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Rajendran NR, Qureshi N, Pourkheirandish M. Genotyping by Sequencing Advancements in Barley. FRONTIERS IN PLANT SCIENCE 2022; 13:931423. [PMID: 36003814 PMCID: PMC9394214 DOI: 10.3389/fpls.2022.931423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Barley is considered an ideal crop to study cereal genetics due to its close relationship with wheat and diploid ancestral genome. It plays a crucial role in reducing risks to global food security posed by climate change. Genetic variations in the traits of interest in crops are vital for their improvement. DNA markers have been widely used to estimate these variations in populations. With the advancements in next-generation sequencing, breeders could access different types of genetic variations within different lines, with single-nucleotide polymorphisms (SNPs) being the most common type. However, genotyping barley with whole genome sequencing (WGS) is challenged by the higher cost and computational demand caused by the large genome size (5.5GB) and a high proportion of repetitive sequences (80%). Genotyping-by-sequencing (GBS) protocols based on restriction enzymes and target enrichment allow a cost-effective SNP discovery by reducing the genome complexity. In general, GBS has opened up new horizons for plant breeding and genetics. Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges. Moreover, a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium. The complete exploitation of GBS advancements will pave the way to a better understanding of crop genetics and offer opportunities for the successful improvement of barley and its close relatives.
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Affiliation(s)
- Nirmal Raj Rajendran
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Naeela Qureshi
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico, Mexico
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
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2
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Abstract
Barley (Hordeum vulgare), one of the most widely cultivated cereal crops, possesses a large genome of 5.1 Gbp. Through various international collaborations, the genome has recently been sequenced and assembled at the chromosome-scale by exploiting available genetic and genomic resources. Many wild and cultivated barley accessions have been collected and preserved around the world. These accessions are crucial to obtain diverse natural and induced barley variants. The barley bioresource project aims to investigate the diversity of this crop based on purified seed and DNA samples of a large number of collected accessions. The long-term goal of this project is to analyse the genome sequences of major barley accessions worldwide. In view of technical limitations, a strategy has been employed to establish the exome structure of a selected number of accessions and to perform high-quality chromosome-scale assembly of the genomes of several major representative accessions. For the future project, an efficient annotation pipeline is essential for establishing the function of genomes and genes as well as for using this information for sequence-based digital barley breeding. In this article, the author reviews the existing barley resources along with their applications and discuss possible future directions of research in barley genomics.
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Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
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3
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A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2020; 21:ijms21072580. [PMID: 32276381 PMCID: PMC7177731 DOI: 10.3390/ijms21072580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 01/04/2023] Open
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.
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Li M, Hensel G, Mascher M, Melzer M, Budhagatapalli N, Rutten T, Himmelbach A, Beier S, Korzun V, Kumlehn J, Börner T, Stein N. Leaf Variegation and Impaired Chloroplast Development Caused by a Truncated CCT Domain Gene in albostrians Barley. THE PLANT CELL 2019; 31:1430-1445. [PMID: 31023840 PMCID: PMC6635869 DOI: 10.1105/tpc.19.00132] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/23/2019] [Indexed: 05/17/2023]
Abstract
Chloroplasts fuel plant development and growth by converting solar energy into chemical energy. They mature from proplastids through the concerted action of genes in both the organellar and the nuclear genome. Defects in such genes impair chloroplast development and may lead to pigment-deficient seedlings or seedlings with variegated leaves. Such mutants are instrumental as tools for dissecting genetic factors underlying the mechanisms involved in chloroplast biogenesis. Characterization of the green-white variegated albostrians mutant of barley (Hordeum vulgare) has greatly broadened the field of chloroplast biology, including the discovery of retrograde signaling. Here, we report identification of the ALBOSTRIANS gene HvAST (also known as Hordeum vulgare CCT Motif Family gene 7, HvCMF7) by positional cloning as well as its functional validation based on independently induced mutants by Targeting Induced Local Lesions in Genomes (TILLING) and RNA-guided clustered regularly interspaced short palindromic repeats-associated protein 9 endonuclease-mediated gene editing. The phenotypes of the independent HvAST mutants imply residual activity of HvCMF7 in the original albostrians allele conferring an imperfect penetrance of the variegated phenotype even at homozygous state of the mutation. HvCMF7 is a homolog of the Arabidopsis (Arabidopsis thaliana) CONSTANS, CO-like, and TOC1 (CCT) Motif transcription factor gene CHLOROPLAST IMPORT APPARATUS2, which was reported to be involved in the expression of nuclear genes essential for chloroplast biogenesis. Notably, in barley we localized HvCMF7 to the chloroplast, without any clear evidence for nuclear localization.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources Group, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- Molecular Genetics Group, Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Goetz Hensel
- Plant Reproductive Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Martin Mascher
- Domestication Genomics Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Michael Melzer
- Structural Cell Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Nagaveni Budhagatapalli
- Plant Reproductive Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Twan Rutten
- Structural Cell Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Axel Himmelbach
- Genomics of Genetic Resources Group, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Sebastian Beier
- Bioinformatics and Information Technology Group, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | | | - Jochen Kumlehn
- Plant Reproductive Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Thomas Börner
- Molecular Genetics Group, Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Nils Stein
- Genomics of Genetic Resources Group, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
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5
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Liu Y, Zhang B, Wen X, Zhang S, Wei Y, Lu Q, Liu Z, Wang K, Liu F, Peng R. Construction and characterization of a bacterial artificial chromosome library for Gossypium mustelinum. PLoS One 2018; 13:e0196847. [PMID: 29771937 PMCID: PMC5957370 DOI: 10.1371/journal.pone.0196847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 04/20/2018] [Indexed: 11/18/2022] Open
Abstract
A bacterial artificial chromosome (BAC) library for G. mustelinum Miers ex G. Watt (AD4) was constructed. Intact nuclei from G. mustelinum (AD4) were used to isolate high molecular weight DNA, which was partially cleaved with Hind III and cloned into pSMART BAC (Hind III) vectors. The BAC library consisted of 208,182 clones arrayed in 542 384-microtiter plates, with an average insert size of 121.72 kb ranging from 100 to 150 kb. About 2% of the clones did not contain inserts. Based on an estimated genome size of 2372 Mb for G. mustelinum, the BAC library was estimated to have a total coverage of 10.50 × genome equivalents. The high capacity library of G. mustelinum will serve as a giant gene resource for map-based cloning of quantitative trait loci or genes associated with important agronomic traits or resistance to Verticillium wilt, physical mapping and comparative genome analysis.
