding and candidate gene mining of yield-related traits in barley.
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Affiliation(s)
- Binbin Du
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Jia Wu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | | | - Chaoyue Sun
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Genlou Sun
- Biology Department, Saint Mary’s University, Halifax, Canada
| | - Jie Zhou
- Lu’an Academy of Agricultural Science, Lu’an, China
| | - Lei Zhang
- Lu’an Academy of Agricultural Science, Lu’an, China
| | | | - Xifeng Ren
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Baowei Lu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
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13
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Xie S, Wang F, Li M, Hu Z, Wang H, Zhang Z, Chen X, Gu Z, Zhang G, Ye L. Enhancing barley yield potential and germination rate: gene editing of HvGA20ox2 and discovery of novel allele sdw1.ZU9. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38739690 DOI: 10.1111/tpj.16798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024]
Abstract
Several dwarf and semi-dwarf genes have been identified in barley. However, only a limited number have been effectively utilized in breeding programs to cultivate lodging resistant varieties. This is due to the common association of dwarf and semi-dwarf traits with negative effects on malt quality. In this study, we employed gene editing to generate three new haplotypes of sdw1/denso candidate gene gibberellin (GA) 20-oxidase2 (GA20ox2). These haplotypes induced a dwarfing phenotype and enhancing yield potential, and promoting seed dormancy, thereby reducing pre-harvest sprouting. Moreover, β-amylase activity in the grains of the mutant lines was significantly increased, which is beneficial for malt quality. The haplotype analysis revealed significant genetic divergence of this gene during barley domestication and selection. A novel allele (sdw1.ZU9), containing a 96-bp fragment in the promoter region of HvGA20ox2, was discovered and primarily observed in East Asian and Russian barley varieties. The 96-bp fragment was associated with lower gene expression, leading to lower plant height but higher germination rate. In conclusion, HvGA20ox2 can be potentially used to develop semi-dwarf barley cultivars with high yield and improved malt quality.
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Affiliation(s)
- Shanggeng Xie
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fengyue Wang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mengdi Li
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Zhongyuan Institute, Zhejiang University, Zhengzhou, 450000, China
| | - Zengjie Hu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Han Wang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhizhong Zhang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiang Chen
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhiye Gu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Guoping Zhang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Zhongyuan Institute, Zhejiang University, Zhengzhou, 450000, China
| | - Lingzhen Ye
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Zhongyuan Institute, Zhejiang University, Zhengzhou, 450000, China
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14
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Gao G, Yan L, Cai Y, Guo Y, Jiang C, He Q, Tasnim S, Feng Z, Liu J, Zhang J, Komatsuda T, Mascher M, Yang P. Most Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley. PLANT COMMUNICATIONS 2024; 5:100828. [PMID: 38297838 PMCID: PMC11121735 DOI: 10.1016/j.xplc.2024.100828] [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: 11/15/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/02/2024]
Abstract
Tibetan weedy barleys reside at the edges of qingke (hulless barley) fields in Tibet (Xizang). The spikes of these weedy barleys contain or lack a brittle rachis, with either two- or six-rowed spikes and either hulled or hulless grains at maturity. Although the brittle rachis trait of Tibetan weedy barleys is similar to that of wild barley (Hordeum vulgare ssp. spontaneum Thell.), these plants share genetic similarity with domesticated barley. The origin of Tibetan weedy barleys continues to be debated. Here, we show that most Tibetan weedy barleys originated from cross-pollinated hybridization of domesticated barleys, followed by hybrid self-pollination and recombination between Non-brittle rachis 1 (btr1) and 2 (btr2). We discovered the specific genetic ancestry of these weedy barleys in South Asian accessions. Tibetan weedy barleys exhibit lower genetic diversity than wild and Chinese landraces/cultivars and share a close relationship with qingke, genetically differing from typical eastern and western barley populations. We classified Tibetan weedy barleys into two groups, brittle rachis (BR) and non-brittle rachis (NBR); these traits align with the haplotypes of the btr1 and btr2 genes. Whereas wild barleys carry haplotype combinations of Btr1 and Btr2, each showing lower proportions in a population, the recombinant haplotype BTR2H8+BTR1H24 is predominant in the BR group. Haplotype block analysis based on whole-genome sequencing revealed two recombination breakpoints, which are present in 80.6% and 16.8% of BR accessions according to marker-assisted analysis. Hybridization events between wild and domesticated barley were rarely detected. These findings support the notion that Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley.
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Affiliation(s)
- Guangqi Gao
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Luxi Yan
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Cai
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland, Germany
| | - Congcong Jiang
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiang He
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sarah Tasnim
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jun Liu
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Zhang
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Takao Komatsuda
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland, Germany
| | - Ping Yang
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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15
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Li B, Jia Y, Xu L, Zhang S, Long Z, Wang R, Guo Y, Zhang W, Jiao C, Li C, Xu Y. Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1282-1298. [PMID: 38124464 PMCID: PMC11022822 DOI: 10.1111/pbi.14264] [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: 05/04/2023] [Revised: 11/09/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023]
Abstract
The repeated emergence of the same trait (convergent evolution) in distinct species is an interesting phenomenon and manifests visibly the power of natural selection. The underlying genetic mechanisms have important implications to understand how the genome evolves under environmental challenges. In cereal crops, both rice and barley can develop black-coloured husk/pericarp due to melanin accumulation. However, it is unclear if this trait shares a common origin. Here, we fine-mapped the barley HvBlp gene controlling the black husk/pericarp trait and confirmed its function by gene silencing. The result was further supported by a yellow husk/pericarp mutant with deletion of the HvBlp gene, derived from gamma ray radiation of the wild-type W1. HvBlp encodes a putative tyrosine transporter homologous to the black husk gene OsBh4 in rice. Surprisingly, synteny and phylogenetic analyses showed that HvBlp and OsBh4 belonged to different lineages resulted from dispersed and tandem duplications, respectively, suggesting that the black husk/pericarp trait has emerged independently. The dispersed duplication (dated at 21.23 MYA) yielding HvBlp occurred exclusively in the common ancestor of Triticeae. HvBlp and OsBh4 displayed converged transcription in husk/pericarp tissues, contributing to the black husk/pericarp trait. Further transcriptome and metabolome data identified critical candidate genes and metabolites related to melanin production in barley. Taken together, our study described a compelling case of convergent evolution resulted from transcriptional convergence after repeated gene duplication, providing valuable genetic insights into phenotypic evolution. The identification of the black husk/pericarp genes in barley also has great potential in breeding for stress-resilient varieties with higher nutritional values.
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Affiliation(s)
- Bo Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Yong Jia
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Le Xu
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Zhoukai Long
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Rong Wang
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Ying Guo
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Wenying Zhang
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
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16
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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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17
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Li Z, Velásquez‐Zapata V, Elmore JM, Li X, Xie W, Deb S, Tian X, Banerjee S, Jørgensen HJL, Pedersen C, Wise RP, Thordal‐Christensen H. Powdery mildew effectors AVR A1 and BEC1016 target the ER J-domain protein HvERdj3B required for immunity in barley. MOLECULAR PLANT PATHOLOGY 2024; 25:e13463. [PMID: 38695677 PMCID: PMC11064805 DOI: 10.1111/mpp.13463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/06/2024] [Accepted: 04/11/2024] [Indexed: 05/05/2024]
Abstract
The barley powdery mildew fungus, Blumeria hordei (Bh), secretes hundreds of candidate secreted effector proteins (CSEPs) to facilitate pathogen infection and colonization. One of these, CSEP0008, is directly recognized by the barley nucleotide-binding leucine-rich-repeat (NLR) receptor MLA1 and therefore is designated AVRA1. Here, we show that AVRA1 and the sequence-unrelated Bh effector BEC1016 (CSEP0491) suppress immunity in barley. We used yeast two-hybrid next-generation interaction screens (Y2H-NGIS), followed by binary Y2H and in planta protein-protein interactions studies, and identified a common barley target of AVRA1 and BEC1016, the endoplasmic reticulum (ER)-localized J-domain protein HvERdj3B. Silencing of this ER quality control (ERQC) protein increased Bh penetration. HvERdj3B is ER luminal, and we showed using split GFP that AVRA1 and BEC1016 translocate into the ER signal peptide-independently. Overexpression of the two effectors impeded trafficking of a vacuolar marker through the ER; silencing of HvERdj3B also exhibited this same cellular phenotype, coinciding with the effectors targeting this ERQC component. Together, these results suggest that the barley innate immunity, preventing Bh entry into epidermal cells, requires ERQC. Here, the J-domain protein HvERdj3B appears to be essential and can be regulated by AVRA1 and BEC1016. Plant disease resistance often occurs upon direct or indirect recognition of pathogen effectors by host NLR receptors. Previous work has shown that AVRA1 is directly recognized in the cytosol by the immune receptor MLA1. We speculate that the AVRA1 J-domain target being inside the ER, where it is inapproachable by NLRs, has forced the plant to evolve this challenging direct recognition.
