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      Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

      research-article
      1 , 1 , 2 , 3 , 4 , 5 , 2 , 6 , 7 , 4 , 2 , 2 , 36 , 2 , 8 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 9 , 1 , 37 , 1 , 10 , 1 , 11 , 1 , 1 , 1 , 1 , 1 , 1 , 12 , 12 , 13 , 13 , 14 , 14 , 15 , 15 , 16 , 15 , 17 , 18 , 19 , 20 , 20 , 21 , 21 , 22 , 23 , 24 , 24 , 24 , 25 , 25 , 26 , 6 , 6 , 27 , 28 , 27 , 29 , 30 , 29 , 31 , 31 , 32 , 33 , 33 , 33 , 34 , 1 , 8 , 35 , 5 , 38 , , 4 , , 2 , 37 , , 1 , 37 ,
      Nature Biotechnology
      Nature Publishing Group US
      Plant domestication, Genome informatics, Plant breeding, Plant immunity, Genome-wide association studies

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          Abstract

          Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

          Abstract

          Exploring the diversity of the wild progenitor of the wheat D subgenome allows for rapid trait discovery.

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          Fitting Linear Mixed-Effects Models Usinglme4

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            Minimap2: pairwise alignment for nucleotide sequences

            Heng Li (2018)
            Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.
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              Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

              Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT2, for representing and searching an expanded model of the human reference genome, in which a large catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate two initial applications of HISAT2: HLA typing, a critical need in human organ transplantation, and DNA fingerprinting, widely used in forensics. These applications are part of HISAT-genotype, with performance not only surpassing earlier computational methods, but matching or exceeding the accuracy of laboratory-based assays.
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                Author and article information

