BACKGROUND: A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with the goal of revealing the structural features of the third largest chromosome in wheat. RESULTS: We assembled 689 informative BAC contigs (hereafter reffered to as contigs) representing 91% of the entire physical length of wheat chromosome 6B. The contigs were integrated into a radiation hybrid (RH) map of chromosome 6B, with one linkage group consisting of 448 loci with 653 markers. The order and direction of 480 contigs, corresponding to 87% of the total length of 6B, were determined. We also characterized the contigs that contained a part of the nucleolus organizer region or centromere based on their positions on the RH map and the assembled BAC clone sequences. Analysis of the virtual gene order along 6B using the information collected for the integrated map revealed the presence of several chromosomal rearrangements, indicating evolutionary events that occurred on chromosome 6B. CONCLUSIONS: We constructed a reliable physical map of chromosome 6B, enabling us to analyze its genomic structure and evolutionary progression. More importantly, the physical map should provide a high-quality and map-based reference sequence that will serve as a resource for wheat chromosome 6B.

Advanced Genomics Laboratory National Institute of Agrobiological Sciences Tsukuba 305 8602 Japan

Bioinformatics Research Unit National Institute of Agrobiological Sciences Tsukuba 305 8602 Japan

Cereal Science Research Center of Tsukuba Nisshin Flour Milling Inc Tsukuba 300 2611 Japan

Core Research Division Organization of Advanced Science and Technology Kobe University Kobe 657 8501 Japan

Institute of Experimental Botany Centre of the Region Haná for Biotechnological and Agricultural Research CZ 78371 Olomouc Czech Republic

Institute of Plant Science and Resources Okayama University Kurashiki 710 0046 Japan

Kihara Institute for Biological Research Yokohama City University Yokohama 244 0813 Japan

Laboratory of Plant Genetics Graduate School of Agricultural Science Kobe University Kobe 657 8501 Japan

Laboratory of Plant Genetics Graduate School of Agriculture Kyoto University Kyoto 606 8502 Japan

Plant Genome Research Unit National Institute of Agrobiological Sciences Tsukuba 305 8602 Japan

Wheat Breeding Group NARO Tohoku Agricultural Research Center Morioka 020 0198 Japan

Zobrazit více v PubMed

Kihara H, Nishiyama I. Genomanalyse bei Triticum und Aegilops. I Genomaffinitäten in tri-, tetra- und pentaploiden Weizenbastarden. Cytologia. 1930;1:270–284.

Sears ER. The aneuploids of common wheat. Missouri Agricultural Experiment Station Research Bulletin. 1954;572:1–58.

Okamoto M. Identification of the chromosomes of common wheat belonging to the A and B genome. Can J Genet Cytol. 1962;4:31–37. doi: 10.1139/g62-005. DOI

Šafář J, Šimková H, Kubaláková M, Číhalíková J, Suchánková P, Bartoš J, et al. Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res. 2010;129:211–223. doi: 10.1159/000313072. PubMed DOI

International Rice Genome Sequencing Project The map-based sequence of the rice genome. Nature. 2005;436:793–800. doi: 10.1038/nature03895. PubMed DOI

International Brachypodium Initiative Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010;463:763–768. doi: 10.1038/nature08747. PubMed DOI

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009;457:551–556. doi: 10.1038/nature07723. PubMed DOI

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009;326:1112–1115. doi: 10.1126/science.1178534. PubMed DOI

The International Barley Genome Sequencing Consortium A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711–716. PubMed

Flavell RB, Rimpau J, Smith DB. Repeated sequence DNA relationships in 4 cereal genomes. Chromosoma. 1977;63:205–22. doi: 10.1007/BF00327450. DOI

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;496:91–95. doi: 10.1038/nature12028. PubMed DOI

Doležel J, Kubaláková M, Paux E, Bartoš J, Feuillet C. Chromosome-based genomics in the cereals. Chromosome Res. 2007;15:51–66. doi: 10.1007/s10577-006-1106-x. PubMed DOI