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Affiliation(s)
- Zizhang Li
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Present address:
Institute for Bioscience and Biotechnology Research & Department of Plant Sciences and Landscape ArchitectureUniversity of MarylandRockvilleMarylandUSA
| | - Valeria Velásquez‐Zapata
- Program in Bioinformatics & Computational BiologyIowa State UniversityAmesIowaUSA
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
- Present address:
GreenLight Biosciences, IncResearch Triangle ParkNorth CarolinaUSA
| | - J. Mitch Elmore
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
- USDA‐Agricultural Research Service, Corn Insects and Crop Genetics Research UnitAmesIowaUSA
- Present address:
USDA‐Agricultural Research Service, Cereal Disease LaboratorySt. PaulMinnesotaUSA
| | - Xuan Li
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Wenjun Xie
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Sohini Deb
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Xiao Tian
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Sagnik Banerjee
- Program in Bioinformatics & Computational BiologyIowa State UniversityAmesIowaUSA
- Department of StatisticsIowa State UniversityAmesIowaUSA
- Present address:
Bristol Myers SquibbSan DiegoCaliforniaUSA
| | - Hans J. L. Jørgensen
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Carsten Pedersen
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Roger P. Wise
- Program in Bioinformatics & Computational BiologyIowa State UniversityAmesIowaUSA
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
- USDA‐Agricultural Research Service, Corn Insects and Crop Genetics Research UnitAmesIowaUSA
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18
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Cosenza F, Shrestha A, Van Inghelandt D, Casale FA, Wu PY, Weisweiler M, Li J, Wespel F, Stich B. Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2385-2402. [PMID: 38330219 PMCID: PMC11016846 DOI: 10.1093/jxb/erae010] [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: 05/17/2023] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Despite their role in plant physiological regulation, a complete overview of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Using a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as to identify new genetic variants by single and multi-population QTL analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected new QTLs for flowering time and plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect, or low-frequency genetic variants underlie the control of these two traits.
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Affiliation(s)
- Francesco Cosenza
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Delphine Van Inghelandt
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Federico A Casale
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Po-Ya Wu
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Marius Weisweiler
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jinquan Li
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Franziska Wespel
- Saatzucht Josef Breun GmbH Co. KG, Amselweg 1, 91074 Herzogenaurach, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
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19
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Bernád V, Al-Tamimi N, Langan P, Gillespie G, Dempsey T, Henchy J, Harty M, Ramsay L, Houston K, Macaulay M, Shaw PD, Raubach S, Mcdonnel KP, Russell J, Waugh R, Khodaeiaminjan M, Negrão S. Unlocking the genetic diversity and population structure of the newly introduced two-row spring European HerItage Barley collecTion (ExHIBiT). FRONTIERS IN PLANT SCIENCE 2024; 15:1268847. [PMID: 38571708 PMCID: PMC10987740 DOI: 10.3389/fpls.2024.1268847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
In the last century, breeding programs have traditionally favoured yield-related traits, grown under high-input conditions, resulting in a loss of genetic diversity and an increased susceptibility to stresses in crops. Thus, exploiting understudied genetic resources, that potentially harbour tolerance genes, is vital for sustainable agriculture. Northern European barley germplasm has been relatively understudied despite its key role within the malting industry. The European Heritage Barley collection (ExHIBiT) was assembled to explore the genetic diversity in European barley focusing on Northern European accessions and further address environmental pressures. ExHIBiT consists of 363 spring-barley accessions, focusing on two-row type. The collection consists of landraces (~14%), old cultivars (~18%), elite cultivars (~67%) and accessions with unknown breeding history (~1%), with 70% of the collection from Northern Europe. The population structure of the ExHIBiT collection was subdivided into three main clusters primarily based on the accession's year of release using 26,585 informative SNPs based on 50k iSelect single nucleotide polymorphism (SNP) array data. Power analysis established a representative core collection of 230 genotypically and phenotypically diverse accessions. The effectiveness of this core collection for conducting statistical and association analysis was explored by undertaking genome-wide association studies (GWAS) using 24,876 SNPs for nine phenotypic traits, four of which were associated with SNPs. Genomic regions overlapping with previously characterised flowering genes (HvZTLb) were identified, demonstrating the utility of the ExHIBiT core collection for locating genetic regions that determine important traits. Overall, the ExHIBiT core collection represents the high level of untapped diversity within Northern European barley, providing a powerful resource for researchers and breeders to address future climate scenarios.
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Affiliation(s)
- Villő Bernád
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Nadia Al-Tamimi
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Patrick Langan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Gary Gillespie
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Timothy Dempsey
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Joey Henchy
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Mary Harty
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Paul D. Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Kevin P. Mcdonnel
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- School of Biosystems Engineering, University College Dublin, Dublin, Ireland
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee, United Kingdom
| | | | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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20
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Basak P, Gurjar MS, Kumar TPJ, Kashyap N, Singh D, Jha SK, Saharan MS. Transcriptome analysis of Bipolaris sorokiniana - Hordeum vulgare provides insights into mechanisms of host-pathogen interaction. Front Microbiol 2024; 15:1360571. [PMID: 38577688 PMCID: PMC10993733 DOI: 10.3389/fmicb.2024.1360571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/01/2024] [Indexed: 04/06/2024] Open
Abstract
Spot blotch disease incited by Bipolaris sorokiniana severely affects the cultivation of barley. The resistance to B. sorokiniana is quantitative in nature and its interaction with the host is highly complex which necessitates in-depth molecular analysis. Thus, the study aimed to conduct the transcriptome analysis to decipher the mechanisms and pathways involved in interactions between barley and B. sorokiniana in both the resistant (EC0328964) and susceptible (EC0578292) genotypes using the RNA Seq approach. In the resistant genotype, 6,283 genes of Hordeum vulgare were differentially expressed out of which 5,567 genes were upregulated and 716 genes were downregulated. 1,158 genes of Hordeum vulgare were differentially expressed in the susceptible genotype, out of which 654 genes were upregulated and 504 genes were downregulated. Several defense-related genes like resistant gene analogs (RGAs), disease resistance protein RPM1, pathogenesis-related protein PRB1-2-like, pathogenesis-related protein 1, thaumatin-like protein PWIR2 and defensin Tm-AMP-D1.2 were highly expressed exclusively in resistant genotype only. The pathways involved in the metabolism and biosynthesis of secondary metabolites were the most prominently represented pathways in both the resistant and susceptible genotypes. However, pathways involved in MAPK signaling, plant-pathogen interaction, and plant hormone signal transduction were highly enriched in resistant genotype. Further, a higher number of pathogenicity genes of B. sorokiniana was found in response to the susceptible genotype. The pathways encoding for metabolism, biosynthesis of secondary metabolites, ABC transporters, and ubiquitin-mediated proteolysis were highly expressed in susceptible genotype in response to the pathogen. 14 and 11 genes of B. sorokiniana were identified as candidate effectors from susceptible and resistant host backgrounds, respectively. This investigation will offer valuable insights in unraveling the complex mechanisms involved in barley- B. sorokiniana interaction.
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Affiliation(s)
- Poulami Basak
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Malkhan Singh Gurjar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Natasha Kashyap
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Dinesh Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra Kumar Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mahender Singh Saharan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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21
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Tucker JR, Badea A, Blackwell BA, MacEachern D, Mills A. Bringing Barley Back: Analysis of Heritage Varieties for Use as Germplasm Sources to Improve Resistance against the Most Devastating, Contemporary Disease in Canada, Fusarium Head Blight ( Fusarium graminearum). PLANTS (BASEL, SWITZERLAND) 2024; 13:799. [PMID: 38592826 PMCID: PMC10974673 DOI: 10.3390/plants13060799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Fusarium head blight (FHB), caused by Fusarium graminearum, is currently the most devastating disease for barley (Hordeum vulgare) in Canada. Associated mycotoxins can compromise grain quality, where deoxynivalenol (DON) is considered particularly damaging due to its frequency of detection. Breeding barley with a lower DON content is difficult, due to the poor adaptation and malt quality of resistance sources. A set of European-derived heritage varieties were screened in an FHB nursery in Charlottetown, PE, with selections tested at Brandon, MB, between 2018-2022. Genetic evaluation demonstrated a distinct clustering of Canadian varieties from the heritage set. At Brandon, 72% of the heritage varieties ranked lower for DON content than did the moderately resistant Canadian check 'AAC Goldman', but resistance was associated with later heading and taller stature. In contrast with Canadian modern malting variety 'AAC Synergy', general deficiencies were observed in yield, enzyme activity, and extract, along with higher protein content. Nonetheless, several resistant varieties were identified with reasonable a heading date and yield, including 'Chevallier Chile', 'Domen', 'Djugay', 'Hannchen', 'Heils Franken', 'Moravian Barley', 'Loosdorfer' with 'Golden Melon', 'Nutans Moskva', and 'Vellavia', these being some of the most promising varieties when malting quality characteristics were also considered. These heritage resources could be used as parents in breeding to develop FHB-resistant malting barley varieties.