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Affiliation(s)
- Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States of America
| | - Xinpeng Wen
- Anyang Institute of Technology, Anyang, Henan, China
| | - Shulin Zhang
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yangyang Wei
- Anyang Institute of Technology, Anyang, Henan, China
| | - Quanwei Lu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Zhen Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- * E-mail: (FL); (RP)
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- * E-mail: (FL); (RP)
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6
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Barley Genome Sequencing and Assembly—A First Version Reference Sequence. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-92528-8_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Braumann I, Dockter C, Beier S, Himmelbach A, Lok F, Lundqvist U, Skadhauge B, Stein N, Zakhrabekova S, Zhou R, Hansson M. Mutations in the gene of the Gα subunit of the heterotrimeric G protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding. Hereditas 2017; 155:10. [PMID: 28878591 PMCID: PMC5583965 DOI: 10.1186/s41065-017-0045-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 08/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Short-culm mutants have been widely used in breeding programs to increase lodging resistance. In barley (Hordeum vulgare L.), several hundreds of short-culm mutants have been isolated over the years. The objective of the present study was to identify the Brachytic1 (Brh1) semi-dwarfing gene and to test its effect on yield and malting quality. RESULTS Double-haploid lines generated through a cross between a brh1.a mutant and the European elite malting cultivar Quench, showed good malting quality but a decrease in yield. Especially the activities of the starch degrading enzymes β-amylase and free limit dextrinase were high. A syntenic approach comparing markers in barley to those in rice (Oryza sativa L.), sorghum (Sorghum bicolor Moench) and brachypodium (Brachypodium distachyon P. Beauv) helped us to identify Brh1 as an orthologue of rice D1 encoding the Gα subunit of a heterotrimeric G protein. We demonstrated that Brh1 is allelic to Ari-m. Sixteen different mutant alleles were described at the DNA level. CONCLUSIONS Mutants in the Brh1 locus are deficient in the Gα subunit of a heterotrimeric G protein, which shows that heterotrimeric G proteins are important regulators of culm length in barley. Mutant alleles do not have any major negative effects on malting quality.
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Affiliation(s)
- Ilka Braumann
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | - Finn Lok
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Smedjevägen 3, SE-23053 Alnarp, Sweden
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | | | - Ruonan Zhou
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, SE-22362 Lund, Sweden
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8
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Beier S, Himmelbach A, Colmsee C, Zhang XQ, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci Data 2017; 4:170044. [PMID: 28448065 PMCID: PMC5407242 DOI: 10.1038/sdata.2017.44] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/09/2017] [Indexed: 12/30/2022] Open
Abstract
Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Xiao-Qi Zhang
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Qisen Zhang
- Australian Export Grains Innovation Centre, South Perth, Western Australia 6151, Australia
| | - Lin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Micha Bayer
- The James Hutton Institute, Dundee DD2 5DA, UK
| | - Daniel Bolser
- European Molecular Biology Laboratory-The European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Stefan Taudien
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Marius Felder
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Alex Hastie
- BioNano Genomics Inc., San Diego, California 92121, USA
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Helena Staňková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Saki Chan
- BioNano Genomics Inc., San Diego, California 92121, USA
| | - María Muñoz-Amatriaín
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, California 92521, USA
| | - Steve Wanamaker
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Lala Aliyeva-Schnorr
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Stefano Grasso
- Department of Agricultural and Environmental Sciences, University of Udine, 33100 Udine, Italy
| | - Jaakko Tanskanen
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Sujie Cao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Brett Chapman
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yong Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xuan Li
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - John K McCooke
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Cong Tan
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Shuya Yin
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Gaofeng Zhou
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Jesse A Poland
- Kansas State University, Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Manhattan, Kansas 66506, USA
| | - Matthew I Bellgard
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | | | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, California 92521, USA
| | - Peter Langridge
- School of Agriculture, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA.,Department of Plant and Microbial Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Paul Kersey
- European Molecular Biology Laboratory-The European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Matthew D Clark
- Earlham Institute, Norwich NR4 7UH, UK.,School of Environmental Sciences, University of East Anglia, Norwich NR4 7UH, UK
| | - Mario Caccamo
- Earlham Institute, Norwich NR4 7UH, UK.,National Institute of Agricultural Botany, Cambridge CB3 0LE, UK
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Matthias Platzer
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Timothy J Close
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Mats Hansson
- Department of Biology, Lund University, 22362 Lund, Sweden
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ilka Braumann
- Carlsberg Research Laboratory, 1799 Copenhagen, Denmark
| | - Chengdao Li
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.,Department of Agriculture and Food, Government of Western Australia, South Perth, Western Australia 6150, Australia.,Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei 434025, China
| | - Robbie Waugh
- The James Hutton Institute, Dundee DD2 5DA, UK.,School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.,School of Plant Biology, University of Western Australia, Crawley 6009, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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9
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Coates BS, Abel CA, Perera OP. Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools. Genome 2016; 60:310-324. [PMID: 28177843 DOI: 10.1139/gen-2016-0067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The lepidopteran pest insect Helicoverpa zea feeds on cultivated corn and cotton across the Americas where control remains challenging owing to the evolution of resistance to chemical and transgenic insecticidal toxins, yet genomic resources remain scarce for this species. A bacterial artificial chromosome (BAC) library having a mean genomic insert size of 145 ± 20 kbp was created from a laboratory strain of H. zea, which provides ∼12.9-fold coverage of a 362.8 ± 8.8 Mbp (0.37 ± 0.09 pg) flow cytometry estimated haploid genome size. Assembly of Illumina HiSeq 2000 reads generated from 14 pools that encompassed all BAC clones resulted in 165 485 genomic contigs (N50 = 3262 bp; 324.6 Mbp total). Long terminal repeat (LTR) protein coding regions annotated from 181 contigs included 30 Ty1/copia, 78 Ty3/gypsy, and 73 BEL/Pao elements, of which 60 (33.1%) encoded all five functional polyprotein (pol) domains. Approximately 14% of LTR elements are distributed non-randomly across pools of BAC clones.