The International Wheat Genome Sequencing Consortium A chromosome-based draft sequence of the hexaploid bred wheat genome. Science. 2014;345:1251788. doi: 10.1126/science.1251788. PubMed DOI

Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Phillippe R, et al. A physical map of the short arm of wheat chromosome 1A. PLoS One. 2013;11:e80272. doi: 10.1371/journal.pone.0080272. PubMed DOI PMC

Lucas SJ, Akpınar BA, Kantar M, Weinstein Z, Aydınoğlu F, Šafář J, et al. Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A. PLoS One. 2013;8:e59542. doi: 10.1371/journal.pone.0059542. PubMed DOI PMC

Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Šimková H, et al. The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biol. 2013;14:R138. doi: 10.1186/gb-2013-14-12-r138. PubMed DOI PMC

Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, et al. A high density physical map of chromosome 1BL advances evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol. 2013;14:R64. doi: 10.1186/gb-2013-14-6-r64. PubMed DOI PMC

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

Poursarebani N, Nussbaumer T, Šimková H, Šafář J, Witsenboer H, van Oeveren J, et al. Whole genome profiling (WGP™) and shotgun sequencing delivers an anchored, gene decorated, physical map assembly of bread wheat chromosome 6A. Plant J. 2014;79:334–347. doi: 10.1111/tpj.12550. PubMed DOI PMC

Cviková K, Cattonaro F, Alaux M, Stein N, Mayer KFX, Doležel J, et al. High-throughput physical map anchoring via BAC-pool sequencing. BMC Plant Biol. 2015;15:99. doi: 10.1186/s12870-015-0429-1. PubMed DOI PMC

Akpinar BA, Magni F, Yuce M, Lucas SJ, Šimková H, Šafář J, et al. The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements. BMC Genomics. 2015;16:453. doi: 10.1186/s12864-015-1641-y. PubMed DOI PMC

Tanaka T, Kobayashi F, Joshi G, Onuki R, Sakai H, Kanamori H, et al. Next-generation survey sequencing and the molecular organization of wheat chromosome 6B. DNA Res. 2014;21:103–114. doi: 10.1093/dnares/dst041. PubMed DOI PMC

Pikaard CS. The epigenetics of nucleolar dominance. Trends Genet. 2000;16:495–500. doi: 10.1016/S0168-9525(00)02113-2. PubMed DOI

Morrison JW. Chromosome behavior in wheat monosomics. Heredity. 1953;7:203–217. doi: 10.1038/hdy.1953.28. DOI

McIntosh RA, Yamazaki Y, Dubcovsky J, Rogers J, Morris C, Apples R, et al. Catalogue of gene symbols for wheat. 2013.

Paux E, Roger D, Badaeva E, Gay G, Bernard M, Sourdille P, et al. Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC end sequencing on chromosome 3B. Plant J. 2006;48:463–474. doi: 10.1111/j.1365-313X.2006.02891.x. PubMed DOI

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

Sears E, Sears L. Proc 5th Int Wheat Genet Symp. New Delhi, India: Agricultural Research Institute; 1978. The telocentric chromosomes of common wheat; pp. 389–407.

van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, et al. Sequence-based physical mapping of complex genomes by whole genome profiling. Genome Res. 2011;21:618–625. doi: 10.1101/gr.112094.110. PubMed DOI PMC

Philippe R, Choulet F, Paux E, van Oeveren J, Tang J, Wittenberg AH, et al. Whole genome profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome. BMC Genomics. 2012;13:47. doi: 10.1186/1471-2164-13-47. PubMed DOI PMC

Soderlund C, Longden I, Mott R. FPC: a system for building contigs from restriction fingerprinted clones. Comput Appl Biosci. 1997;13:523–535. PubMed

Ishikawa G, Yonemaru J, Saito M, Nakamura T. PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes. BMC Genomics. 2007;8:135. doi: 10.1186/1471-2164-8-135. PubMed DOI PMC