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Affiliation(s)
- James R. Tucker
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB R7A 5Y3, Canada;
| | - Ana Badea
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB R7A 5Y3, Canada;
| | - Barbara A. Blackwell
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
| | - Dan MacEachern
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada; (D.M.); (A.M.)
| | - Aaron Mills
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada; (D.M.); (A.M.)
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22
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Vinje MA, Simmons CH. Characterization of barley (Horduem vulgare) lys3 mutants identifies genes under the regulation of the prolamin-box binding transcription factor and elucidates its role in endosperm promoter methylation during grain development. Mol Genet Genomics 2024; 299:17. [PMID: 38416243 DOI: 10.1007/s00438-024-02112-x] [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: 09/26/2023] [Accepted: 12/24/2023] [Indexed: 02/29/2024]
Abstract
Barley ranks fourth in global cereal production and is primarily grown for animal feed and malt. Hordeins, the principal barley seed storage proteins, are homologous to wheat gluten and when ingested elicit an immune response in people with Coeliac disease. Risø 1508 is a chemically induced barley mutant with low hordein levels imparted by the lys3.a locus that is reported to be caused by an SNP in the barley prolamin-box binding factor gene (BPBF). Reports suggest the lys3.a locus prevents CG DNA demethylation at the Hor2 (B-hordein) promoter during grain development subsequently causing hypermethylation and inhibiting gene expression. In lys3.a mutants, endosperm-specific β-amylase (Bmy1) and Hor2 are similarly downregulated during grain development and thus we hypothesize that the inability to demethylate the Bmy1 promoter CG islands is also causing Bmy1 downregulation. We use whole-genome bisulfite sequencing and mRNA-seq on developing endosperms from two lys3.a mutants and a lys3.b mutant to determine all downstream genes affected by lys3 mutations. RNAseq analysis identified 306 differentially expressed genes (DEGs) shared between all mutants and their parents and 185 DEGs shared between both lys3.a mutants and their parents. Global DNA methylation levels and promoter CG DNA methylation levels were not significantly different between the mutants and their parents and thus refute the hypothesis that the lys3.a mutant's phenotype is caused by dysregulation of demethylation during grain development. The majority of DEGs were downregulated (e.g., B- and C-hordeins and Bmy1), but some DEGs were upregulated (e.g., β-glucosidase, D-hordein) suggesting compensatory effects and potentially explaining the low β-glucan phenotype observed in lys3.a germplasm. These findings have implications on human health and provide novel insight to barley breeders regarding the use of BPBF transcription factor mutants to create gluten-free barley varieties.
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Affiliation(s)
- Marcus A Vinje
- USDA, Agricultural Research Service, Cereal Crops Research Unit, Madison, WI, 53726, USA.
| | - Carl H Simmons
- USDA, Agricultural Research Service, Cereal Crops Research Unit, Madison, WI, 53726, USA
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23
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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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24
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Hong Y, Zhang M, Zhu J, Zhang Y, Lv C, Guo B, Wang F, Xu R. Genome-wide association studies reveal novel loci for grain size in two-rowed barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:58. [PMID: 38407646 DOI: 10.1007/s00122-024-04562-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024]
Abstract
KEY MESSAGE SNP-based and InDel-based GWAS on multi-environment data identified genomic regions associated with barley grain size. Barley yield and quality are greatly influenced by grain size. Improving barley grain size in breeding programs requires knowledge of genetic loci and alleles in germplasm resources. In this study, a collection of 334 worldwide two-rowed barley accessions with extensive genetic diversity was evaluated for grain size including grain length (GL), grain width (GW), and thousand-grain weight (TGW) across six independent field trials. Significant differences were observed in genotype and environments for all measured traits. SNP- and InDel-based GWAS were applied to dissect the genetic architecture of grain size with an SLAF-seq strategy. Two approaches using the FarmCPU model revealed 38 significant marker-trait associations (MTAs) with PVE ranging from 0.01% to 20.68%. Among these MTAs, five were on genomic regions where no previously reported QTL for grain size. Superior alleles of TGW-associated SNP233060 and GL-associated InDel11006 exhibited significantly higher levels of phenotype. The significant MTAs could be used in marker-assisted selection breeding.
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Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Juan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yuhang Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Chao Lv
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Baojian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Feifei Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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25
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Gao S, Su Z, Ma J, Ma J, Liu C, Li H, Zheng Z. Identification of a novel and plant height-independent QTL for coleoptile length in barley and validation of its effect using near isogenic lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:53. [PMID: 38381194 PMCID: PMC10881613 DOI: 10.1007/s00122-024-04561-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
KEY MESSAGE This study reported the identification and validation of novel QTL conferring coleoptile length in barley and predicted candidate genes underlying the largest effect QTL based on orthologous analysis and comparison of the whole genome assemblies for both parental genotypes of the mapping population. Coleoptile length (CL) is one of the most important agronomic traits in cereal crops due to its direct influence on the optimal depth for seed sowing which facilitates better seedling establishment. Varieties with longer coleoptiles are preferred in drought-prone areas where less moisture maintains at the top layer of the soil. Compared to wheat, genetic study on coleoptile length is limited in barley. Here, we reported a study on detecting the genomic regions associated with CL in barley by assessing a population consisting of 201 recombinant inbred lines. Four putative QTL conferring CL were consistently identified on chromosomes 1H, 5H, 6H, and 7H in each of the trials conducted. Of these QTL, the two located on chromosomes 5H and 6H (designated as Qcl.caf-5H and Qcl.caf-6H) are likely novel and Qcl.caf-5H showed the most significant effect explaining up to 30.9% of phenotypic variance with a LOD value of 15.1. To further validate the effect of this putative QTL, five pairs of near isogenic lines (NILs) were then developed and assessed. Analysis of the NILs showed an average difference of 21.0% in CL between the two isolines. Notably, none of the other assessed morphological characteristics showed consistent differences between the two isolines for each pair of the NILs. Candidate genes underlying the Qcl.caf-5H locus were also predicted by employing orthologous analysis and comparing the genome assemblies for both parental genotypes of the mapping population in the present study. Taken together, these findings expand our understanding on genetic basis of CL and will be indicative for further gene cloning and functional analysis underly this locus in barley.
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Affiliation(s)
- Shang Gao
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China
| | - Zhouyang Su
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, 7205, Australia
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Huihui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China.
| | - Zhi Zheng
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
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26
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Vladejić J, Kovacik M, Zwyrtková J, Szurman-Zubrzycka M, Doležel J, Pecinka A. Zeocin-induced DNA damage response in barley and its dependence on ATR. Sci Rep 2024; 14:3119. [PMID: 38326519 PMCID: PMC10850495 DOI: 10.1038/s41598-024-53264-0] [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: 07/11/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
DNA damage response (DDR) is an essential mechanism by which living organisms maintain their genomic stability. In plants, DDR is important also for normal growth and yield. Here, we explored the DDR of a temperate model crop barley (Hordeum vulgare) at the phenotypic, physiological, and transcriptomic levels. By a series of in vitro DNA damage assays using the DNA strand break (DNA-SB) inducing agent zeocin, we showed reduced root growth and expansion of the differentiated zone to the root tip. Genome-wide transcriptional profiling of barley wild-type and plants mutated in DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (hvatr.g) revealed zeocin-dependent, ATR-dependent, and zeocin-dependent/ATR-independent transcriptional responses. Transcriptional changes were scored also using the newly developed catalog of 421 barley DDR genes with the phylogenetically-resolved relationships of barley SUPRESSOR OF GAMMA 1 (SOG1) and SOG1-LIKE (SGL) genes. Zeocin caused up-regulation of specific DDR factors and down-regulation of cell cycle and histone genes, mostly in an ATR-independent manner. The ATR dependency was obvious for some factors associated with DDR during DNA replication and for many genes without an obvious connection to DDR. This provided molecular insight into the response to DNA-SB induction in the large and complex barley genome.