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Affiliation(s)
- Brad S Coates
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA.,b Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Craig A Abel
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Omaththage P Perera
- c USDA-ARS, Southern Insect Management Research Unit, 141 Experiment Station Road, P.O. Box 346, Stoneville, MS 38776, USA
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10
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Daneri-Castro SN, Svensson B, Roberts TH. Barley germination: Spatio-temporal considerations for designing and interpreting ‘omics’ experiments. J Cereal Sci 2016. [DOI: 10.1016/j.jcs.2016.05.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Beier S, Himmelbach A, Schmutzer T, Felder M, Taudien S, Mayer KFX, Platzer M, Stein N, Scholz U, Mascher M. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1511-22. [PMID: 26801048 PMCID: PMC5066668 DOI: 10.1111/pbi.12511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 05/02/2023]
Abstract
Hierarchical shotgun sequencing remains the method of choice for assembling high-quality reference sequences of complex plant genomes. The efficient exploitation of current high-throughput technologies and powerful computational facilities for large-insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole-genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high-quality assemblies of a large number of clones to assemble map-based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Marius Felder
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Stefan Taudien
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Klaus F X Mayer
- Plant Genome and System Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
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12
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Jost M, Taketa S, Mascher M, Himmelbach A, Yuo T, Shahinnia F, Rutten T, Druka A, Schmutzer T, Steuernagel B, Beier S, Taudien S, Scholz U, Morgante M, Waugh R, Stein N. A Homolog of Blade-On-Petiole 1 and 2 (BOP1/2) Controls Internode Length and Homeotic Changes of the Barley Inflorescence. PLANT PHYSIOLOGY 2016; 171:1113-27. [PMID: 27208226 PMCID: PMC4902598 DOI: 10.1104/pp.16.00124] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/08/2016] [Indexed: 05/17/2023]
Abstract
Inflorescence architecture in small-grain cereals has a direct effect on yield and is an important selection target in breeding for yield improvement. We analyzed the recessive mutation laxatum-a (lax-a) in barley (Hordeum vulgare), which causes pleiotropic changes in spike development, resulting in (1) extended rachis internodes conferring a more relaxed inflorescence, (2) broadened base of the lemma awns, (3) thinner grains that are largely exposed due to reduced marginal growth of the palea and lemma, and (4) and homeotic conversion of lodicules into two stamenoid structures. Map-based cloning enforced by mapping-by-sequencing of the mutant lax-a locus enabled the identification of a homolog of BLADE-ON-PETIOLE1 (BOP1) and BOP2 as the causal gene. Interestingly, the recently identified barley uniculme4 gene also is a BOP1/2 homolog and has been shown to regulate tillering and leaf sheath development. While the Arabidopsis (Arabidopsis thaliana) BOP1 and BOP2 genes act redundantly, the barley genes contribute independent effects in specifying the developmental growth of vegetative and reproductive organs, respectively. Analysis of natural genetic diversity revealed strikingly different haplotype diversity for the two paralogous barley genes, likely affected by the respective genomic environments, since no indication for an active selection process was detected.
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Affiliation(s)
- Matthias Jost
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Shin Taketa
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Takahisa Yuo
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Fahimeh Shahinnia
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Arnis Druka
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Burkhard Steuernagel
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Stefan Taudien
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Michele Morgante
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Robbie Waugh
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
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13
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Schneider LM, Adamski NM, Christensen CE, Stuart DB, Vautrin S, Hansson M, Uauy C, von Wettstein-Knowles P. The Cer-cqu gene cluster determines three key players in a β-diketone synthase polyketide pathway synthesizing aliphatics in epicuticular waxes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2715-2730. [PMID: 26962211 PMCID: PMC4861019 DOI: 10.1093/jxb/erw105] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Aliphatic compounds on plant surfaces, called epicuticular waxes, are the first line of defense against pathogens and pests, contribute to reducing water loss and determine other important phenotypes. Aliphatics can form crystals affecting light refraction, resulting in a color change and allowing identification of mutants in their synthesis or transport. The present study discloses three such Eceriferum (cer) genes in barley - Cer-c, Cer-q and Cer-u - known to be tightly linked and functioning in a biochemical pathway forming dominating amounts of β-diketone and hydroxy-β-diketones plus some esterified alkan-2-ols. These aliphatics are present in many Triticeae as well as dicotyledons such as Eucalyptus and Dianthus. Recently developed genomic resources and mapping populations in barley defined these genes to a small region on chromosome arm 2HS. Exploiting Cer-c and -u potential functions pinpointed five candidates, of which three were missing in apparent cer-cqu triple mutants. Sequencing more than 50 independent mutants for each gene confirmed their identification. Cer-c is a chalcone synthase-like polyketide synthase, designated diketone synthase (DKS), Cer-q is a lipase/carboxyl transferase and Cer-u is a P450 enzyme. All were highly expressed in pertinent leaf sheath tissue of wild type. A physical map revealed the order Cer-c, Cer-u, Cer-q with the flanking genes 101kb apart, confirming they are a gene cluster, Cer-cqu. Homology-based modeling suggests that many of the mutant alleles affect overall protein structure or specific active site residues. The rich diversity of identified mutations will facilitate future studies of three key enzymes involved in synthesis of plant apoplast waxes.
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Affiliation(s)
- Lizette M Schneider
- Biology Department, Copenhagen University, Copenhagen DK-2200, Denmark Biology Department, Lund University, SW-22362 Lund, Sweden
| | | | | | - David B Stuart
- Biology Department, Lund University, SW-22362 Lund, Sweden
| | - Sonia Vautrin
- INRA-Centre National de Ressources Génomiques Végétales, F-31326 Castanet Tolosan, France
| | - Mats Hansson
- Biology Department, Lund University, SW-22362 Lund, Sweden
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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14
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Yeo FKS, Wang Y, Vozabova T, Huneau C, Leroy P, Chalhoub B, Qi XQ, Niks RE, Marcel TC. Haplotype divergence and multiple candidate genes at Rphq2, a partial resistance QTL of barley to Puccinia hordei. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:289-304. [PMID: 26542283 PMCID: PMC4733143 DOI: 10.1007/s00122-015-2627-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 10/17/2015] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Rphq2, a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars. ABSTRACT Partial and non-host resistances to rust fungi in barley (Hordeum vulgare) may be based on pathogen-associated molecular pattern (PAMP)-triggered immunity. Understanding partial resistance may help to understand non-host resistance, and vice versa. We constructed two non-gridded BAC libraries from cultivar Vada and line SusPtrit. Vada is immune to non-adapted Puccinia rust fungi, and partially resistant to P. hordei. SusPtrit is susceptible to several non-adapted rust fungi, and has been used for mapping QTLs for non-host and partial resistance. The BAC libraries help to identify genes determining the natural variation for partial and non-host resistances of barley to rust fungi. A major-effect QTL, Rphq2, for partial resistance to P. hordei was mapped in a complete Vada and an incomplete SusPtrit contig. The physical distance between the markers flanking Rphq2 was 195 Kbp in Vada and at least 226 Kbp in SusPtrit. This marker interval was predicted to contain 12 genes in either accession, of which only five genes were in common. The haplotypes represented by Vada and SusPtrit were found in 57 and 43%, respectively, of a 194 barley accessions panel. The lack of homology between the two haplotypes probably explains the suppression of recombination in the Rphq2 area and limit further genetic resolution in fine mapping. The possible candidate genes for Rphq2 encode peroxidases, kinases and a member of seven-in-absentia protein family. This result suggests that Rphq2 does not belong to the NB-LRR gene family and does not resemble any of the partial resistance genes cloned previously.
