Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

Nature Biotechnology

Volumn 35, Issue 8, 2017, Pages 793-796

  Thind, Anupriya Kaur ^a   Wicker, Thomas ^a   Šimková, Hana ^b   Fossati, Dario ^c   Moullet, Odile ^c   Brabant, Cécile ^c   Vrána, Jan ^b   Doležel, Jaroslav ^b   Krattinger, Simon G ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b PALACKÝ UNIVERSITY   (Czech Republic)

^c Institute for Plant Production Sciences Agroscope   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CROPS; GENE ENCODING; PLANTS (BOTANY);

ARABIDOPSIS THALIANA; COMPLEXITY REDUCTION; ETHYL METHANESULFONATE; HEXAPLOID WHEAT; HIGH-QUALITY SEQUENCES; IMMUNE RECEPTORS; LEAF RUST RESISTANCE GENES; MOLECULAR MARKER;

CLONING;

MESYLIC ACID ETHYL ESTER; MOLECULAR MARKER; PLANT PROTEIN;

ARABIDOPSIS THALIANA; ARTICLE; CHROMOSOME ANALYSIS; CULTIVAR; GENE MAPPING; GENETIC RESISTANCE; HEXAPLOIDY; LEAF RUST; MOLECULAR CLONING; NONHUMAN; PHENOTYPE; PLANT GENOME; PRIORITY JOURNAL; WHEAT; BIOTECHNOLOGY; FOOD GRAIN; GENETIC LINKAGE; GENETICS; PLANT GENE; PROCEDURES;

BIOTECHNOLOGY; CLONING, MOLECULAR; EDIBLE GRAIN; GENES, PLANT; GENETIC LINKAGE; TRITICUM;

EID: 85027272000     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3877     Document Type: Article

References (46)