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Affiliation(s)
- Jovanka Vladejić
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Martin Kovacik
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jana Zwyrtková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia.
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27
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Jöst M, Soltani O, Kappel C, Janiak A, Chmielewska B, Szurman-Zubrzycka M, McKim SM, Lenhard M. The gain-of-function mutation blf13 in the barley orthologue of the rice growth regulator NARROW LEAF1 is associated with increased leaf width. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:850-867. [PMID: 37837419 DOI: 10.1093/jxb/erad403] [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: 05/23/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023]
Abstract
Canopy architecture in cereals plays an important role in determining yield. Leaf width represents one key aspect of this canopy architecture. However, our understanding of leaf width control in cereals remains incomplete. Classical mutagenesis studies in barely identified multiple morphological mutants, including those with differing leaf widths. Of these, we characterized the broad leaf13 (blf13) mutant in detail. Mutant plants form wider leaves due to increased post-initiation growth and cell proliferation. The mutant phenotype perfectly co-segregated with a missense mutation in the HvHNT1 gene which affected a highly conserved region of the encoded protein, orthologous to the rice NARROW LEAF1 (NAL1) protein. Causality of this mutation for the blf13 phenotype is further supported by correlative transcriptomic analyses and protein-protein interaction studies showing that the mutant HvNHT1 protein interacts more strongly with a known interactor than wild-type HvHNT1. The mutant HvHNT1 protein also showed stronger homodimerization compared with wild-type HvHNT1, and homology modelling suggested an additional interaction site between HvHNT1 monomers due to the blf13 mutation. Thus, the blf13 mutation parallels known gain-of-function NAL1 alleles in rice that increase leaf width and grain yield, suggesting that the blf13 mutation may have a similar agronomic potential in barley.
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Affiliation(s)
- Moritz Jöst
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ouad Soltani
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Agnieszka Janiak
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Poland
| | - Beata Chmielewska
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Poland
| | - Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Poland
| | - Sarah M McKim
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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28
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Aleksza D, Spiridon A, Tarkka M, Hauser MT, Hann S, Causon T, Kratena N, Stanetty C, George TS, Russell J, Oburger E. Phytosiderophore pathway response in barley exposed to iron, zinc or copper starvation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111919. [PMID: 37992897 DOI: 10.1016/j.plantsci.2023.111919] [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: 07/18/2023] [Revised: 10/04/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
Efficient micronutrient acquisition is a critical factor in selecting micronutrient dense crops for human consumption. Enhanced exudation and re-uptake of metal chelators, so-called phytosiderophores, by roots of graminaceous plants has been implicated in efficient micronutrient acquisition. We compared PS biosynthesis and exudation as a response mechanism to either Fe, Zn or Cu starvation. Two barley (Hordeum vulgare L.) lines with contrasting micronutrient grain yields were grown hydroponically and PS exudation (LC-MS) and root gene expression (RNAseq) were determined after either Fe, Zn, or Cu starvation. The response strength of the PS pathway was micronutrient dependent and decreased in the order Fe > Zn > Cu deficiency. We observed a stronger expression of PS pathway genes and greater PS exudation in the barley line with large micronutrient grain yield suggesting that a highly expressed PS pathway might be an important trait involved in high micronutrient accumulation. In addition to several metal specific transporters, we also found that the expression of IRO2 and bHLH156 transcription factors was not only induced under Fe but also under Zn and Cu deficiency. Our study delivers important insights into the role of the PS pathway in the acquisition of different micronutrients.
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Affiliation(s)
- David Aleksza
- University of Natural Resources and Life Sciences, Department of Forest and Soil Science, Institute of Soil Research, Konrad-Lorenz Strasse 24, Tulln an der Donau 3430, Austria; University of Natural Resources and Life Sciences, Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Andreea Spiridon
- University of Natural Resources and Life Sciences, Department of Forest and Soil Science, Institute of Soil Research, Konrad-Lorenz Strasse 24, Tulln an der Donau 3430, Austria
| | - Mika Tarkka
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil Ecology, Theodor-Lieser-Strasse 4, D-06120 Halle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Marie-Theres Hauser
- University of Natural Resources and Life Sciences, Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Stephan Hann
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Analytical Chemistry, Muthgasse 18, 1190 Vienna, Austria
| | - Tim Causon
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Analytical Chemistry, Muthgasse 18, 1190 Vienna, Austria
| | - Nicolas Kratena
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060 Vienna, Austria
| | - Christian Stanetty
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060 Vienna, Austria
| | | | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Eva Oburger
- University of Natural Resources and Life Sciences, Department of Forest and Soil Science, Institute of Soil Research, Konrad-Lorenz Strasse 24, Tulln an der Donau 3430, Austria.
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29
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Helmsorig G, Walla A, Rütjes T, Buchmann G, Schüller R, Hensel G, von Korff M. early maturity 7 promotes early flowering by controlling the light input into the circadian clock in barley. PLANT PHYSIOLOGY 2024; 194:849-866. [PMID: 37951242 PMCID: PMC10828213 DOI: 10.1093/plphys/kiad551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/26/2023] [Indexed: 11/13/2023]
Abstract
Breeding for variation in photoperiod response is crucial to adapt crop plants to various environments. Plants measure changes in day length by the circadian clock, an endogenous timekeeper that allows plants to anticipate changes in diurnal and seasonal light-dark cycles. Here, we describe the early maturity 7 (eam7) locus in barley (Hordeum vulgare), which interacts with PHOTOPERIOD 1 (Ppd-H1) to cause early flowering under non-inductive short days. We identify LIGHT-REGULATED WD 1 (LWD1) as a putative candidate to underlie the eam7 locus in barley as supported by genetic mapping and CRISPR-Cas9-generated lwd1 mutants. Mutations in eam7 cause a significant phase advance and a misregulation of core clock and clock output genes under diurnal conditions. Early flowering was linked to an upregulation of Ppd-H1 during the night and consequent induction of the florigen FLOWERING LOCUS T1 under short days. We propose that EAM7 controls photoperiodic flowering in barley by controlling the light input into the clock and diurnal expression patterns of the major photoperiod response gene Ppd-H1.
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Affiliation(s)
- Gesa Helmsorig
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Agatha Walla
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Thea Rütjes
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Gabriele Buchmann
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Rebekka Schüller
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Götz Hensel
- Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow's Needs”, 40223 Düsseldorf, Germany
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
- Division of Molecular Biology, Centre of the Region Hana for Biotechnological and Agriculture Research, Faculty of Science, Palacký University, CZ-779 00 Olomouc, Czech
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow's Needs”, 40223 Düsseldorf, Germany
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30
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Brabham HJ, Gómez De La Cruz D, Were V, Shimizu M, Saitoh H, Hernández-Pinzón I, Green P, Lorang J, Fujisaki K, Sato K, Molnár I, Šimková H, Doležel J, Russell J, Taylor J, Smoker M, Gupta YK, Wolpert T, Talbot NJ, Terauchi R, Moscou MJ. Barley MLA3 recognizes the host-specificity effector Pwl2 from Magnaporthe oryzae. THE PLANT CELL 2024; 36:447-470. [PMID: 37820736 PMCID: PMC10827324 DOI: 10.1093/plcell/koad266] [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] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat (NLRs) immune receptors directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley (Hordeum vulgare) NLR gene Mildew locus a (Mla) has undergone functional diversification, and the proteins encoded by different Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei [Bgh]). Here, we show that Mla3 also confers resistance to the rice blast fungus Magnaporthe oryzae in a dosage-dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is Pathogenicity toward Weeping Lovegrass 2 (Pwl2), a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.
