BACKGROUND: The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. METHODS: In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. RESULTS: A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of 42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored earlier to the D-genome. CONCLUSION: This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.

Department of Computer Science and Information Technology St Cloud State University St Cloud MN 56301 USA

Department of Computer Science Slippery Rock University Slippery Rock PA 16057 USA

Department of Computer Sciences North Dakota State University Fargo ND 58102 USA

Department of Plant Pathology Kansas State University Manhattan KS 66506 5502 USA

Department of Plant Sciences North Dakota State University Fargo ND 58102 USA

Department of Plant Sciences University of California Davis CA 95616 USA

Diversity Arrays Technology Pty Limited 1 Wilf Crane Crescent Yarralumla ACT2600 Australia

Faculty of Science Palacký University 783 71 Olomouc Czech Republic

Institute of Experimental Botany Šlechtitelů 31 783 71 Olomouc Czech Republic

USDA ARS Cereal Disease Laboratory University of Minnesota St Paul MN 55108 USA

USDA ARS Western Regional Research Center Albany CA 94710 USA

Zobrazit více v PubMed

Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, et al. A physical map of the 1-gigabase bread wheat chromosome 3B. Science. 2008;322:101–104. doi: 10.1126/science.1161847. PubMed DOI

Peters JL, Cnudde F, Gerats T. Forward genetics and map- based cloning approaches. Trends Plant Sci. 2003;8:484–491. doi: 10.1016/j.tplants.2003.09.002. PubMed DOI

Xue S, Zhang Z, Lin F, Kong Z, Cao Y, Li C, et al. A high-density intervarietal map of the wheat genome enriched with markers derived from expressed sequence tags. Theor Appl Genet. 2008;117:181–189. doi: 10.1007/s00122-008-0764-9. PubMed DOI

Saintenac C, Falque M, Martin OC, Paux E, Feuillet C, Sourdille P. Detailed recombination studies along chromosome 3B provide new insights on crossover distribution in wheat (Triticum aestivum L.) Genetics. 2009;181:393–403. doi: 10.1534/genetics.108.097469. PubMed DOI PMC

Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, 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 U S A. 2013;110(19):7940–7945. doi: 10.1073/pnas.1219082110. PubMed DOI PMC

Börner A, Schumann E, Fürste A, Cöster H, Leithold B, Röder MS, et al. Mapping of quantitative trait loci for agronomic important characters in hexaploid wheat (Triticum aestivum L.) Theor Appl Genet. 2002;105:921–936. doi: 10.1007/s00122-002-0994-1. PubMed DOI

Kulwal PL, Kumar N, Kumar A, Gupta RK, Balyan HS, Gupta PK. Gene networks in hexaploid wheat: interacting quantitative trait loci for grain protein content. Funct Integr Genome. 2005;5:254–259. doi: 10.1007/s10142-005-0136-3. PubMed DOI

Echeverry-Solarte M, Kumar A, Kianian SF, Mantovani E, Simsek S, Alamri MS, et al. Genome-wide genetic dissection of supernumerary spikelet and related traits in common wheat (Triticum aestivum L.). Plant Genome. 2014; 7. doi: 10.3835/plantgenome2014.03.0013. PubMed

Echeverry-Solarte M, Kumar A, Kianian SF, Mantovani E, McClean PE, Deckard EL, et al. Genome-wide mapping of spike-related and agronomic traits in a common wheat population derived from a supernumerary spikelet (SS) parent and an elite parent. Plant Genome. 2015;8. doi: 10.3835/plantgenome2014.12.0089. PubMed

Echeverry-Solarte M, Kumar A, Kianian SF, Simsek S, Alamri MS, Mantovani E, et al. New QTL alleles for quality-related traits in spring wheat revealed by RIL population derived from supernumerary × non-supernumerary spikelet genotypes. Theor Appl Genet. 2015;128(5):893-912. doi: 10.1007/s00122-015-2478-0. PubMed

Dubcovsky J, Dvorak J. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science. 2007;316:1862–1866. doi: 10.1126/science.1143986. PubMed DOI PMC

