Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago long-range linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.

Department of Plant and Microbial Biology University of Zurich Zurich Switzerland

Institute for Plant Production Sciences Agroscope Switzerland

Institute of Experimental Botany Centre of the Region Haná for Biotechnological and Agricultural Research Olomouc Czech Republic

Zobrazit více v PubMed

Cell. 2002 Mar 22;108(6):743-54 PubMed

Mol Syst Biol. 2011 Oct 11;7:539 PubMed

BMC Plant Biol. 2014 Dec 30;14:379 PubMed

Genome Biol. 2015 Sep 02;16:183 PubMed

Plant Biotechnol J. 2013 Jan;11(1):23-32 PubMed

Genome Biol. 2016 Oct 31;17 (1):221 PubMed

Nat Biotechnol. 2016 Jun;34(6):652-5 PubMed

BMC Genomics. 2008 Jun 19;9:294 PubMed

Cytogenet Genome Res. 2010 Jul;129(1-3):211-23 PubMed

Genome Res. 2016 Mar;26(3):342-50 PubMed

PLoS One. 2013;8(1):e54101 PubMed

Genome Biol. 2015 Feb 26;16:48 PubMed

Proc Natl Acad Sci U S A. 2011 May 3;108(18):7619-24 PubMed

Bioinformatics. 2014 Aug 1;30(15):2114-20 PubMed

Nature. 2013 Apr 4;496(7443):91-5 PubMed

Science. 2013 Aug 16;341(6147):786-8 PubMed

Theor Appl Genet. 2002 Jun;104(8):1362-1372 PubMed

Science. 2014 Jul 18;345(6194):1249721 PubMed

Plant Cell. 2004 Oct;16(10):2822-35 PubMed

Plant J. 2016 Aug;87(4):403-19 PubMed

Methods Mol Biol. 2000;132:243-58 PubMed

Nature. 2010 Feb 11;463(7282):763-8 PubMed

Funct Integr Genomics. 2012 Aug;12(3):397-416 PubMed

Nat Genet. 2012 Jun 03;44(7):803-7 PubMed

Nat Biotechnol. 2013 Dec;31(12):1119-25 PubMed

Genome. 2003 Oct;46(5):893-905 PubMed

Theor Appl Genet. 2017 Jan;130(1):1-12 PubMed

Theor Appl Genet. 2007 Oct;115(6):877-84 PubMed

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7940-5 PubMed

Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13436-41 PubMed

Genetics. 2000 Dec;156(4):2033-41 PubMed

PLoS One. 2013;8(2):e57994 PubMed

PLoS One. 2011;6(7):e21614 PubMed

Nat Genet. 2016 Dec;48(12 ):1576-1580 PubMed

PLoS One. 2011;6(8):e23501 PubMed

Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PubMed

A single NLR gene confers resistance to leaf and stripe rust in wheat

Sexy ways: approaches to studying plant sex chromosomes

Barley MLA3 recognizes the host-specificity effector Pwl2 from Magnaporthe oryzae

Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Flow Cytometric Analysis and Sorting of Plant Chromosomes

Flow karyotyping of wheat-Aegilops additions facilitate dissecting the genomes of Ae. biuncialis and Ae. geniculata into individual chromosomes

A lineage-specific Exo70 is required for receptor kinase-mediated immunity in barley

Capturing Wheat Phenotypes at the Genome Level

Transfer of the ph1b Deletion Chromosome 5B From Chinese Spring Wheat Into a Winter Wheat Line and Induction of Chromosome Rearrangements in Wheat-Aegilops biuncialis Hybrids

Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62

Long-range assembly of sequences helps to unravel the genome structure and small variation of the wheat-Haynaldia villosa translocated chromosome 6VS.6AL

Chromosome analysis and sorting

Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing

The Coiled-Coil NLR Rph1, Confers Leaf Rust Resistance in Barley Cultivar Sudan

Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene

Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

Integration of Genetic and Cytogenetic Maps and Identification of Sex Chromosome in Garden Asparagus (Asparagus officinalis L.)