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Affiliation(s)
- Helen J Brabham
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- 2Blades, Evanston, IL 60201, USA
| | - Diana Gómez De La Cruz
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Vincent Were
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Motoki Shimizu
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
| | - Hiromasa Saitoh
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | | | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jennifer Lorang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Koki Fujisaki
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - James Russell
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yogesh Kumar Gupta
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- 2Blades, Evanston, IL 60201, USA
| | - Tom Wolpert
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ryohei Terauchi
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto 617-0001, Japan
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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31
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Kazakova E, Gorbatova I, Khanova A, Shesterikova E, Pishenin I, Prazyan A, Podlutskii M, Blinova Y, Bitarishvili S, Bondarenko E, Smirnova A, Lychenkova M, Bondarenko V, Korol M, Babina D, Makarenko E, Volkova P. Radiation Hormesis in Barley Manifests as Changes in Growth Dynamics Coordinated with the Expression of PM19L-like, CML31-like, and AOS2-like. Int J Mol Sci 2024; 25:974. [PMID: 38256048 PMCID: PMC10815718 DOI: 10.3390/ijms25020974] [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: 12/13/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
The stimulation of growth and development of crops using ionising radiation (radiation hormesis) has been reported by many research groups. However, specific genes contributing to the radiation stimulation of plant growth are largely unknown. In this work, we studied the impact of the low-dose γ-irradiation of barley seeds on the growth dynamics and gene expression of eight barley cultivars in a greenhouse experiment. Our findings confirmed that candidate genes of the radiation growth stimulation, previously established in barley seedlings (PM19L-like, CML31-like, and AOS2-like), are significant in radiation hormesis throughout ontogeny. In γ-stimulated cultivars, the expression of these genes was aligned with the growth dynamics, yield parameters, and physiological conditions of plants. We identified contrasting cultivars for future gene editing and found that the γ-stimulated cultivar possessed some specific abiotic stress-responsive elements in the promotors of candidate genes, possibly revealing a new level of radiation hormesis effect execution. These results can be used in creating new productive barley cultivars, ecological toxicology of radionuclides, and eustress biology studies.
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Affiliation(s)
- Elizaveta Kazakova
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Irina Gorbatova
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Anastasia Khanova
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Ekaterina Shesterikova
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Ivan Pishenin
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Alexandr Prazyan
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Mikhail Podlutskii
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Yana Blinova
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Sofia Bitarishvili
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Ekaterina Bondarenko
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Alena Smirnova
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Maria Lychenkova
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Vladimir Bondarenko
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Marina Korol
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Daria Babina
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
| | - Ekaterina Makarenko
- Laboratory of Molecular and Cellular Radiobiology, Russian Institute of Radiology and Agroecology of National Research Centre “Kurchatov Institute”, 249035 Obninsk, Russia; (E.K.); (I.G.); (A.K.); (E.S.); (I.P.); (A.P.); (Y.B.); (S.B.); (E.B.); (A.S.); (M.L.); (V.B.); (M.K.); (D.B.)
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Du B, Wu J, Wang M, Wu J, Sun C, Zhang X, Ren X, Wang Q. Detection of consensus genomic regions and candidate genes for quality traits in barley using QTL meta-analysis. FRONTIERS IN PLANT SCIENCE 2024; 14:1319889. [PMID: 38283973 PMCID: PMC10811794 DOI: 10.3389/fpls.2023.1319889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
Improving barley grain quality is a major goal in barley breeding. In this study, a total of 35 papers focusing on quantitative trait loci (QTLs) mapping for barley quality traits published since 2000 were collected. Among the 454 QTLs identified in these studies, 349 of them were mapped onto high-density consensus maps, which were used for QTL meta-analysis. Through QTL meta-analysis, the initial QTLs were integrated into 41 meta-QTLs (MQTLs) with an average confidence interval (CI) of 1. 66 cM, which is 88.9% narrower than that of the initial QTLs. Among the 41 identified MQTLs, 25 were subsequently validated in publications using genome-wide association study (GWAS). From these 25 validated MQTLs, ten breeder's MQTLs were selected. Synteny analysis comparing barley and wheat MQTLs revealed orthologous relationships between eight breeder's MQTLs and 45 wheat MQTLs. Additionally, 17 barley homologs associated with rice quality traits were identified within the regions of the breeder's MQTLs through comparative analysis. The findings of this study provide valuable insights for molecular marker-assisted breeding and the identification of candidate genes related to quality traits in barley.
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Affiliation(s)
- Binbin Du
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Jindong Wu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Meng Wang
- Xingtai Agriculture and Rural Bureau, Xingtai, Hebei, China
| | - Jia Wu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Chaoyue Sun
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Xingen Zhang
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Xifeng Ren
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qifei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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Cheng J, Jia Y, Hill C, He T, Wang K, Guo G, Shabala S, Zhou M, Han Y, Li C. Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement. J Adv Res 2024:S2090-1232(23)00408-3. [PMID: 38199453 DOI: 10.1016/j.jare.2023.12.021] [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: 05/27/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
INTRODUCTION Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the "Green Revolution", modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known. OBJECTIVES This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits. METHODS Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8a in barley and RNA-seq was conducted to compare the transcriptome between wild type and mutants. Also, field trials in multiple environments were performed to detect the functional haplotypes. RESULTS There were ten GA2oxs that distinctly expressed in shoot, tiller, inflorescence, grain, embryo and root. Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA4 level. RNA-seq analysis revealed that genes involved in starch and sucrose metabolism were significantly decreased in the inflorescence of ga2ox8a mutants. Furthermore, haplotype analysis revealed one naturally occurring HvGA2ox8a haplotype was associated with decreased plant height, early flowering and wider and heavier seed. CONCLUSION Our results demonstrate the potential of manipulating GA2ox genes to fine tune GA signalling and biofunctions in desired plant tissues and open a promising avenue for minimising the trade-off effects of Green Revolution semi-dwarfing genes on grain size and weight. The knowledge will promote the development of next generation barley cultivars with better adaptation to a changing climate.
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Affiliation(s)
- Jingye Cheng
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia; Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Jia
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Camilla Hill
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia
| | - Tianhua He
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia
| | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ganggang Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia.
| | - Yong Han
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
| | - Chengdao Li
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
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Li Y, Wei ZZ, Sela H, Govta L, Klymiuk V, Roychowdhury R, Chawla HS, Ens J, Wiebe K, Bocharova V, Ben-David R, Pawar PB, Zhang Y, Jaiwar S, Molnár I, Doležel J, Coaker G, Pozniak CJ, Fahima T. Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69. PLANT COMMUNICATIONS 2024; 5:100646. [PMID: 37415333 PMCID: PMC10811346 DOI: 10.1016/j.xplc.2023.100646] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/10/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023]
Abstract
Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.
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Affiliation(s)
- Yinghui Li
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Zhen-Zhen Wei
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Hanan Sela
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Liubov Govta
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Rajib Roychowdhury
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Harmeet Singh Chawla
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Jennifer Ens
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Krystalee Wiebe
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Valeria Bocharova
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Roi Ben-David
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO) - Volcani Center, Rishon Lezion 7505101, Israel
| | - Prerna B Pawar
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Yuqi Zhang
- Department of Crop Genomics and Bioinformatics, China Agricultural University, Beijing 100094, China
| | - Samidha Jaiwar
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Gitta Coaker
- Plant Pathology Department, University of California, Davis, Davis, CA 95616, USA
| | - Curtis J Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel.
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Xia X, Liu L, Cai K, Song X, Yue W, Wang J. A splicing site change between exon 5 and 6 of the nuclear-encoded chloroplast-localized HvYGL8 gene results in reduced chlorophyll content and plant height in barley. FRONTIERS IN PLANT SCIENCE 2023; 14:1327246. [PMID: 38192692 PMCID: PMC10773589 DOI: 10.3389/fpls.2023.1327246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
The chloroplast is an important cellular organelle and metabolic hub, which is not only responsible for plant photosynthesis but is also involved in the de novo biosynthesis of pigments, fatty acids, and hormone metabolisms. Several genes that are responsible for rice leaf color variations have been reported to be directly or indirectly involved in chlorophyll biosynthesis and chloroplast development, whereas a few genes have been functionally confirmed to be responsible for leaf color changes in barley at the molecular level. In this study, we obtained a yellow leaf and dwarf ygl8 mutant from the progeny of Morex (a variety of barley) seeds treated with EMS. We performed bulked-segregant analysis (BSA) and RNA-seq analysis and targeted a UMP kinase encoding gene, YGL8, which generated a splicing site change between exon 5 and 6 of YGL8 due to a G to A single-nucleotide transition in the 5th exon/intron junction in the ygl8 mutant. The splicing site change between exon 5 and 6 of YGL8 had no effects on chloroplast subcellular localization but resulted in an additional loop in the UMP kinase domain, which might disturb the access of the substrates. On one hand, the splicing site change between exon 5 and 6 of YGL8 downregulated the transcriptional expression of chloroplast-encoded genes and chlorophyll-biosynthesis-related genes in a temperature-dependent manner in the ygl8 mutant. On the other hand, the downregulation of bioactive GA-biosynthesis-related GA20ox genes and cell-wall-cellulose-biosynthesis-related CesA genes was also observed in the ygl8 mutant, which led to a reduction in plant height. Our study will facilitate the understanding of the regulation of leaf color and plant height in barley.