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Affiliation(s)
- F K S Yeo
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- Department of Plant Science and Environmental Ecology, Faculty of Resource Science and Technology, University Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Y Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - T Vozabova
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- The Institute of Botany of the Academy of Science of the Czech Republic, Zámek 1, 252 43, Průhonice, Czech Republic
| | - C Huneau
- INRA, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
- Université d'Evry Val d'Essonne, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
| | - P Leroy
- INRA, UMR1095, Genetics Diversity and Ecophysiology of Cereals, 63039, Clermont-Ferrand, France
- Université Blaise Pascal, UMR1095, Genetics Diversity and Ecophysiology of Cereals, 63039, Clermont-Ferrand, France
| | - B Chalhoub
- INRA, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
- Université d'Evry Val d'Essonne, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
| | - X Q Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - R E Niks
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands.
| | - T C Marcel
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- INRA, UMR1290, BIOGER, 78850, Thiverval-Grignon, France
- AgroParisTech, UMR1290, BIOGER, 78850, Thiverval-Grignon, France
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15
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Tavakol E, Okagaki R, Verderio G, Shariati J V, Hussien A, Bilgic H, Scanlon MJ, Todt NR, Close TJ, Druka A, Waugh R, Steuernagel B, Ariyadasa R, Himmelbach A, Stein N, Muehlbauer GJ, Rossini L. The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning. PLANT PHYSIOLOGY 2015; 168:164-74. [PMID: 25818702 PMCID: PMC4424007 DOI: 10.1104/pp.114.252882] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/26/2015] [Indexed: 05/18/2023]
Abstract
Tillers are vegetative branches that develop from axillary buds located in the leaf axils at the base of many grasses. Genetic manipulation of tillering is a major objective in breeding for improved cereal yields and competition with weeds. Despite this, very little is known about the molecular genetic bases of tiller development in important Triticeae crops such as barley (Hordeum vulgare) and wheat (Triticum aestivum). Recessive mutations at the barley Uniculme4 (Cul4) locus cause reduced tillering, deregulation of the number of axillary buds in an axil, and alterations in leaf proximal-distal patterning. We isolated the Cul4 gene by positional cloning and showed that it encodes a BROAD-COMPLEX, TRAMTRACK, BRIC-À-BRAC-ankyrin protein closely related to Arabidopsis (Arabidopsis thaliana) BLADE-ON-PETIOLE1 (BOP1) and BOP2. Morphological, histological, and in situ RNA expression analyses indicate that Cul4 acts at axil and leaf boundary regions to control axillary bud differentiation as well as the development of the ligule, which separates the distal blade and proximal sheath of the leaf. As, to our knowledge, the first functionally characterized BOP gene in monocots, Cul4 suggests the partial conservation of BOP gene function between dicots and monocots, while phylogenetic analyses highlight distinct evolutionary patterns in the two lineages.
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Affiliation(s)
- Elahe Tavakol
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Ron Okagaki
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Gabriele Verderio
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Vahid Shariati J
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Ahmed Hussien
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Hatice Bilgic
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Mike J Scanlon
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Natalie R Todt
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Timothy J Close
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Arnis Druka
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Robbie Waugh
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Burkhard Steuernagel
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Ruvini Ariyadasa
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Axel Himmelbach
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Nils Stein
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Gary J Muehlbauer
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Laura Rossini
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
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Ui H, Sameri M, Pourkheirandish M, Chang MC, Shimada H, Stein N, Komatsuda T, Handa H. High-resolution genetic mapping and physical map construction for the fertility restorer Rfm1 locus in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:283-90. [PMID: 25412992 DOI: 10.1007/s00122-014-2428-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/08/2014] [Indexed: 05/11/2023]
Abstract
High-resolution genetic linkage mapping and BAC physical mapping narrowed the fertility restorer locus Rfm1 in barley to a sub-centimorgan genetic interval and a 208-kb physical interval. Rfm1 restores the fertility of msm1 and msm2 male-sterile cytoplasms in barley. The fertility restoration gene is located on the short arm of chromosome 6H (6HS), and we pursued a positional cloning of this gene. Starting from a previous result that has delimited Rfm1 within a 10.8 cM region on 6HS, we developed novel CAPS and SSR markers tightly linked to the gene in barley using the sequence information from the syntenic region of rice and barley genome assemblies. Next, we performed fine mapping of the Rfm1 locus. To isolate recombinants, we surveyed 3,638 F2 plants derived from a cross between the CMS strain and the Rf strain with adjacent markers (NAS2090 and NAS1080). This analysis identified 175 recombinant plants from the F2 population to build a high-resolution map with nine markers tightly linked to the Rfm1 locus. Rfm1 was located within the 0.14 cM region delimited by two markers (NAS9113 and NAS9200). Using these flanking markers as well as marker cosegregating with Rfm1 (NAS9133), we screened the BAC libraries of the cultivar Morex, an rfm1 carrier. We isolated 11 BAC clones and constructed a BAC physical map using their fingerprints. Finally, we delimited the Rfm1 locus encompassing the rfm1 allele on a 208-kb contig composed of three minimally overlapping BAC clones. This precise localization of the Rfm1 locus in the barley genome is expected to greatly accelerate the future map-based cloning of the Rfm1 gene by sequence analysis and its genetic transformation for the complementation of cytoplasmic male-sterile plants.
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Affiliation(s)
- Hajime Ui
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2, Kan-non-dai, Tsukuba, 305-8602, Japan
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17
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Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis. Mol Genet Genomics 2014; 289:921-33. [PMID: 24859131 DOI: 10.1007/s00438-014-0862-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
Abstract
The para rubber tree is the most widely cultivated tree species for producing natural rubber (NR) latex. Unfortunately, rubber tree characteristics such as a long life cycle, heterozygous genetic backgrounds, and poorly understood genetic profiles are the obstacles to breeding new rubber tree varieties, such as those with improved NR yields. Recent evidence has revealed the potential importance of controlling microRNA (miRNA) decay in some aspects of NR regulation. To gain a better understanding of miRNAs and their relationship with rubber tree gene regulation networks, large genomic DNA insert-containing libraries were generated to complement the incomplete draft genome sequence and applied as a new powerful tool to predict a function of interested genes. Bacterial artificial chromosome and fosmid libraries, containing a total of 120,576 clones with an average insert size of 43.35 kb, provided approximately 2.42 haploid genome equivalents of coverage based on the estimated 2.15 gb rubber tree genome. Based on these library sequences, the precursors of 1 member of rubber tree-specific miRNAs and 12 members of conserved miRNAs were successfully identified. A panel of miRNAs was characterized for phytohormone response by precisely identifying phytohormone-responsive motifs in their promoter sequences. Furthermore, the quantitative real-time PCR on ethylene stimulation of rubber trees was performed to demonstrate that the miR2118, miR159, miR164 and miR166 are responsive to ethylene, thus confirmed the prediction by genomic DNA analysis. The cis-regulatory elements identified in the promoter regions of these miRNA genes help augment our understanding of miRNA gene regulation and provide a foundation for further investigation of the regulation of rubber tree miRNAs.
