A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

被引：68

作者：

Ariyadasa, Ruvini ^{[1
]}

Mascher, Martin ^{[1
]}

Nussbaumer, Thomas ^{[2
]}

Schulte, Daniela ^{[1
]}

Frenkel, Zeev ^{[3
]}

Poursarebani, Naser ^{[1
]}

Zhou, Ruonan ^{[1
]}

Steuernagel, Burkhard ^{[1
]}

Gundlach, Heidrun ^{[2
]}

Taudien, Stefan ^{[4
]}

Felder, Marius ^{[4
]}

Platzer, Matthias ^{[4
]}

Himmelbach, Axel ^{[1
]}

Schmutzer, Thomas ^{[1
]}

Hedley, Pete E. ^{[5
]}

Muehlbauer, Gary J. ^{[6
,7
]}

Scholz, Uwe ^{[1
]}

Korol, Abraham ^{[3
]}

Mayer, Klaus F. X. ^{[2
]}

Waugh, Robbie ^{[5
]}

Langridge, Peter ^{[8
]}

Graner, Andreas ^{[1
]}

Stein, Nils ^{[1
]}

机构：

[1] Leibniz Inst Plant Genet & Crop Plant Res, D-06466 Gatersleben, Stadt Seeland, Germany

[2] Helmholtz Zentrum Munchen, Munich Informat Ctr Prot Sequence, Inst Bioinformat & Syst Biol, D-85764 Neuherberg, Germany

[3] Univ Haifa, Inst Evolut, IL-31905 Haifa, Israel

[4] Fritz Lipmann Inst, Leibniz Inst Age Res, D-07745 Jena, Germany

[5] James Hutton Inst, Dundee DD25DE, Scotland

[6] Univ Minnesota, Dept Agron & Plant Genet, St Paul, MN 55108 USA

[7] Univ Minnesota, Dept Plant Biol, St Paul, MN 55108 USA

[8] Univ Adelaide, Australian Ctr Plant Funct Genom, Glen Osmond, SA 5064, Australia

来源：

PLANT PHYSIOLOGY | 2014年 / 164卷 / 01期

基金：

澳大利亚研究理事会; 英国生物技术与生命科学研究理事会;

关键词：

HORDEUM-VULGARE; DISEASE RESISTANCE; GENOME ANALYSIS; COMPLEX GENOME; DRAFT GENOME; GENE; WHEAT; IDENTIFICATION; RECOMBINATION; ADAPTATION;

D O I：

10.1104/pp.113.228213

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

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.

引用

页码：412 / 423

页数：12

共 59 条

[41] Recognition specificity and RAR1/SGT1 dependence in barley Mla disease resistance genes to the powdery mildew fungus [J].

Shen, QH ;

Zhou, FS ;

Bieri, S ;

Haizel, T ;

Shirasu, K ;

Schulze-Lefert, P .

PLANT CELL, 2003, 15 (03) :732-744

[42] A novel class of eukaryotic zinc-binding proteins is required for disease resistance signaling in barley and development in C-elegans [J].

Shirasu, K ;

Lahaye, T ;

Tan, MW ;

Zhou, FS ;

Azevedo, C ;

Schulze-Lefert, P .

CELL, 1999, 99 (04) :355-366

[43] Contigs built with fingerprints, markers, and FPCV4.7 [J].

Soderlund, C ;

Humphray, S ;

Dunham, A ;

French, L .

GENOME RESEARCH, 2000, 10 (11) :1772-1787

[44] The eukaryotic translation initiation factor 4E confers multiallelic recessive Bymovirus resistance in Hordeum vulgare (L.) [J].

Stein, N ;

Perovic, D ;

Kumlehn, J ;

Pellio, B ;

Stracke, S ;

Streng, S ;

Ordon, F ;

Graner, A .

PLANT JOURNAL, 2005, 42 (06) :912-922

[45] De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley [J].

Steuernagel, Burkhard ;

Taudien, Stefan ;

Gundlach, Heidrun ;

Seidel, Michael ;

Ariyadasa, Ruvini ;

Schulte, Daniela ;

Petzold, Andreas ;

Felder, Marius ;

Graner, Andreas ;

Scholz, Uwe ;

Mayer, Klaus F. X. ;

Platzer, Matthias ;

Stein, Nils .

BMC GENOMICS, 2009, 10

[46] Boron-toxicity tolerance in barley arising from efflux transporter amplification [J].

Sutton, Tim ;

Baumann, Ute ;

Hayes, Julie ;

Collins, Nicholas C. ;

Shi, Bu-Jun ;

Schnurbusch, Thorsten ;

Hay, Alison ;

Mayo, Gwenda ;

Pallotta, Margaret ;

Tester, Mark ;

Langridge, Peter .

SCIENCE, 2007, 318 (5855) :1446-1449

[47] Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway [J].

Taketa, Shin ;

Amano, Satoko ;

Tsujino, Yasuhiro ;

Sato, Tomohiko ;

Saisho, Daisuke ;

Kakeda, Katsuyuki ;

Nomura, Mika ;

Suzuki, Toshisada ;

Matsumoto, Takashi ;

Sato, Kazuhiro ;

Kanamori, Hiroyuki ;

Kawasaki, Shinji ;

Takeda, Kazuyoshi .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (10) :4062-4067

[48] Sequencing of BAC pools by different next generation sequencing platforms and strategies [J].

Taudien S. ;

Steuernagel B. ;

Ariyadasa R. ;

Schulte D. ;

Schmutzer T. ;

Groth M. ;

Felder M. ;

Petzold A. ;

Scholz U. ;

Mayer K.F. ;

Stein N. ;

Platzer M. .

BMC Research Notes, 4 (1)

[49] The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley [J].

Turner, A ;

Beales, J ;

Faure, S ;

Dunford, RP ;

Laurie, DA .

SCIENCE, 2005, 310 (5750) :1031-1034

[50]

van Hintum T, 2003, DEV PL GEN, V7, P247, DOI 10.1016/S0168-7972(03)80014-2

← 1 2 3 4 5 6 →