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Affiliation(s)
- Xue Xia
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
- College of Advanced Agricultural Sciences, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Lei Liu
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
| | - Kangfeng Cai
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
| | - Xiujuan Song
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
- College of Advanced Agricultural Sciences, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Wenhao Yue
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
| | - Junmei Wang
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
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Ahmar S, Hensel G, Gruszka D. CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives. Biotechnol Adv 2023; 69:108248. [PMID: 37666372 DOI: 10.1016/j.biotechadv.2023.108248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland.
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Qian J, Ibrahim HMM, Erz M, Kümmel F, Panstruga R, Kusch S. Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen. Mob DNA 2023; 14:17. [PMID: 37964319 PMCID: PMC10648671 DOI: 10.1186/s13100-023-00305-6] [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: 08/07/2023] [Accepted: 10/18/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND The genome of the obligate biotrophic phytopathogenic barley powdery mildew fungus Blumeria hordei is inflated due to highly abundant and possibly active transposable elements (TEs). In the absence of the otherwise common repeat-induced point mutation transposon defense mechanism, noncoding RNAs could be key for regulating the activity of TEs and coding genes during the pathogenic life cycle. RESULTS We performed time-course whole-transcriptome shotgun sequencing (RNA-seq) of total RNA derived from infected barley leaf epidermis at various stages of fungal pathogenesis and observed significant transcript accumulation and time point-dependent regulation of TEs in B. hordei. Using a manually curated consensus database of 344 TEs, we discovered phased small RNAs mapping to 104 consensus transposons, suggesting that RNA interference contributes significantly to their regulation. Further, we identified 5,127 long noncoding RNAs (lncRNAs) genome-wide in B. hordei, of which 823 originated from the antisense strand of a TE. Co-expression network analysis of lncRNAs, TEs, and coding genes throughout the asexual life cycle of B. hordei points at extensive positive and negative co-regulation of lncRNAs, subsets of TEs and coding genes. CONCLUSIONS Our work suggests that similar to mammals and plants, fungal lncRNAs support the dynamic modulation of transcript levels, including TEs, during pivotal stages of host infection. The lncRNAs may support transcriptional diversity and plasticity amid loss of coding genes in powdery mildew fungi and may give rise to novel regulatory elements and virulence peptides, thus representing key drivers of rapid evolutionary adaptation to promote pathogenicity and overcome host defense.
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Affiliation(s)
- Jiangzhao Qian
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Heba M M Ibrahim
- Department of Biosystems, Division of Plant Biotechnics, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, 3001, Leuven, Belgium
- Present address: Institute of Bio- and Geosciences IBG-2, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Myriam Erz
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
- Present address: Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-Von-Linné-Weg 10, 50829, Cologne, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
- Present address: Institute of Bio- and Geosciences IBG-4, Forschungszentrum Jülich, 52425, Jülich, Germany.
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Chen G, Mishina K, Wang Q, Zhu H, Tagiri A, Kikuchi S, Sassa H, Oono Y, Komatsuda T. Organ-enriched gene expression during floral morphogenesis in wild barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:887-902. [PMID: 37548103 DOI: 10.1111/tpj.16416] [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: 05/31/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 08/08/2023]
Abstract
Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (Hordeum. vulgare) has unique floral morphogenesis. Wild barley (H. vulgare ssp. spontaneum), which is the immediate ancestor of cultivated barley (H. vulgare ssp. vulgare), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ-specific transcriptome atlas for wild barley floral organs. Genome-wide transcription profiles indicated that 22 838 protein-coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ-enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ-enriched expression influence the biological processes in floral organs. The co-expression regulatory network showed that the expression of 690 genes targeted by MADS-box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.
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Affiliation(s)
- Gang Chen
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Hongjing Zhu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Akemi Tagiri
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Jinan, 252100, China
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Ritzinger M, Sallam AH, Smith KP, Case AJ, Wodarek J, Curland RD, Dill-Macky R, Steffenson BJ. Genome-Wide Association Mapping of Bacterial Leaf Streak Resistance in Two Elite Barley Breeding Panels. PHYTOPATHOLOGY 2023; 113:2119-2126. [PMID: 37069124 DOI: 10.1094/phyto-10-22-0402-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Bacterial leaf streak (BLS), caused chiefly by the pathogen Xanthomonas translucens pv. translucens, is becoming an increasingly important foliar disease of barley in the Upper Midwest. The deployment of resistant cultivars is the most economical and practical method of control. To identify sources of BLS resistance, we evaluated two panels of breeding lines from the University of Minnesota (UMN) and Anheuser-Busch InBev (ABI) barley improvement programs for reaction to strain CIX95 in the field at St. Paul and Crookston, MN, in 2020 and 2021. The percentage of resistant lines in the UMN and ABI panels with mid-season maturity was 1.8% (6 of 333 lines) and 5.2% (13 of 251 lines), respectively. Both panels were genotyped with the barley 50K iSelect SNP array, and then a genome-wide association study was performed. A single, highly significant association was identified for BLS resistance on chromosome 6H in the UMN panel. This association was also identified in the ABI panel. Seven other significant associations were detected in the ABI panel: two each on chromosomes 1H, 2H, and 3H and one on chromosome 5H. Of the eight associations identified in the panels, five were novel. The discovery of resistance in elite breeding lines will hasten the time needed to develop and release a BLS-resistant cultivar.
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Affiliation(s)
- Mitch Ritzinger
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | | | - Joseph Wodarek
- University of Minnesota, Northwest Research and Outreach Center, Crookston, MN 56716
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Polturak G, Misra RC, El-Demerdash A, Owen C, Steed A, McDonald HP, Wang J, Saalbach G, Martins C, Chartrain L, Wilkinson B, Nicholson P, Osbourn A. Discovery of isoflavone phytoalexins in wheat reveals an alternative route to isoflavonoid biosynthesis. Nat Commun 2023; 14:6977. [PMID: 37914713 PMCID: PMC10620232 DOI: 10.1038/s41467-023-42464-3] [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: 07/17/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
Isoflavones are a group of phenolic compounds mostly restricted to plants of the legume family, where they mediate important interactions with plant-associated microbes, including in defense from pathogens and in nodulation. Their well-studied health promoting attributes have made them a prime target for metabolic engineering, both for bioproduction of isoflavones as high-value molecules, and in biofortification of food crops. A key gene in their biosynthesis, isoflavone synthase, was identified in legumes over two decades ago, but little is known about formation of isoflavones outside of this family. Here we identify a specialized wheat-specific isoflavone synthase, TaCYP71F53, which catalyzes a different reaction from the leguminous isoflavone synthases, thus revealing an alternative path to isoflavonoid biosynthesis and providing a non-transgenic route for engineering isoflavone production in wheat. TaCYP71F53 forms part of a biosynthetic gene cluster that produces a naringenin-derived O-methylated isoflavone, 5-hydroxy-2',4',7-trimethoxyisoflavone, triticein. Pathogen-induced production and in vitro antimicrobial activity of triticein suggest a defense-related role for this molecule in wheat. Genomic and metabolic analyses of wheat ancestral grasses further show that the triticein gene cluster was introduced into domesticated emmer wheat through natural hybridization ~9000 years ago, and encodes a pathogen-responsive metabolic pathway that is conserved in modern bread wheat varieties.
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Affiliation(s)
- Guy Polturak
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK.
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | | | - Amr El-Demerdash
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
- Division of Organic Chemistry, Department of Chemistry, School of Sciences, Mansoura University, Mansoura, 35516, Egypt
| | - Charlotte Owen
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Andrew Steed
- Crop Genetics Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Hannah P McDonald
- Molecular Microbiology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - JiaoJiao Wang
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
- Tsinghua-Peking Joint Center for Life Sciences, and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | | | - Carlo Martins
- Proteomics Facility, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - Barrie Wilkinson
- Molecular Microbiology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Paul Nicholson
- Crop Genetics Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Anne Osbourn
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK.
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41
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Shanmugaraj N, Rajaraman J, Kale S, Kamal R, Huang Y, Thirulogachandar V, Garibay-Hernández A, Budhagatapalli N, Tandron Moya YA, Hajirezaei MR, Rutten T, Hensel G, Melzer M, Kumlehn J, von Wirén N, Mock HP, Schnurbusch T. Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence. THE PLANT CELL 2023; 35:3973-4001. [PMID: 37282730 PMCID: PMC10615218 DOI: 10.1093/plcell/koad164] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/17/2023] [Accepted: 06/04/2023] [Indexed: 06/08/2023]
Abstract
Leaf and floral tissue degeneration is a common feature in plants. In cereal crops such as barley (Hordeum vulgare L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of the inflorescence meristem dome, which is followed basipetally by the degeneration of floral primordia and the central axis. Due to its quantitative nature and environmental sensitivity, inflorescence PTD constitutes a complex, multilayered trait affecting final grain number. This trait appears to be highly predictable and heritable under standardized growth conditions, consistent with a developmentally programmed mechanism. To elucidate the molecular underpinnings of inflorescence PTD, we combined metabolomic, transcriptomic, and genetic approaches to show that barley inflorescence PTD is accompanied by sugar depletion, amino acid degradation, and abscisic acid responses involving transcriptional regulators of senescence, defense, and light signaling. Based on transcriptome analyses, we identified GRASSY TILLERS1 (HvGT1), encoding an HD-ZIP transcription factor, as an important modulator of inflorescence PTD. A gene-edited knockout mutant of HvGT1 delayed PTD and increased differentiated apical spikelets and final spikelet number, suggesting a possible strategy to increase grain number in cereals. We propose a molecular framework that leads to barley PTD, the manipulation of which may increase yield potential in barley and other related cereals.