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18
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Zeng Q, Yuan F, Xu X, Shi X, Nie X, Zhuang H, Chen X, Wang Z, Wang X, Huang L, Han D, Kang Z. Construction and characterization of a bacterial artificial chromosome library for the hexaploid wheat line 92R137. BIOMED RESEARCH INTERNATIONAL 2014; 2014:845806. [PMID: 24895618 PMCID: PMC4026951 DOI: 10.1155/2014/845806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/26/2014] [Accepted: 04/18/2014] [Indexed: 11/18/2022]
Abstract
For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sublibraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymes HindIII and BamHI. The BAC library was composed of total 765,696 clones, of which 390,144 were from the HindIII digestion and 375,552 from the BamHI digestion. Through pulsed-field gel electrophoresis (PFGE) analysis of 453 clones randomly selected from the HindIII sublibrary and 573 clones from the BamHI sublibrary, the average insert sizes were estimated as 129 and 113 kb, respectively. Thus, the HindIII sublibrary was estimated to have a 3.01-fold coverage and the BamHI sublibrary a 2.53-fold coverage based on the estimated hexaploid wheat genome size of 16,700 Mb. The 765,696 clones were arrayed in 1,994 384-well plates. All clones were also arranged into plate pools and further arranged into 5-dimensional (5D) pools. The probability of identifying a clone corresponding to any wheat DNA sequence (such as gene Yr26 for stripe rust resistance) from the library was estimated to be more than 99.6%. Through polymerase chain reaction screening the 5D pools with Xwe173, a marker tightly linked to Yr26, six BAC clones were successfully obtained. These results demonstrate that the BAC library is a valuable genomic resource for positional cloning of Yr26 and other genes of interest.
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Affiliation(s)
- Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hua Zhuang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianming Chen
- Wheat Genetics, Quality, Physiology, and Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, and Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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PROTEIN DISULFIDE ISOMERASE LIKE 5-1 is a susceptibility factor to plant viruses. Proc Natl Acad Sci U S A 2014; 111:2104-9. [PMID: 24481254 DOI: 10.1073/pnas.1320362111] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein disulfide isomerases (PDIs) catalyze the correct folding of proteins and prevent the aggregation of unfolded or partially folded precursors. Whereas suppression of members of the PDI gene family can delay replication of several human and animal viruses (e.g., HIV), their role in interactions with plant viruses is largely unknown. Here, using a positional cloning strategy we identified variants of PROTEIN DISULFIDE ISOMERASE LIKE 5-1 (HvPDIL5-1) as the cause of naturally occurring resistance to multiple strains of Bymoviruses. The role of wild-type HvPDIL5-1 in conferring susceptibility was confirmed by targeting induced local lesions in genomes for induced mutant alleles, transgene-induced complementation, and allelism tests using different natural resistance alleles. The geographical distribution of natural genetic variants of HvPDIL5-1 revealed the origin of resistance conferring alleles in domesticated barley in Eastern Asia. Higher sequence diversity was correlated with areas with increased pathogen diversity suggesting adaptive selection for bymovirus resistance. HvPDIL5-1 homologs are highly conserved across species of the plant and animal kingdoms implying that orthologs of HvPDIL5-1 or other closely related members of the PDI gene family may be potential susceptibility factors to viruses in other eukaryotic species.
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Pasquariello M, Barabaschi D, Himmelbach A, Steuernagel B, Ariyadasa R, Stein N, Gandolfi F, Tenedini E, Bernardis I, Tagliafico E, Pecchioni N, Francia E. The barley Frost resistance-H2 locus. Funct Integr Genomics 2014; 14:85-100. [PMID: 24442711 DOI: 10.1007/s10142-014-0360-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
Frost resistance-H2 (Fr-H2) is a major QTL affecting freezing tolerance in barley, yet its molecular basis is still not clearly understood. To gain a better insight into the structural characterization of the locus, a high-resolution linkage map developed from the Nure × Tremois cross was initially implemented to map 13 loci which divided the 0.602 cM total genetic distance into ten recombination segments. A PCR-based screening was then applied to identify positive bacterial artificial chromosome (BAC) clones from two genomic libraries of the reference genotype Morex. Twenty-six overlapping BACs from the integrated physical-genetic map were 454 sequenced. Reads assembled in contigs were subsequently ordered, aligned and manually curated in 42 scaffolds. In a total of 1.47 Mbp, 58 protein-coding sequences were identified, 33 of which classified according to similarity with sequences in public databases. As three complete barley C-repeat Binding Factors (HvCBF) genes were newly identified, the locus contained13 full-length HvCBFs, four Related to AP2 Triticeae (RAPT) genes, and at least five CBF pseudogenes. The final overall assembly of Fr-H2 includes more than 90 % of target region: all genes were identified along the locus, and a general survey of Repetitive Elements obtained. We believe that this gold-standard sequence for the Morex Fr-H2 will be a useful genomic tool for structural and evolutionary comparisons with Fr-H2 in winter-hardy cultivars along with Fr-2 of other Triticeae crops.
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Affiliation(s)
- Marianna Pasquariello
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad. Besta, 42122, Reggio Emilia, Italy,
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21
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Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley PE, Muehlbauer GJ, Scholz U, Korol A, Mayer KF, Waugh R, Langridge P, Graner A, Stein N. A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. PLANT PHYSIOLOGY 2014; 164:412-23. [PMID: 24243933 PMCID: PMC3875818 DOI: 10.1104/pp.113.228213] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/13/2013] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.
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22
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García-Cegarra A, Merlo MA, Ponce M, Portela-Bens S, Cross I, Manchado M, Rebordinos L. A preliminary genetic map in Solea senegalensis (Pleuronectiformes, Soleidae) using BAC-FISH and next-generation sequencing. Cytogenet Genome Res 2013; 141:227-40. [PMID: 24107490 DOI: 10.1159/000355001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This article presents the first physical mapping carried out in the Senegalese sole (Solea senegalensis), an important marine fish species of Southern Europe. Eight probes were designated to pick up genes of interest in aquaculture (candidate genes) from a bacterial artificial chromosome (BAC) library using a method of rapid screening based on a 4-dimension PCR. Seven known and 3 unknown clones were isolated and labeled. The 10 BAC clones were used as probes to map the karyotype of the species by fluorescence in situ hybridization (FISH). Nine out of the 10 clones were localized in only 1 chromosome pair, whereas the remaining one hybridized on 2 chromosome pairs. The 2-color FISH experiments showed colocation of 4 probes in 2 chromosome pairs. In addition, 2-color FISH was carried out both with 5S rDNA and the BAC containing the lysozyme gene published previously. This first genetic map of the Senegalese sole represents a starting point for future studies of the sole genome. In addition, 7 out of the 10 BAC clones were sequenced using next-generation sequencing, and bioinformatic characterization of the sequences was carried out. Hence the anchoring of the sequences to specific chromosomes or chromosome arms is now possible, leading to an initial scaffold of the Senegalese sole genome.