Ishikawa G, Nakamura T, Ashida T, Saito M, Nasuda S, Endo TR, et al. Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers. Theor Appl Genet. 2009;118:499–514. doi: 10.1007/s00122-008-0916-y. PubMed DOI

Mayer KFX, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, et al. Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell. 2011;23:1249–1263. doi: 10.1105/tpc.110.082537. PubMed DOI PMC

Kobayashi F, Takumi S, Handa H. Identification of quantitative trait loci for ABA responsiveness at the seedling stage associated with ABA-regulated gene expression in common wheat. Theor Appl Genet. 2010;121:629–641. doi: 10.1007/s00122-010-1335-4. PubMed DOI

Tiwari VK, Riera-Lizarazu O, Gunn HL, Lopez K, Iqbal MJ, Kianian S, 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:e48815. doi: 10.1371/journal.pone.0048815. PubMed DOI PMC

Endo TR, Gill BS. The deletion stocks of common wheat. J Hered. 1996;87:295–307. doi: 10.1093/oxfordjournals.jhered.a023003. DOI

Qi L, Echalier B, Friebe B, Gill BS. Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct Integr Genomics. 2003;3:39–55. PubMed

Sourdille P, Singh S, Cadalen T, Brown-Guedira GL, Gay G, Qi L, 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. doi: 10.1007/s10142-004-0106-1. PubMed DOI

La Rota M, Sorrells ME. Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics. 2004;4:34–46. doi: 10.1007/s10142-003-0098-2. PubMed DOI

Randhawa HS, Dilbirlig M, Sidhu D, Erayman M, Sandhu D, Bondareva S, et al. Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags. Genetics. 2004;168:677–686. doi: 10.1534/genetics.104.034843. PubMed DOI PMC

Barker RF, Harberd NP, Jarvis MG, Flavell RB. Structure and evolution of the intergenic region in a ribosomal DNA repeat unit of wheat. J Mol Biol. 1988;201:1–17. doi: 10.1016/0022-2836(88)90434-2. PubMed DOI

Flavell RB, O’Dell M. Ribosomal RNA genes on homoeologous chromosomes of group 5 and 6 in hexaploid wheat. Heredity. 1976;37:377–385. doi: 10.1038/hdy.1976.102. DOI

Gerlach WL, Bedbrook JR. Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res. 1979;7:1870–1885. doi: 10.1093/nar/7.7.1869. PubMed DOI PMC

Mizuno H, Sasaki T, Matsumoto T. Characterization of internal structure of the nucleolar organizing region in rice (Oryza sativa L.) Cytogenet Genome Res. 2008;121:282–285. doi: 10.1159/000138898. PubMed DOI

Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice. 2013;6:4. doi: 10.1186/1939-8433-6-4. PubMed DOI PMC

Fujisawa M, Yamagata H, Kamiya K, Nakamura M, Saji S, Kanamori H, et al. Sequence comparison of distal and proximal ribosomal DNA arrays in rice (Oryza sativa L.) chromosome 9S and analysis of their flanking regions. Theor Appl Genet. 2006;113:419–428. doi: 10.1007/s00122-006-0307-1. PubMed DOI

Komuro S, Endo R, Shikata K, Kato A. Genomic and chromosomal distribution patterns of various repeated DNA sequences in wheat revealed by a fluorescence in situ hybridization procedure. Genome. 2013;56:131–137. doi: 10.1139/gen-2013-0003. PubMed DOI

Li B, Choulet F, Heng Y, Hao W, Paux E, Liu Z, et al. Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure. Plant J. 2013;73:952–965. doi: 10.1111/tpj.12086. PubMed DOI

Fukui KN, Suzuki G, Kagudah ES, Rahman S, Apples R, Yamamoto M, et al. Physical arrangement of retrotransposon-related repeats in centromeric regions of wheat. Plant Cell Physiol. 2001;42:189–196. doi: 10.1093/pcp/pce026. PubMed DOI