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Affiliation(s)
- Nandhakumar Shanmugaraj
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Sandip Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Venkatasubbu Thirulogachandar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Adriana Garibay-Hernández
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Nagaveni Budhagatapalli
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Yudelsy Antonia Tandron Moya
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Mohammed R Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
- Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Halle 06120,Germany
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Rodríguez Del Río Á, Monteagudo A, Contreras-Moreira B, Kiss T, Mayer M, Karsai I, Igartua E, Casas AM. Diversity of gene expression responses to light quality in barley. Sci Rep 2023; 13:17143. [PMID: 37816785 PMCID: PMC10564772 DOI: 10.1038/s41598-023-44263-8] [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: 01/06/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Light quality influence on barley development is poorly understood. We exposed three barley genotypes with either sensitive or insensitive response to two light sources producing different light spectra, fluorescent bulbs, and metal halide lamps, keeping constant light intensity, duration, and temperature. Through RNA-seq, we identified the main genes and pathways involved in the genotypic responses. A first analysis identified genotypic differences in gene expression of development-related genes, including photoreceptors and flowering time genes. Genes from the vernalization pathway of light quality-sensitive genotypes were affected by fluorescent light. In particular, vernalization-related repressors reacted differently: HvVRN2 did not experience relevant changes, whereas HvOS2 expression increased under fluorescent light. To identify the genes primarily related to light quality responses, and avoid the confounding effect of plant developmental stage, genes influenced by development were masked in a second analysis. Quantitative expression levels of PPD-H1, which influenced HvVRN1 and HvFT1, explained genotypic differences in development. Upstream mechanisms (light signaling and circadian clock) were also altered, but no specific genes linking photoreceptors and the photoperiod pathway were identified. The variety of light-quality sensitivities reveals the presence of possible mechanisms of adaptation of winter and facultative barley to latitudinal variation in light quality, which deserves further research.
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Affiliation(s)
- Álvaro Rodríguez Del Río
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
- Centro de Biotecnología y Genómica de Plantas, UPM/INIA-CSIC, Madrid, Spain
| | - Arantxa Monteagudo
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
| | - Bruno Contreras-Moreira
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
| | - Tibor Kiss
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
- Center for Research and Development, Food and Wine Center of Excellence, Eszterházy Károly Catholic University, Eger, Hungary
| | - Marianna Mayer
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
| | - Ildikó Karsai
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
| | - Ernesto Igartua
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain.
| | - Ana M Casas
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
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Liu J, Liu F, Pan W. Improving the Completeness of Chromosome-Level Assembly by Recalling Sequences from Lost Contigs. Genes (Basel) 2023; 14:1926. [PMID: 37895275 PMCID: PMC10606404 DOI: 10.3390/genes14101926] [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: 07/11/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
For a long time, the construction of complete reference genomes for complex eukaryotic genomes has been hindered by the limitations of sequencing technologies. Recently, the Pacific Biosciences (PacBio) HiFi data and Oxford Nanopore Technologies (ONT) Ultra-Long data, leveraging their respective advantages in accuracy and length, have provided an opportunity for generating complete chromosome sequences. Nevertheless, for the majority of genomes, the chromosome-level assemblies generated using existing methods still miss a high proportion of sequences due to losing small contigs in the step of assembly and scaffolding. To address this shortcoming, in this paper, we propose a novel method that is able to identify and fill the gaps in the chromosome-level assembly by recalling the sequences in the lost small contigs. Experimental results on both real and simulated datasets demonstrate that this method is able to improve the completeness of the chromosome-level assembly.
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Affiliation(s)
- Junyang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China;
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (ICR, CAAS), Shenzhen 518120, China
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China;
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang 455000, China
| | - Weihua Pan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (ICR, CAAS), Shenzhen 518120, China
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Contreras-Moreira B, Saraf S, Naamati G, Casas AM, Amberkar SS, Flicek P, Jones AR, Dyer S. GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation. Genome Biol 2023; 24:223. [PMID: 37798615 PMCID: PMC10552430 DOI: 10.1186/s13059-023-03071-z] [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: 06/07/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts .
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Affiliation(s)
- Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
- Estación Experimental Aula Dei-CSIC, 50059, Zaragoza, Spain.
| | - Shradha Saraf
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ana M Casas
- Estación Experimental Aula Dei-CSIC, 50059, Zaragoza, Spain
| | - Sandeep S Amberkar
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
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Duan Y, Han M, Grimm M, Schierstaedt J, Imani J, Cardinale M, Le Jean M, Nesme J, Sørensen SJ, Schikora A. Hordeum vulgare differentiates its response to beneficial bacteria. BMC PLANT BIOLOGY 2023; 23:460. [PMID: 37789272 PMCID: PMC10548682 DOI: 10.1186/s12870-023-04484-5] [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: 06/23/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND In nature, beneficial bacteria triggering induced systemic resistance (ISR) may protect plants from potential diseases, reducing yield losses caused by diverse pathogens. However, little is known about how the host plant initially responds to different beneficial bacteria. To reveal the impact of different bacteria on barley (Hordeum vulgare), bacterial colonization patterns, gene expression, and composition of seed endophytes were explored. RESULTS This study used the soil-borne Ensifer meliloti, as well as Pantoea sp. and Pseudomonas sp. isolated from barley seeds, individually. The results demonstrated that those bacteria persisted in the rhizosphere but with different colonization patterns. Although root-leaf translocation was not observed, all three bacteria induced systemic resistance (ISR) against foliar fungal pathogens. Transcriptome analysis revealed that ion- and stress-related genes were regulated in plants that first encountered bacteria. Iron homeostasis and heat stress responses were involved in the response to E. meliloti and Pantoea sp., even if the iron content was not altered. Heat shock protein-encoding genes responded to inoculation with Pantoea sp. and Pseudomonas sp. Furthermore, bacterial inoculation affected the composition of seed endophytes. Investigation of the following generation indicated that the enhanced resistance was not heritable. CONCLUSIONS Here, using barley as a model, we highlighted different responses to three different beneficial bacteria as well as the influence of soil-borne Ensifer meliloti on the seed microbiome. In total, these results can help to understand the interaction between ISR-triggering bacteria and a crop plant, which is essential for the application of biological agents in sustainable agriculture.
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Affiliation(s)
- Yongming Duan
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Min Han
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Maja Grimm
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Jasper Schierstaedt
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ) - Department Plant-Microbe Systems, Theodor-Echtermeyer Weg 1, 14979, Großbeeren, Germany
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Jafargholi Imani
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies, University of Salento, SP6 Lecce- Monteroni, Lecce, 73100, Italy
- Institute of Applied Microbiology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Marie Le Jean
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR 7360 CNRS, Université de Lorraine, 8 rue du Général Delestraint, Metz, 57070, France
| | - Joseph Nesme
- Department of Biology, Section of Microbiology, Copenhagen University, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Søren J Sørensen
- Department of Biology, Section of Microbiology, Copenhagen University, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Adam Schikora
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany.
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Farooqi MQU, Moody D, Bai G, Bernardo A, St. Amand P, Diggle AJ, Rengel Z. Genetic characterization of root architectural traits in barley ( Hordeum vulgare L.) using SNP markers. FRONTIERS IN PLANT SCIENCE 2023; 14:1265925. [PMID: 37860255 PMCID: PMC10582755 DOI: 10.3389/fpls.2023.1265925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/05/2023] [Indexed: 10/21/2023]
Abstract
Increasing attention is paid to providing new tools to breeders for targeted breeding for specific root traits that are beneficial in low-fertility, drying soils; however, such information is not available for barley (Hordeum vulgare L.). A panel of 191 barley accessions (originating from Australia, Europe, and Africa) was phenotyped for 26 root and shoot traits using the semi-hydroponic system and genotyped using 21 062 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). The population structure analysis of the barley panel identified six distinct groups. We detected 1199 significant (P<0.001) marker-trait associations (MTAs) with r2 values up to 0.41. The strongest MTAs were found for root diameter in the top 20 cm and the longest root length. Based on the physical locations of these MTAs in the barley reference genome, we identified 37 putative QTLs for the root traits, and three QTLs for shoot traits, with nine QTLs located in the same physical regions. The genomic region 640-653 Mb on chromosome 7H was significant for five root length-related traits, where 440 annotated genes were located. The putative QTLs for various root traits identified in this study may be useful for genetic improvement regarding the adaptation of new barley cultivars to suboptimal environments and abiotic stresses.