1. Mago, R. et al. Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC Plant Biol. 14, 379 (2014).
2. Jordan, K.W. et al. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol. 16, 48 (2015).
3. Chia, J.M. et al. Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44, 803-807 (2012).
4. Rawat, N. et al. Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight. Nat. Genet. 48, 1576-1580 (2016).
5. Putnam, N.H. et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26, 342-350 (2016).
6. FAO. The State of the World's Land and Water Resources for Food and Agriculture (SOLAW)-Managing Systems at Risk (Food and Agriculture Organization of the United Nations, Rome and Earthscan, London, 2011).
7. Krattinger, S.G., Wicker, T. & Keller, B. in Genetics and Genomics of the Triticeae (eds. Feuillet, C. & Muehlbauer, G.J.) 337-357 (Springer, New York, 2009).
8. Stein, N., Feuillet, C., Wicker, T., Schlagenhauf, E. & Keller, B. Subgenome chromosome walking in wheat: a 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.). Proc. Natl. Acad. Sci. USA 97, 13436-13441 (2000).
9. Ay, F. & Noble, W.S. Analysis methods for studying the 3D architecture of the genome. Genome Biol. 16, 183 (2015).
10. Burton, J.N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119-1125 (2013).
11. Kolmer, J. Leaf rust of wheat: pathogen biology, variation and host resistance. Forests 4, 70-84 (2013).
12. Dyck, P.L. & Kerber, E.R. Inheritance in hexaploid wheat of adult-plant leaf rust resistance derived from Aegilops squarrosa. Can. J. Genet. Cytol. 12, 175-180 (1970).
13. Hiebert, C.W., Thomas, J.B., Somers, D.J., McCallum, B.D. & Fox, S.L. Microsatellite mapping of adult-plant leaf rust resistance gene Lr22a in wheat. Theor. Appl. Genet. 115, 877-884 (2007).
14. Pretorius, Z.A., Rijkenberg, F.H.J. & Wilcoxson, R.D. Characterization of adult-plant resistance to leaf rust of wheat conferred by the gene Lr22a. Plant Dis. 71, 542-545 (1987).
15. Kolmer, J.A. Virulence in Puccinia recondita f. sp. tritici isolates from Canada to genes for adult-plant resistance to wheat leaf rust. Plant Dis. 81, 267-271 (1997).
16. McCallum, B.D., Seto-Goh, P. & Xue, A. Physiologic specialization of Puccinia triticina, the causal agent of wheat leaf rust, in Canada in 2009. Can. J. Plant Pathol. 35, 338-345 (2013).
17. Moullet, O. & Schori, A. Maintaining the efficiency of MAS method in cereals while reducing the costs. J. Plant Breed. Genet. 2, 97-100 (2014).
18. Doležel, J. et al. Chromosomes in the flow to simplify genome analysis. Funct. Integr. Genomics 12, 397-416 (2012).
19. Safár, J. et al. Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet. Genome Res. 129, 211-223 (2010).
20. Luo, M.C. et al. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc. Natl. Acad. Sci. USA 110, 7940-7945 (2013).
21. Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
22. Belkhadir, Y., Nimchuk, Z., Hubert, D.A., Mackey, D. & Dangl, J.L. Arabidopsis RIN4 negatively regulates disease resistance mediated by RPS2 and RPM1 downstream or independent of the NDR1 signal modulator and is not required for the virulence functions of bacterial type III effectors AvrRpt2 or AvrRpm1. Plant Cell 16, 2822-2835 (2004).
23. Mackey, D., Holt, B.F. III, Wiig, A. & Dangl, J.L. RIN4 interacts with Pseudomonas syringae type III effector molecules and is required for RPM1-mediated resistance in Arabidopsis. Cell 108, 743-754 (2002).
24. Steuernagel, B. et al. Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat. Biotechnol. 34, 652-655 (2016).
25. Sánchez-Martín, J. et al. Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biol. 17, 221 (2016).
26. Gardiner, L.J. et al. Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat. Plant J. 87, 403-419 (2016).
27. Choulet, F. et al. Structural and functional partitioning of bread wheat chromosome 3B. Science 345, 1249721 (2014).
28. Gottlieb, A. et al. Insular organization of gene space in grass genomes. PLoS One 8, e54101 (2013).
29. Stein, N., Herren, G. & Keller, B. A new DNA extraction method for high-throughput marker analysis in a large-genome species such as Triticum aestivum. Plant Breed. 120, 354-356 (2001).
30. Singla, J. et al. Characterization of Lr75: a partial, broad-spectrum leaf rust resistance gene in wheat. Theor. Appl. Genet. 130, 1-12 (2017).
31. Periyannan, S. et al. The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science 341, 786-788 (2013).
32. Vrána, J. et al. Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156, 2033-2041 (2000).
33. Kubaláková, M., Vrána, J., Cíhalíková, J., Simková, H. & Doležel, J. Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 104, 1362-1372 (2002).
34. Giorgi, D. et al. FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy. PLoS One 8, e57994 (2013).
35. Kubaláková, M. et al. Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. Genome 46, 893-905 (2003).
36. Simková, H. et al. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley. BMC Genomics 9, 294 (2008).
37. Šimková, H., Číhalíková, J., Vrána, J., Lysák, M.A. & Doležel, J. Preparation of HMW DNA from plant nuclei and chromosomes isolated from root tips. Biol. Plant. 46, 369-373 (2003).
38. Bolger, A.M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
39. Chapman, J.A. et al. Meraculous: de novo genome assembly with short paired-end reads. PLoS One 6, e23501 (2011).
40. International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463, 763-768 (2010).
41. Shatalina, M. et al. Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno. Plant Biotechnol. J. 11, 23-32 (2013).
42. Jia, J. et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496, 91-95 (2013).
43. Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
44. Gao, Z., Chung, E.H., Eitas, T.K. & Dangl, J.L. Plant intracellular innate immune receptor Resistance to Pseudomonas syringae pv. maculicola 1 (RPM1) is activated at, and functions on, the plasma membrane. Proc. Natl. Acad. Sci. USA 108, 7619-7624 (2011).
45. Helft, L. et al. LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains. PLoS One 6, e21614 (2011).
46. Retief, J.D. Phylogenetic analysis using PHYLIP. Methods Mol. Biol. 132, 243-258 (2000).