                Contributors
                a.bentley@cgiar.org
                bkeller@botinst.uzh.ch
                jpoland@ksu.edu
                brande.wulff@kaust.edu.sa
                Journal
                Nat Biotechnol
                Nat Biotechnol
                Nature Biotechnology
                Nature Publishing Group US (New York )
                1087-0156
                1546-1696
                1 November 2021
                1 November 2021
                2022
                : 40
                : 3
                : 422-431
                Affiliations
                [1 ]GRID grid.14830.3e, ISNI 0000 0001 2175 7246, John Innes Centre, Norwich Research Park, ; Norwich, UK
                [2 ]GRID grid.36567.31, ISNI 0000 0001 0737 1259, Department of Plant Pathology and Wheat Genetics Resource Center, , Kansas State University, ; Manhattan, KS USA
                [3 ]GRID grid.473327.6, ISNI 0000 0004 0604 4346, Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, ; Colonia, Uruguay
                [4 ]GRID grid.7400.3, ISNI 0000 0004 1937 0650, Department of Plant and Microbial Biology, , University of Zurich, ; Zurich, Switzerland
                [5 ]GRID grid.17595.3f, ISNI 0000 0004 0383 6532, The John Bingham Laboratory, , NIAB, ; Cambridge, UK
                [6 ]GRID grid.25152.31, ISNI 0000 0001 2154 235X, Crop Development Centre, Department of Plant Sciences, , University of Saskatchewan, ; Saskatoon, Saskatchewan Canada
                [7 ]GRID grid.17091.3e, ISNI 0000 0001 2288 9830, Faculty of Land and Food Systems, , The University of British Columbia, ; Vancouver, British Columbia Canada
                [8 ]GRID grid.418934.3, ISNI 0000 0001 0943 9907, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, ; Seeland, Germany
                [9 ]GRID grid.27871.3b, ISNI 0000 0000 9750 7019, National Key Laboratory of Crop Genetics and Germplasm Enhancement, , Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, ; Nanjing, China
                [10 ]GRID grid.1010.0, ISNI 0000 0004 1936 7304, School of Agriculture, Food and Wine, , University of Adelaide, ; Glen Osmond, South Australia Australia
                [11 ]GRID grid.6292.f, ISNI 0000 0004 1757 1758, Department of Agricultural and Food Sciences, Alma Mater Studiorum, , University of Bologna, ; Bologna, Italy
                [12 ]GRID grid.7048.b, ISNI 0000 0001 1956 2722, Department of Agroecology, Global Rust Reference Center, , Aarhus University, ; Slagelse, Denmark
                [13 ]Texas A&M AgriLife Research, Amarillo, TX USA
                [14 ]GRID grid.12136.37, ISNI 0000 0004 1937 0546, Institute for Cereal Crops Improvement, School of Plant Sciences and Food Security, , Tel Aviv University, ; Tel Aviv, Israel
                [15 ]GRID grid.5173.0, ISNI 0000 0001 2298 5320, Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, , University of Natural Resources and Life Sciences, ; Vienna, Austria
                [16 ]GRID grid.8570.a, ISNI 0000 0001 2152 4506, Laboratory of Plant Breeding, Department of Agronomy, Faculty of Agriculture, , Universitas Gadjah Mada, ; Yogyakarta, Indonesia
                [17 ]GRID grid.411528.b, ISNI 0000 0004 0611 9352, Department of Agronomy and Plant Breeding, , Ilam University, ; Ilam, Iran
                [18 ]Institute of Botany, Plant Physiology and Genetics, Tajik National Academy of Sciences, Dushanbe, Tajikistan
                [19 ]GRID grid.14830.3e, ISNI 0000 0001 2175 7246, Germplasm Resources Unit, , John Innes Centre, Norwich Research Park, ; Norwich, UK
                [20 ]GRID grid.17635.36, ISNI 0000000419368657, Department of Plant Pathology, , University of Minnesota, ; Saint Paul, MN USA
                [21 ]GRID grid.412577.2, ISNI 0000 0001 2176 2352, School of Agricultural Biotechnology, , Punjab Agricultural University, ; Ludhiana, India
                [22 ]GRID grid.493032.f, Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, ; Canberra, Australian Capital Territory Australia
                [23 ]GRID grid.418376.f, ISNI 0000 0004 1800 7673, Wheat Research Department, , Field Crops Research Institute, Agricultural Research Center, ; Giza, Egypt
                [24 ]GRID grid.421605.4, ISNI 0000 0004 0447 4123, Earlham Institute, Norwich Research Park, ; Norwich, UK
                [25 ]GRID grid.426256.1, QIAGEN Aarhus A/S, ; Aarhus, Denmark
                [26 ]GRID grid.164295.d, ISNI 0000 0001 0941 7177, Department of Plant Science and Landscape Architecture, , University of Maryland, ; College Park, MD USA
                [27 ]GRID grid.464345.4, Institute of Crop Science, Chinese Academy of Agricultural Sciences, ; Beijing, China
                [28 ]GRID grid.80510.3c, ISNI 0000 0001 0185 3134, Triticeae Research Institute, , Sichuan Agricultural University, ; Chengdu, China
                [29 ]GRID grid.512835.8, USDA-ARS Cereal Crops Research Unit, , Edward T. Schafer Agricultural Research Center, ; Fargo, ND USA
                [30 ]USDA-ARS, Plant Science Research Unit, Raleigh, NC USA
                [31 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Plant Sciences, , University of California, ; Davis, CA USA
                [32 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Plant and Microbial Biology, , University of California, ; Berkeley, CA USA
                [33 ]GRID grid.4567.0, ISNI 0000 0004 0483 2525, Plant Genome and Systems Biology, , Helmholtz Center Munich, ; Neuherberg, Germany
                [34 ]GRID grid.6936.a, ISNI 0000000123222966, Faculty of Life Sciences, , Technical University Munich, ; Weihenstephan, Germany
                [35 ]GRID grid.421064.5, ISNI 0000 0004 7470 3956, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, ; Leipzig, Germany
                [36 ]Present Address: Bayer R&D Services LLC, Kansas City, MO USA
                [37 ]GRID grid.45672.32, ISNI 0000 0001 1926 5090, Present Address: Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), , King Abdullah University of Science and Technology (KAUST), ; Thuwal, Saudi Arabia
                [38 ]GRID grid.433436.5, ISNI 0000 0001 2289 885X, Present Address: International Maize and Wheat Improvement Center (CIMMYT), ; Texcoco, Mexico
                Author information