Liu Z, Yue W, Li D, Wang RR, Kong X, Lu K, et al. Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres. Chromosoma. 2008;10:445–456. doi: 10.1007/s00412-008-0161-9. PubMed DOI

Qi L, Friebe B, Zhang P, Gill BS. A molecular-cytogenetic method for locating genes to pericentromeric regions facilitates a genomewide comparison of synteny between the centromeric regions of wheat and rice. Genetics. 2009;183:1235–1247. doi: 10.1534/genetics.109.107409. PubMed DOI PMC

Rustenholz C, Choulet F, Laugier C, Šafář J, Šimková H, Doležel J, et al. A 3,000-Loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. Plant Physiol. 2011;157:1596–1608. doi: 10.1104/pp.111.183921. PubMed DOI PMC

Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, et al. Structural and functional partitioning of bread wheat chromosome 3B. Science. 2014;345:1249721–1. doi: 10.1126/science.1249721. PubMed DOI

Gale MD, Devos KM. Comparative genetics in the grasses. Proc Natl Acad Sci U S A. 1998;95:1971–1974. doi: 10.1073/pnas.95.5.1971. PubMed DOI PMC

Devos KM. Updating the ‘Crop Circle’. Curr Opin Plant Biol. 2005;8:155–162. doi: 10.1016/j.pbi.2005.01.005. PubMed DOI

Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, et al. Palaeogenomics of plants: synteny-based modeling of extinct ancestors. Trends Plant Sci. 2010;15:479–487. doi: 10.1016/j.tplants.2010.06.001. PubMed DOI

Luo M-C, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, et al. A 4-gigabase physical map unlock the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc Natl Acad Sci U S A. 2013;110:7940–7945. doi: 10.1073/pnas.1219082110. PubMed DOI PMC

Vrána J, Kubaláková M, Šimková H, Číhalíková J, Lysák MA, Doležel J. Flow-sorting of mitotic chromosomes in common wheat (Triticum aestivum L.) Genetics. 2000;156:2033–2041. PubMed PMC

Janda J, Šafář J, Kubaláková M, Bartoš J, Kovářová P, Suchánková P, et al. Advanced resources for plant genomics: BAC library specific for the short arm of wheat chromosome 1B. Plant J. 2006;47:977–986. doi: 10.1111/j.1365-313X.2006.02840.x. PubMed DOI

Šimková H, Šafář J, Kubaláková M, Suchánková P, Číhalíková J, Robert-Quatre H, et al. BAC libraries from wheat chromosome 7D: efficient tool for positional cloning of aphid resistance genes. J Biomed Biotechnol. 2011;2011:302543. PubMed PMC

Nelson W, Soderlund C. Integrating sequence with FPC fingerprint maps. Nucleic Acids Res. 2009;37:e36. doi: 10.1093/nar/gkp034. PubMed DOI PMC

Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. doi: 10.1093/nar/25.17.3389. PubMed DOI PMC

Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K. TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol. 2009;150:1135–1146. doi: 10.1104/pp.109.138214. PubMed DOI PMC

Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, et al. Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol. 2011;156:20–28. doi: 10.1104/pp.110.171579. PubMed DOI PMC

Birnboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979;7:1513–1523. doi: 10.1093/nar/7.6.1513. PubMed DOI PMC

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

Huang X, Madan A. CAP3: A DNA Sequence Assembly Program. Genome Res. 1999;9:868–877. doi: 10.1101/gr.9.9.868. PubMed DOI PMC

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: An information aesthetic for comparative genomics. Genome Res. 2009;19:1639–1645. doi: 10.1101/gr.092759.109. PubMed DOI PMC

Armachea J-P, Jarascha A, Angera AM, Villab E, Beckera T, Bhushana S, et al. Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution. Proc Natl Acad Sci U S A. 2010;107:19748–19753. doi: 10.1073/pnas.1009999107. PubMed DOI PMC

Features of the organization of bread wheat chromosome 5BS based on physical mapping

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A