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Affiliation(s)
- M. Q. U. Farooqi
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | | | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Amy Bernardo
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Paul St. Amand
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Art J. Diggle
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Zed Rengel
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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Li B, Yang Q, Yang L, Zhou X, Deng L, Qu L, Guo D, Hui R, Guo Y, Liu X, Wang T, Fan L, Li M, Yan M. A gap-free reference genome reveals structural variations associated with flowering time in rapeseed ( Brassica napus). HORTICULTURE RESEARCH 2023; 10:uhad171. [PMID: 37841499 PMCID: PMC10569240 DOI: 10.1093/hr/uhad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/20/2023] [Indexed: 10/17/2023]
Abstract
Allopolyploid oilseed rape (Brassica napus) is an important oil crop and vegetable. However, the latest version of its reference genome, with collapsed duplications, gaps, and other issues, prevents comprehensive genomic analysis. Herein, we report a gap-free assembly of the rapeseed cv. Xiang5A genome using a combination of ONT (Oxford Nanopore Technologies) ultra-long reads, PacBio high-fidelity reads, and Hi-C datasets. It includes gap-free assemblies of all 19 chromosomes and telomere-to-telomere assemblies of eight chromosomes. Compared with previously published genomes of B. napus, our gap-free genome, with a contig N50 length of 50.70 Mb, has complete assemblies of 9 of 19 chromosomes without manual intervention, and greatly improves contiguity and completeness, thereby representing the highest quality genome assembly to date. Our results revealed that B. napus Xiang5A underwent nearly complete triplication and allotetraploidy relative to Arabidopsis thaliana. Using the gap-free assembly, we found that 917 flowering-related genes were affected by structural variation, including BnaA03.VERNALIZATION INSENSITIVE 3 and BnaC04.HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1. These genes may play crucial roles in regulating flowering time and facilitating the adaptation of Xiang5A in the Yangtze River Basin of China. This reference genome provides a valuable genetic resource for rapeseed functional genomic studies and breeding.
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Affiliation(s)
- Bao Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Qian Yang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Lulu Yang
- Department of Cell Biology and Genetics, Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, China
| | - Xing Zhou
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Lichao Deng
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Liang Qu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Dengli Guo
- Department of Cell Biology and Genetics, Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, China
| | - Rongkui Hui
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Yiming Guo
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Xinhong Liu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Tonghua Wang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Lianyi Fan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Mei Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
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Chen C, Jost M, Outram MA, Friendship D, Chen J, Wang A, Periyannan S, Bartoš J, Holušová K, Doležel J, Zhang P, Bhatt D, Singh D, Lagudah E, Park RF, Dracatos PM. A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley. Nat Commun 2023; 14:5468. [PMID: 37673864 PMCID: PMC10482968 DOI: 10.1038/s41467-023-41021-2] [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: 12/19/2022] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
Leaf rust, caused by Puccinia hordei, is one of the most widespread and damaging foliar diseases affecting barley. The barley leaf rust resistance locus Rph7 has been shown to have unusually high sequence and haplotype divergence. In this study, we isolate the Rph7 gene using a fine mapping and RNA-Seq approach that is confirmed by mutational analysis and transgenic complementation. Rph7 is a pathogen-induced, non-canonical resistance gene encoding a protein that is distinct from other known plant disease resistance proteins in the Triticeae. Structural analysis using an AlphaFold2 protein model suggests that Rph7 encodes a putative NAC transcription factor with a zinc-finger BED domain with structural similarity to the N-terminal DNA-binding domain of the NAC transcription factor (ANAC019) from Arabidopsis. A global gene expression analysis suggests Rph7 mediates the activation and strength of the basal defence response. The isolation of Rph7 highlights the diversification of resistance mechanisms available for engineering disease control in crops.
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Affiliation(s)
- Chunhong Chen
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Matthias Jost
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Megan A Outram
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Dorian Friendship
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Jian Chen
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Aihua Wang
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Sambasivam Periyannan
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
- The University of Southern Queensland, School of Agriculture and Environmental Science, Centre for Crop Health, Toowoomba, QLD, 4350, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Peng Zhang
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Dhara Bhatt
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Davinder Singh
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Evans Lagudah
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia.
| | - Robert F Park
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia.
| | - Peter M Dracatos
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia.
- La Trobe Institute for Sustainable Agriculture & Food (LISAF), Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
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Huang L, Gao G, Jiang C, Guo G, He Q, Zong Y, Liu C, Yang P. Generating homozygous mutant populations of barley microspores by ethyl methanesulfonate treatment. ABIOTECH 2023; 4:202-212. [PMID: 37970468 PMCID: PMC10638298 DOI: 10.1007/s42994-023-00108-6] [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: 01/12/2023] [Accepted: 05/31/2023] [Indexed: 11/17/2023]
Abstract
Induced mutations are important for genetic research and breeding. Mutations induced by physical or chemical mutagenesis are usually heterozygous during the early generations. However, mutations must be fixed prior to phenotyping or field trials, which requires additional rounds of self-pollination. Microspore culture is an effective method to produce double-haploid (DH) plants that are fixed homozygotes. In this study, we conducted ethyl methanesulfonate (EMS)-induced mutagenesis of microspore cultures of barley (Hordeum vulgare) cultivar 'Hua30' and landrace 'HTX'. The EMS concentrations were negatively correlated with the efficiency of callus induction and the frequency of mutant plant regeneration. The two genotypes showed different regeneration efficiencies. The phenotypic variation of the regenerated M1 plants and the presence of genome-wide nucleotide mutations, revealed by whole-genome sequencing, highlight the utility of EMS-induced mutagenesis of isolated microspore cultures for developing DH mutants. Genome-wide analysis of the mutation frequency in the regenerated plants revealed that a considerable proportion of mutations resulted from microspore culture (somaclonal variation) rather than EMS-induced mutagenesis. In addition to producing a population of 1972 homozygous mutant lines that are available for future field trials, this study lays the foundation for optimizing the regeneration efficiency of DH plants and the richness of mutations (mainly by fine-tuning the mutagen dosage).
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Affiliation(s)
- Linli Huang
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Guimei Guo
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yingjie Zong
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Chenghong Liu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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50
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Espinosa E, Bautista R, Fernandez I, Larrosa R, Zapata EL, Plata O. Comparing assembly strategies for third-generation sequencing technologies across different genomes. Genomics 2023; 115:110700. [PMID: 37598732 DOI: 10.1016/j.ygeno.2023.110700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
Abstract
The recent advent of long-read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), has led to substantial accuracy and computational cost improvements. However, de novo whole-genome assembly still presents significant challenges related to the computational cost and the quality of the results. Accordingly, sequencing accuracy and throughput continue to improve, and many tools are constantly emerging. Therefore, selecting the correct sequencing platform, the proper sequencing depth and the assembly tools are necessary to perform high-quality assembly. This paper evaluates the primary assembly reconstruction from recent hybrid and non-hybrid pipelines on different genomes. We find that using PacBio high-fidelity long-read (HiFi) plays an essential role in haplotype construction with respect to ONT reads. However, we observe a substantial improvement in the correctness of the assembly from high-fidelity ONT datasets and combining it with HiFi or short-reads.
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Affiliation(s)
- Elena Espinosa
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain.
| | - Rocio Bautista
- Supercomputing and Bioinnovation Center, University of Malaga, C. Severo Ochoa, 34, Malaga 29590, Spain.
| | - Ivan Fernandez
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain; Departament d'Arquitectura de Computadors, Universitat Politècnica de Catalunya, C. Jordi Girona, 1-3, Barcelona 08034, Spain.
| | - Rafael Larrosa
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain; Supercomputing and Bioinnovation Center, University of Malaga, C. Severo Ochoa, 34, Malaga 29590, Spain.
| | - Emilio L Zapata
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain; Supercomputing and Bioinnovation Center, University of Malaga, C. Severo Ochoa, 34, Malaga 29590, Spain.
| | - Oscar Plata
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain.
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