                http://orcid.org/0000-0002-6632-2171
                http://orcid.org/0000-0003-2689-0112
                http://orcid.org/0000-0002-3864-0631
                http://orcid.org/0000-0002-1429-2716
                http://orcid.org/0000-0002-4370-8565
                http://orcid.org/0000-0003-0665-5094
                http://orcid.org/0000-0002-7733-0185
                http://orcid.org/0000-0002-6458-8697
                http://orcid.org/0000-0001-5935-2578
                http://orcid.org/0000-0003-4936-1694
                http://orcid.org/0000-0003-2920-4720
                http://orcid.org/0000-0002-6162-4795
                http://orcid.org/0000-0002-4323-9009
                http://orcid.org/0000-0001-7070-3623
                http://orcid.org/0000-0002-8800-4764
                http://orcid.org/0000-0002-7271-8914
                http://orcid.org/0000-0003-4692-5001
                http://orcid.org/0000-0001-5838-9328
                http://orcid.org/0000-0001-9899-4557
                http://orcid.org/0000-0002-8284-7728
                http://orcid.org/0000-0002-4914-2697
                http://orcid.org/0000-0001-7969-8760
                http://orcid.org/0000-0003-4748-2900
                http://orcid.org/0000-0001-9186-3386
                http://orcid.org/0000-0002-0801-5093
                http://orcid.org/0000-0002-6045-9169
                http://orcid.org/0000-0001-8736-4568
                http://orcid.org/0000-0003-4311-5935
                http://orcid.org/0000-0002-0748-2351
                http://orcid.org/0000-0002-0060-3114
                http://orcid.org/0000-0002-2695-5521
                http://orcid.org/0000-0002-8447-2886
                http://orcid.org/0000-0001-7961-5363
                http://orcid.org/0000-0001-9793-0340
                http://orcid.org/0000-0002-8599-9479
                http://orcid.org/0000-0002-6234-1789
                http://orcid.org/0000-0002-7789-6875
                http://orcid.org/0000-0002-4719-3220
                http://orcid.org/0000-0001-5508-1125
                http://orcid.org/0000-0002-3377-4040
                http://orcid.org/0000-0001-7000-2034
                http://orcid.org/0000-0002-1958-2827
                http://orcid.org/0000-0002-9653-3287
                http://orcid.org/0000-0002-0427-6528
                http://orcid.org/0000-0002-9744-5887
                http://orcid.org/0000-0002-1679-0700
                http://orcid.org/0000-0002-5543-1911
                http://orcid.org/0000-0003-1194-7796
                http://orcid.org/0000-0001-6484-1077
                http://orcid.org/0000-0002-9814-1770
                http://orcid.org/0000-0001-6373-6013
                http://orcid.org/0000-0001-5519-4357
                http://orcid.org/0000-0003-2379-9225
                http://orcid.org/0000-0002-7856-1399
                http://orcid.org/0000-0003-4044-4346
                Article
                1058
                10.1038/s41587-021-01058-4
                8926922
                34725503
                30583d84-c85a-4d38-9d68-d93ee5569160
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 1 February 2021
                : 16 August 2021
                Funding
                Funded by: Fulbright Association
                Funded by: FundRef https://doi.org/10.13039/501100000268, RCUK | Biotechnology and Biological Sciences Research Council (BBSRC);
                Award ID: BB/P016855/1
                Award ID: BB/P016855/1
                Award ID: BB/N019113/1
                Award ID: BB/P016855/1
                Award ID: BBS/E/J/000PR8000
                Award ID: BB/P016855/1
                Award ID: BB/P016855/1
                Award ID: BBS/E/T/000PR9817
                Award ID: BBS/E/T/000PR9814
                Award ID: BB/I002561/1
                Award ID: BB/P016855/1
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100005825, United States Department of Agriculture | National Institute of Food and Agriculture (NIFA);
                Funded by: FundRef https://doi.org/10.13039/100008921, Ministry of Agriculture - Saskatchewan (Ministry of Agriculture);
                Award ID: 20180095
                Award ID: 20180095
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100000288, Royal Society;
                Award ID: UF150081
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100012774, Innovationsfonden (Innovation Fund Denmark);
                Award ID: 4105-00022B
                Award ID: 4105-00022B
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100010447, Kementerian Riset, Teknologi dan Pendidikan Tinggi (Ministry of Research, Technology and Higher Education of the Republic of Indonesia);
                Funded by: FundRef https://doi.org/10.13039/501100001407, Department of Biotechnology, Ministry of Science and Technology (DBT);
                Award ID: BT/PR30871/BIC/101/1159/2018
                Award ID: BT/IN/Indo-UK/CGAT/14/PC/2014-15
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100001809, National Natural Science Foundation of China (National Science Foundation of China);
                Award ID: 91731305
                Award ID: 31661143007
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100005196, Chinese Academy of Agricultural Sciences (CAAS);
                Award ID: CAAS-DRW202002
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000199, U.S. Department of Agriculture (United States Department of Agriculture);
                Funded by: FundRef https://doi.org/10.13039/100000001, National Science Foundation (NSF);
                Award ID: IOS-1238231
                Award ID: 1822162
                Award ID: 1339389
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100001711, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation);
                Award ID: 310030B_182833
                Award Recipient :
                Categories
                Article
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                © The Author(s), under exclusive licence to Springer Nature America, Inc. 2022

                Biotechnology
                plant domestication,genome informatics,plant breeding,plant immunity,genome-wide association studies

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