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Affiliation(s)
- A García-Cegarra
- Laboratorio de Genética, Facultad de Ciencias del Mar y Ambientales - CACYTMAR, Puerto Real, Spain
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23
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Poursarebani N, Ariyadasa R, Zhou R, Schulte D, Steuernagel B, Martis MM, Graner A, Schweizer P, Scholz U, Mayer K, Stein N. Conserved synteny-based anchoring of the barley genome physical map. Funct Integr Genomics 2013. [PMID: 23812960 DOI: 10.1007/s10142‐013‐0327‐2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gene order is largely collinear in the small-grained cereals, a feature which has proved helpful in both marker development and positional cloning. The accuracy of a virtual gene order map ("genome zipper") for barley (Hordeum vulgare), developed by combining a genetic map of this species with a large number of gene locations obtained from the maps constructed in other grass species, was evaluated here both at the genome-wide level and at the fine scale in a representative segment of the genome. Comparing the whole genome "genome zipper" maps with a genetic map developed by using transcript-derived markers, yielded an accuracy of >94 %. The fine-scale comparison involved a 14 cM segment of chromosome arm 2HL. One hundred twenty-eight genes of the "genome zipper" interval were analysed. Over 95 % (45/47) of the polymorphic markers were genetically mapped and allocated to the expected region of 2HL, following the predicted order. A further 80 of the 128 genes were assigned to the correct chromosome arm 2HL by analysis of wheat-barley addition lines. All 128 gene-based markers developed were used to probe a barley bacterial artificial chromosome (BAC) library, delivering 26 BAC contigs from which all except two were anchored to the targeted zipper interval. The results demonstrate that the gene order predicted by the "genome zipper" is remarkably accurate and that the "genome zipper" represents a highly efficient informational resource for the systematic identification of gene-based markers and subsequent physical map anchoring of the barley genome.
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Affiliation(s)
- Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research-IPK, Corrensstr. 3, 06466 Seeland, OT, Gatersleben, Germany
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24
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Poursarebani N, Ariyadasa R, Zhou R, Schulte D, Steuernagel B, Martis MM, Graner A, Schweizer P, Scholz U, Mayer K, Stein N. Conserved synteny-based anchoring of the barley genome physical map. Funct Integr Genomics 2013; 13:339-50. [PMID: 23812960 DOI: 10.1007/s10142-013-0327-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/17/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
Gene order is largely collinear in the small-grained cereals, a feature which has proved helpful in both marker development and positional cloning. The accuracy of a virtual gene order map ("genome zipper") for barley (Hordeum vulgare), developed by combining a genetic map of this species with a large number of gene locations obtained from the maps constructed in other grass species, was evaluated here both at the genome-wide level and at the fine scale in a representative segment of the genome. Comparing the whole genome "genome zipper" maps with a genetic map developed by using transcript-derived markers, yielded an accuracy of >94 %. The fine-scale comparison involved a 14 cM segment of chromosome arm 2HL. One hundred twenty-eight genes of the "genome zipper" interval were analysed. Over 95 % (45/47) of the polymorphic markers were genetically mapped and allocated to the expected region of 2HL, following the predicted order. A further 80 of the 128 genes were assigned to the correct chromosome arm 2HL by analysis of wheat-barley addition lines. All 128 gene-based markers developed were used to probe a barley bacterial artificial chromosome (BAC) library, delivering 26 BAC contigs from which all except two were anchored to the targeted zipper interval. The results demonstrate that the gene order predicted by the "genome zipper" is remarkably accurate and that the "genome zipper" represents a highly efficient informational resource for the systematic identification of gene-based markers and subsequent physical map anchoring of the barley genome.
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Affiliation(s)
- Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research-IPK, Corrensstr. 3, 06466 Seeland, OT, Gatersleben, Germany
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25
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Silvar C, Perovic D, Nussbaumer T, Spannagl M, Usadel B, Casas A, Igartua E, Ordon F. Towards positional isolation of three quantitative trait loci conferring resistance to powdery mildew in two Spanish barley landraces. PLoS One 2013; 8:e67336. [PMID: 23826271 PMCID: PMC3691219 DOI: 10.1371/journal.pone.0067336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/17/2013] [Indexed: 01/09/2023] Open
Abstract
Three quantitative trait loci (QTL) conferring broad spectrum resistance to powdery mildew, caused by the fungus Blumeria graminis f. sp. hordei, were previously identified on chromosomes 7HS, 7HL and 6HL in the Spanish barley landrace-derived lines SBCC097 and SBCC145. In the present work, a genome-wide putative linear gene index of barley (Genome Zipper) and the first draft of the physical, genetic and functional sequence of the barley genome were used to go one step further in the shortening and explicit demarcation on the barley genome of these regions conferring resistance to powdery mildew as well as in the identification of candidate genes. First, a comparative analysis of the target regions to the barley Genome Zippers of chromosomes 7H and 6H allowed the development of 25 new gene-based molecular markers, which slightly better delimit the QTL intervals. These new markers provided the framework for anchoring of genetic and physical maps, figuring out the outline of the barley genome at the target regions in SBCC097 and SBCC145. The outermost flanking markers of QTLs on 7HS, 7HL and 6HL defined a physical area of 4 Mb, 3.7 Mb and 3.2 Mb, respectively. In total, 21, 10 and 16 genes on 7HS, 7HL and 6HL, respectively, could be interpreted as potential candidates to explain the resistance to powdery mildew, as they encode proteins of related functions with respect to the known pathogen defense-related processes. The majority of these were annotated as belonging to the NBS-LRR class or protein kinase family.
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Affiliation(s)
- Cristina Silvar
- Department of Ecology, Plant and Animal Biology, University of Coruña, A Coruña, Spain.
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26
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Shavrukov Y, Bovill J, Afzal I, Hayes JE, Roy SJ, Tester M, Collins NC. HVP10 encoding V-PPase is a prime candidate for the barley HvNax3 sodium exclusion gene: evidence from fine mapping and expression analysis. PLANTA 2013; 237:1111-22. [PMID: 23277165 DOI: 10.1007/s00425-012-1827-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 12/05/2012] [Indexed: 05/20/2023]
Abstract
In cereals, a common salinity tolerance mechanism is to limit accumulation of Na(+) in the shoot. In a cross between the barley variety Barque-73 (Hordeum vulgare ssp. vulgare) and the accession CPI-71284 of wild barley (H. vulgare ssp. spontaneum), the HvNax3 locus on chromosome 7H was found to determine a ~10-25 % difference in leaf Na(+) accumulation in seedlings grown in saline hydroponics, with the beneficial exclusion trait originating from the wild parent. The Na(+) exclusion allele was also associated with a 13-21 % increase in shoot fresh weight. The HvNax3 locus was delimited to a 0.4 cM genetic interval, where it cosegregated with the HVP10 gene for vacuolar H(+)-pyrophosphatase (V-PPase). Sequencing revealed that the mapping parents encoded identical HVP10 proteins, but salinity-induced mRNA expression of HVP10 was higher in CPI-71284 than in Barque-73, in both roots and shoots. By contrast, the expression of several other genes predicted by comparative mapping to be located in the HvNax3 interval was similar in the two parent lines. Previous work demonstrated roles for V-PPase in ion transport and salinity tolerance. We therefore considered transcription levels of HVP10 to be a possible basis for variation in shoot Na(+) accumulation and biomass production controlled by the HvNax3 locus under saline conditions. Potential mechanisms linking HVP10 expression patterns to the observed phenotypes are discussed.