Goss S, Harris H. New method for mapping genes in human chromosomes. Nature. 1975;255:680–684. doi: 10.1038/255680a0. PubMed DOI

Kumar A, Bassi FM, Paux E, Al-Azzam O, Michalak de Jimenez M, Denton AM, et al. DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. BMC Genomics. 2012;13:339. doi: 10.1186/1471-2164-13-339. PubMed DOI PMC

Tiwari VK, Riera-Lizarazu O, Gunn HL, Lopez K, Iqbal MJ, Kianian SF, et al. Endosperm tolerance of paternal aneuploidy allows radiation-hybrid mapping of the wheat D-genome and a measure of γ-ray induced chromosome breaks. PLoS One. 2012;7(11):e48815. doi: 10.1371/journal.pone.0048815. PubMed DOI PMC

Kumar A, Simons K, Iqbal MJ, de Jiménez M, Bassi FM, Ghavami F, et al. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii accession AL8/78. BMC Genomics. 2012;13:597. doi: 10.1186/1471-2164-13-597. PubMed DOI PMC

Faraut T, de Givry S, Hitte C, Lahbib-Mansais Y, Morisson M, Milan D, et al. Contribution of radiation hybrids to genome mapping in domestic animals. Cytogenet Genome Res. 2009;126:21–33. doi: 10.1159/000245904. PubMed DOI

Lewin HA, Larkin DM, Pontius J, O’Brien SJ. Every genome sequence needs a good map. Genome Res. 2009;19:1925–1928. doi: 10.1101/gr.094557.109. PubMed DOI PMC

Kumar A, Bassi FM, Michalack de Jimenez M, Ghavami F, Mazaheri M, Simons K, et al. Radiation Hybrids: A valuable Tool for Genetic, Genomic and Functional Analysis of Plant Genomes. In: Tuberosa R, Graner A, Frison E, et al., editors. Genomics of Plant Genetic Resources. Netherlands: Springer; 2014. pp. 285–318.

Brenchley R, Spannagl M, Pfeifer M, Barker GLA, D’Amore R, Allen AM, et al. Analysis of the bread wheat genome using whole- genome shotgun sequencing. Nature. 2012;491:705–710. doi: 10.1038/nature11650. PubMed DOI PMC

Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, et al. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature. 2013;496:87–90. doi: 10.1038/nature11997. PubMed DOI

Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature. 2013;496(7443):91–95. doi: 10.1038/nature12028. PubMed DOI

Doležel J, Šimková H, Kubaláková M, Šafář J, Suchánková P, Číhalíková J, et al. Chromosome genomics in the Triticeae. In: Feuillet C, Muehlbauer GJ, et al., editors. Genetics and genomics of the Triticeae. Berlin: Springer; 2009. pp. 285–316.

Huang BE, George AW, Forrest KL, Kilian A, Hayden MJ, Morell MK, et al. A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol J. 2012;10:826–839. doi: 10.1111/j.1467-7652.2012.00702.x. PubMed DOI

Hossain KG, Riera-lizarazu O, Kalavacharla V, Vales MI, Maan SS, Kianian SF. Radiation hybrid mapping of the species cytoplasm-specific (scsae) gene in wheat. Genetics. 2004;168:415–423. doi: 10.1534/genetics.103.022590. PubMed DOI PMC

Kalavacharla V, Hossain K, Gu Y, Riera-Lizarazu O, Vales MI, Bhamidimarri S, et al. High-resolution radiation hybrid map of wheat chromosome 1D. Genetics. 2006;173:1089–1099. doi: 10.1534/genetics.106.056481. PubMed DOI PMC

Marques E, de Givry S, Stothard P, Murdoch B, Wang Z, Womack J, et al. A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly. BMC Genomics. 2007;8:254. doi: 10.1186/1471-2164-8-254. PubMed DOI PMC

Karere GM, Froenicke L, Millon L, Womack JE, Lyons LA. A high-resolution radiation hybrid map of rhesus macaque chromosome 5 identifies rearrangements in the genome assembly. Genomics. 2008;92:210–218. doi: 10.1016/j.ygeno.2008.05.013. PubMed DOI PMC