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Affiliation(s)
- Yuri Shavrukov
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia.
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27
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Carmona A, Friero E, de Bustos A, Jouve N, Cuadrado A. Cytogenetic diversity of SSR motifs within and between Hordeum species carrying the H genome: H. vulgare L. and H. bulbosum L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:949-61. [PMID: 23242107 DOI: 10.1007/s00122-012-2028-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 11/28/2012] [Indexed: 05/10/2023]
Abstract
Non-denaturing FISH (ND-FISH) was used to compare the distribution of four simple sequence repeats (SSRs)-(AG) n , (AAG) n , (ACT) n and (ATC) n -in somatic root tip metaphase spreads of 12 barley (H. vulgare ssp. vulgare) cultivars, seven lines of their wild progenitor H. vulgare ssp. spontaneum, and four lines of their close relative H. bulbosum, to determine whether the range of molecular diversity shown by these highly polymorphic sequences is reflected at the chromosome level. In both, the cultivated and wild barleys, clusters of AG and ATC repeats were invariant. In contrast, clusters of AAG and ACT showed polymorphism. Karyotypes were prepared after the identification of their seven pairs of homologous chromosomes. Variation between these homologues was only observed in one wild accession that showed the segregation of a reciprocal translocation involving chromosomes 5H and 7H. The two subspecies of H. vulgare analysed were no different in terms of their SSRs. Only AAG repeats were found clustered strongly on the chromosomes of all lines of H. bulbosum examined. Wide variation was seen between homologous chromosomes within and across these lines. These results are the first to provide insight into the cytogenetic diversity of SSRs in barley and its closest relatives. Differences in the abundance and distribution of each SSR analysed, between H. vulgare and H. bulbosum, suggest that these species do not share the same H genome, and support the idea that these species are not very closely related. Southern blotting experiments revealed the complex organization of these SSRs, supporting the findings made with ND-FISH.
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Affiliation(s)
- Alejandro Carmona
- Department of Cell Biology and Genetics, University of Alcalá, 28871, Alcalá de Henares (Madrid), Spain
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28
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Heckmann S, Macas J, Kumke K, Fuchs J, Schubert V, Ma L, Novák P, Neumann P, Taudien S, Platzer M, Houben A. The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:555-65. [PMID: 23078243 DOI: 10.1111/tpj.12054] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/11/2012] [Accepted: 10/16/2012] [Indexed: 05/18/2023]
Abstract
In higher plants, the large-scale structure of monocentric chromosomes consists of distinguishable eu- and heterochromatic regions, the proportions and organization of which depend on a species' genome size. To determine whether the same interplay is maintained for holocentric chromosomes, we investigated the distribution of repetitive sequences and epigenetic marks in the woodrush Luzula elegans (3.81 Gbp/1C). Sixty-one per cent of the L. elegans genome is characterized by highly repetitive DNA, with over 30 distinct sequence families encoding an exceptionally high diversity of satellite repeats. Over 33% of the genome is composed of the Angela clade of Ty1/copia LTR retrotransposons, which are uniformly dispersed along the chromosomes, while the satellite repeats occur as bands whose distribution appears to be biased towards the chromosome termini. No satellite showed an almost chromosome-wide distribution pattern as expected for a holocentric chromosome and no typical centromere-associated LTR retrotransposons were found either. No distinguishable large-scale patterns of eu- and heterochromatin-typical epigenetic marks or early/late DNA replicating domains were found along mitotic chromosomes, although super-high-resolution light microscopy revealed distinguishable interspersed units of various chromatin types. Our data suggest a correlation between the centromere and overall genome organization in species with holocentric chromosomes.
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Affiliation(s)
- Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
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29
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Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R. Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics 2012. [PMID: 23161406 DOI: 10.1007/s10142‐012‐0300‐5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
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Affiliation(s)
- C Feuillet
- INRA-UBP UMR 1095 Genetics and Diversity of Cereals, Clermont-Ferrand, France.
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30
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Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R. Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics 2012; 12:573-83. [PMID: 23161406 PMCID: PMC3508266 DOI: 10.1007/s10142-012-0300-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 11/26/2022]
Abstract
The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
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Affiliation(s)
- C Feuillet
- INRA-UBP UMR 1095 Genetics and Diversity of Cereals, Clermont-Ferrand, France.
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31
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A physical, genetic and functional sequence assembly of the barley genome. Nature 2012; 491:711-6. [PMID: 23075845 DOI: 10.1038/nature11543] [Citation(s) in RCA: 934] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/30/2012] [Indexed: 12/13/2022]
Abstract
Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.
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32
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Huynh BL, Mather DE, Schreiber AW, Toubia J, Baumann U, Shoaei Z, Stein N, Ariyadasa R, Stangoulis JCR, Edwards J, Shirley N, Langridge P, Fleury D. Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley. PLANT MOLECULAR BIOLOGY 2012; 80:299-314. [PMID: 22864927 DOI: 10.1007/s11103-012-9949-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/23/2012] [Indexed: 05/21/2023]
Abstract
Fructans are soluble carbohydrates with health benefits and possible roles in plant adaptation. Fructan biosynthetic genes were isolated using comparative genomics and physical mapping followed by BAC sequencing in barley. Genes encoding sucrose:sucrose 1-fructosyltransferase (1-SST), fructan:fructan 1-fructosyltransferase (1-FFT) and sucrose:fructan 6-fructosyltransferase (6-SFT) were clustered together with multiple copies of vacuolar invertase genes and a transposable element on two barley BAC. Intron-exon structures of the genes were similar. Phylogenetic analysis of the fructosyltransferases and invertases in the Poaceae showed that the fructan biosynthetic genes may have evolved from vacuolar invertases. Quantitative real-time PCR was performed using leaf RNA extracted from three wheat cultivars grown under different conditions. The 1-SST, 1-FFT and 6-SFT genes had correlated expression patterns in our wheat experiment and in existing barley transcriptome database. Single nucleotide polymorphism (SNP) markers were developed and successfully mapped to a major QTL region affecting wheat grain fructan accumulation in two independent wheat populations. The alleles controlling high- and low- fructan in parental lines were also found to be associated in fructan production in a diverse set of 128 wheat lines. To the authors' knowledge, this is the first report on the mapping and sequencing of a fructan biosynthetic gene cluster and in particular, the isolation of a novel 1-FFT gene from barley.
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Affiliation(s)
- Bao-Lam Huynh
- Australian Centre for Plant Functional Genomics and School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond 5064, South Australia,
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33
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Advances in genomics for flatfish aquaculture. GENES AND NUTRITION 2012; 8:5-17. [PMID: 22903900 DOI: 10.1007/s12263-012-0312-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 08/02/2012] [Indexed: 10/28/2022]
Abstract
Fish aquaculture is considered to be one of the most sustainable sources of protein for humans. Many different species are cultured worldwide, but among them, marine flatfishes comprise a group of teleosts of high commercial interest because of their highly prized white flesh. However, the aquaculture of these fishes is seriously hampered by the scarce knowledge on their biology. In recent years, various experimental 'omics' approaches have been applied to farmed flatfishes to increment the genomic resources available. These tools are beginning to identify genetic markers associated with traits of commercial interest, and to unravel the molecular basis of different physiological processes. This article summarizes recent advances in flatfish genomics research in Europe. We focus on the new generation sequencing technologies, which can produce a massive amount of DNA sequencing data, and discuss their potentials and applications for de novo genome sequencing and transcriptome analysis. The relevance of these methods in nutrigenomics and foodomics approaches for the production of healthy animals, as well as high quality and safety products for the consumer, is also briefly discussed.
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34
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Zakhrabekova S, Gough SP, Braumann I, Müller AH, Lundqvist J, Ahmann K, Dockter C, Matyszczak I, Kurowska M, Druka A, Waugh R, Graner A, Stein N, Steuernagel B, Lundqvist U, Hansson M. Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley. Proc Natl Acad Sci U S A 2012; 109:4326-4331. [PMID: 22371569 DOI: 10.1073/pnas.1113009109\r1113009109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Time to flowering has an important impact on yield and has been a key trait in the domestication of crop plants and the spread of agriculture. In 1961, the cultivar Mari (mat-a.8) was the very first induced early barley (Hordeum vulgare L.) mutant to be released into commercial production. Mari extended the range of two-row spring barley cultivation as a result of its photoperiod insensitivity. Since its release, Mari or its derivatives have been used extensively across the world to facilitate short-season adaptation and further geographic range extension. By exploiting an extended historical collection of early-flowering mutants of barley, we identified Praematurum-a (Mat-a), the gene responsible for this key adaptive phenotype, as a homolog of the Arabidopsis thaliana circadian clock regulator Early Flowering 3 (Elf3). We characterized 87 induced mat-a mutant lines and identified >20 different mat-a alleles that had clear mutations leading to a defective putative ELF3 protein. Expression analysis of HvElf3 and Gigantea in mutant and wild-type plants demonstrated that mat-a mutations disturb the flowering pathway, leading to the early phenotype. Alleles of Mat-a therefore have important and demonstrated breeding value in barley but probably also in many other day-length-sensitive crop plants, where they may tune adaptation to different geographic regions and climatic conditions, a critical issue in times of global warming.
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35
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Advances in BAC-based physical mapping and map integration strategies in plants. J Biomed Biotechnol 2012; 2012:184854. [PMID: 22500080 PMCID: PMC3303678 DOI: 10.1155/2012/184854] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 10/26/2011] [Accepted: 11/11/2011] [Indexed: 12/29/2022] Open
Abstract
In the advent of next-generation sequencing (NGS) platforms, map-based sequencing strategy has been recently suppressed being too expensive and laborious. The detailed studies on NGS drafts alone indicated these assemblies remain far from gold standard reference quality, especially when applied on complex genomes. In this context the conventional BAC-based physical mapping has been identified as an important intermediate layer in current hybrid sequencing strategy. BAC-based physical map construction and its integration with high-density genetic maps have benefited from NGS and high-throughput array platforms. This paper addresses the current advancements of BAC-based physical mapping and high-throughput map integration strategies to obtain densely anchored well-ordered physical maps. The resulted maps are of immediate utility while providing a template to harness the maximum benefits of the current NGS platforms.
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36
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Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley. Proc Natl Acad Sci U S A 2012; 109:4326-31. [PMID: 22371569 DOI: 10.1073/pnas.1113009109] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Time to flowering has an important impact on yield and has been a key trait in the domestication of crop plants and the spread of agriculture. In 1961, the cultivar Mari (mat-a.8) was the very first induced early barley (Hordeum vulgare L.) mutant to be released into commercial production. Mari extended the range of two-row spring barley cultivation as a result of its photoperiod insensitivity. Since its release, Mari or its derivatives have been used extensively across the world to facilitate short-season adaptation and further geographic range extension. By exploiting an extended historical collection of early-flowering mutants of barley, we identified Praematurum-a (Mat-a), the gene responsible for this key adaptive phenotype, as a homolog of the Arabidopsis thaliana circadian clock regulator Early Flowering 3 (Elf3). We characterized 87 induced mat-a mutant lines and identified >20 different mat-a alleles that had clear mutations leading to a defective putative ELF3 protein. Expression analysis of HvElf3 and Gigantea in mutant and wild-type plants demonstrated that mat-a mutations disturb the flowering pathway, leading to the early phenotype. Alleles of Mat-a therefore have important and demonstrated breeding value in barley but probably also in many other day-length-sensitive crop plants, where they may tune adaptation to different geographic regions and climatic conditions, a critical issue in times of global warming.
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Shi X, Zeng H, Xue Y, Luo M. A pair of new BAC and BIBAC vectors that facilitate BAC/BIBAC library construction and intact large genomic DNA insert exchange. PLANT METHODS 2011; 7:33. [PMID: 21985432 PMCID: PMC3213141 DOI: 10.1186/1746-4811-7-33] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Accepted: 10/11/2011] [Indexed: 05/25/2023]
Abstract
BACKGROUND Large-insert BAC and BIBAC libraries are important tools for structural and functional genomics studies of eukaryotic genomes. To facilitate the construction of BAC and BIBAC libraries and the transfer of complete large BAC inserts into BIBAC vectors, which is desired in positional cloning, we developed a pair of new BAC and BIBAC vectors. RESULTS The new BAC vector pIndigoBAC536-S and the new BIBAC vector BIBAC-S have the following features: 1) both contain two 18-bp non-palindromic I-SceI sites in an inverted orientation at positions that flank an identical DNA fragment containing the lacZ selection marker and the cloning site. Large DNA inserts can be excised from the vectors as single fragments by cutting with I-SceI, allowing the inserts to be easily sized. More importantly, because the two vectors contain different antibiotic resistance genes for transformant selection and produce the same non-complementary 3' protruding ATAA ends by I-SceI that suppress self- and inter-ligations, the exchange of intact large genomic DNA inserts between the BAC and BIBAC vectors is straightforward; 2) both were constructed as high-copy composite vectors. Reliable linearized and dephosphorylated original low-copy pIndigoBAC536-S and BIBAC-S vectors that are ready for library construction can be prepared from the high-copy composite vectors pHZAUBAC1 and pHZAUBIBAC1, respectively, without the need for additional preparation steps or special reagents, thus simplifying the construction of BAC and BIBAC libraries. BIBAC clones constructed with the new BIBAC-S vector are stable in both E. coli and Agrobacterium. The vectors can be accessed through our website http://GResource.hzau.edu.cn. CONCLUSIONS The two new vectors and their respective high-copy composite vectors can largely facilitate the construction and characterization of BAC and BIBAC libraries. The transfer of complete large genomic DNA inserts from one vector to the other is made straightforward.
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Affiliation(s)
- Xue Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyang Zeng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yadong Xue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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