Marone D, Panio G, Ficco DBM, Russo MA, De Vita P, et al. Characterization of wheat DArT markers: genetic and functional features. Mol Genet Genomics. 2012;287:741–753. doi: 10.1007/s00438-012-0714-8. PubMed DOI

Somers DJ, Isaac P, Edwards K. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.) Theor Appl Genet. 2004;109:1105–1114. doi: 10.1007/s00122-004-1740-7. PubMed DOI

Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, et al. Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet. 2005;110:550–560. doi: 10.1007/s00122-004-1871-x. PubMed DOI

Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, et al. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet. 2006;113:1409–1420. doi: 10.1007/s00122-006-0365-4. PubMed DOI

Wang YY, Sun XY, Zhao Y, Kong FM, Guo Y, Zhang GZ, et al. Enrichment of a common wheat genetic map and QTL mapping for fatty acid content in grain. Plant Sci. 2011;181(1):65–75. doi: 10.1016/j.plantsci.2011.03.020. PubMed DOI

Sorrells ME, Gustafson JP, Somers D, Chao S, Benscher D, Guedira-Brown G, et al. Reconstruction of the synthetic W7984 x Opata M85 wheat reference population. Genome. 2011;54:875–882. doi: 10.1139/g11-054. PubMed DOI

Mézard C. Meiotic recombination hotspots in plants. Biochem Soc Trans. 2006;34:part 4. doi: 10.1042/BST0340531. PubMed DOI

Michael TP, Jackson S. The First 50 Plant Genomes. Plant Genome. 2013; 6 (no. 2)

Friesen TL, Xu SS, Harris MO. Stem rust, tan spot, Stagonospora nodorum blotch, and hessian fly resistance in Langdon durum–Aegilops tauschii synthetic hexaploid wheat lines. Crop Sci. 2008;48:1062–1070. doi: 10.2135/cropsci2007.08.0463. DOI

de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T. CARTHAGENE: multipopulation integrated genetic and radiated hybrid mapping. Bioinformatics. 2005;21:1703–1704. doi: 10.1093/bioinformatics/bti222. PubMed DOI

Al-Azzam O, Al-Nimer L, Chitraranjan C, Denton AM, Kumar A, Bassi F, Iqbal MJ, Kianian SF. Network-based Filtering of Unreliable Markers in Genome Mapping. In: Proc. 10th International Conference on Machine Learning and Applications (ICMLA), Honolulu, HI, 2011:19–24. 10.1109/ICMLA.2011.103.

Seetan RI, Denton AM, Al-Azzam O, Kumar A, Iqbal MJ, Kianian SF. Reliable Radiation Hybrid Maps: An Efficient Scalable Clustering-Based Approach. IEEE/ACM Trans Comput Biol Bioinform. 2014;11:788–800. doi: 10.1109/TCBB.2014.2329310. PubMed DOI

Francki MG, Walker E, Crawford AC, Broughton S, Ohm HW, Barclay I, et al. Comparison of genetic and cytogenetic maps of hexaploid wheat (Triticum aestivum L.) using SSR and DArT markers. Mol Genet Genomics. 2009;281:181–191. doi: 10.1007/s00438-008-0403-9. PubMed DOI

Sourdille P, Singh S, Cadalen T, Brown-Guedira GL, Gay G, et al. Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.). Funct Integr Genomics. 2004;4:12–25. PubMed

Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002;93:77–78. doi: 10.1093/jhered/93.1.77. PubMed DOI

Derrien T, Andre C, Galibert F, Hitte C. AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps. Bioinformatics. 2007;23(4):498–499. doi: 10.1093/bioinformatics/btl618. PubMed DOI

A linkage map of Aegilops biuncialis reveals significant genomic rearrangements compared to bread wheat

DArTseq genotyping facilitates identification of Aegilops biuncialis chromatin introgressed into bread wheat Mv9kr1

Identification of New QTLs for Dietary Fiber Content in Aegilops biuncialis

Unlocking the Genetic Diversity and Population Structure of a Wild Gene Source of Wheat, Aegilops biuncialis Vis., and Its Relationship With the Heading Time

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A