The bread wheat (Triticum aestivum L.) genotype "Chinese Spring" ("CS") is the reference base in wheat genetics and genomics. Pericentric rearrangements in this genotype were systematically assessed by analyzing homoeoloci for a set of nonredundant genes from Brachypodium distachyon, Triticum urartu, and Aegilops tauschii in the CS chromosome shotgun sequence obtained from individual chromosome arms flow-sorted from CS aneuploid lines. Based on patterns of their homoeologous arm locations, 551 genes indicated the presence of pericentric inversions in at least 10 of the 21 chromosomes. Available data from deletion bin-mapped expressed sequence tags and genetic mapping in wheat indicated that all inversions had breakpoints in the low-recombinant gene-poor pericentromeric regions. The large number of putative intrachromosomal rearrangements suggests the presence of extensive structural differences among the three subgenomes, at least some of which likely occurred during the production of the aneuploid lines of this hexaploid wheat genotype. These differences could have significant implications in wheat genome research where comparative approaches are used such as in ordering and orientating sequence contigs and in gene cloning.

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

CSIRO Agriculture Flagship St Lucia Queensland Australia

CSIRO Agriculture Flagship St Lucia Queensland Australia School of Plant Biology The University of Western Australia Perth Western Australia Australia

CSIRO Agriculture Flagship St Lucia Queensland Australia Triticeae Research Institute Sichuan Agricultural University Wenjiang Chengdu China

Department of Crop and Soil Sciences and Department of Plant Biology University of Georgia

Triticeae Research Institute Sichuan Agricultural University Wenjiang Chengdu China

Zobrazit více v PubMed

Anderson J, Ogihara Y, Sorrells ME, Tanksley SD. Development of a chromosomal arm map for wheat based on RFLP markers. Theor Appl Genet. 1992;83:1035–1043. PubMed

Berkman PJ, et al. Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J. 2011;9:768–775. PubMed

Berkman PJ, et al. Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet. 2012;124:423–432. PubMed

Berkman PJ, et al. Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnol J. 2013;11:564–571. PubMed

Blanco A, et al. A genetic linkage map of durum wheat. Theor Appl Genet. 1998;97:721–728.

Brenchley R, et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 2012;491:705–710. PubMed PMC

Carollo V, et al. GrainGenes 2.0. An improved resource for the small-grains community. Plant Physiol. 2005;139:643–651. PubMed PMC

Carvalho CM, et al. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome. Nat Genet. 2011;43:1074–1081. PubMed PMC

Choulet F, et al. Structural and functional partitioning of bread wheat chromosome 3B. Science. 2014;345:1249721. PubMed

Clark KA, Krysan PJ. Chromosomal translocations are a common phenomenon in Arabidopsis thaliana T-DNA insertion lines. Plant J. 2010;64:990–1001. PubMed PMC

Conley E, et al. A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice. Genetics. 2004;168:625–637. PubMed PMC

Danilova TV, Friebe B, Gill BS. Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theor Appl Genet. 2014;127:715–730. PubMed PMC

Devos KM, Dubcovsky J, Dvořák J, Chinoy C, Gale MD. Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination. Theor Appl Genet. 1995;91:282–288. PubMed

Devos KM, et al. Chromosome aberrations in wheat nullisomic-tetrasomic and ditelosomic lines. Cereal Res Commun. 1999;27:231–237.

Devos KM. Updating the ‘crop circle’. Curr Opin Plant Biol. 2005;8:155–162. PubMed

Dvořák J, Luo M-C, Yang Z-L. Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing Aegilops species. Genetics. 1998;148:423–434. PubMed PMC

Dvořák J, Yang Z-L, You FM, Luo M-C. Deletion polymorphism in wheat chromosome regions with contrasting recombination rates. Genetics. 2004;168:1665–1675. PubMed PMC

Endo T, Gill B. The deletion stocks of common wheat. J Hered. 1996;87:295–307.

Feldman M, et al. Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics. 1997;147:1381–1387. PubMed PMC

Gill BS, et al. A workshop report on wheat genome sequencing international genome research on wheat consortium. Genetics. 2004;168:1087–1096. PubMed PMC

Gordon L, et al. Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Res. 2007;17:1603–1613. PubMed PMC

Hernandez P, et al. Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J. 2012;69:377–386. PubMed

International Wheat Genome Sequencing Consortium (IWGSC) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. 2014;345:1251788. PubMed

Jia J, et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature. 2013;496:91–95. PubMed

Ling H-Q, et al. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature. 2013;496:87–90. PubMed

Linkiewicz A, et al. A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice. Genetics. 2004;168:665–676. PubMed PMC

Liu C, Atkinson M, Chinoy C, Devos KM, Gale MD. Nonhomoeologous translocations between group 4, 5 and 7 chromosomes within wheat and rye. Theor Appl Genet. 1992;83:305–312. PubMed

Ma J, et al. Sequence-based analysis of translocations and inversions in bread wheat (Triticum aestivum L.) PLoS One. 2013;8:e79329. PubMed PMC

Mickelson-Young L, Endo T, Gill B. A cytogenetic ladder-map of the wheat homoeologous group-4 chromosomes. Theor Appl Genet. 1995;90:1007–1011. PubMed

Miftahudin, et al. Analysis of expressed sequence tag loci on wheat chromosome group 4. Genetics. 2004;168:651–663. PubMed PMC

Mizuno KI, Miyabe I, Schalbetter SA, Carr AM, Murray JM. Recombination-restarted replication makes inverted chromosome fusions at inverted repeats. Nature. 2013;493:246–249. PubMed PMC

Moore G, Devos K, Wang Z, Gale M. Cereal genome evolution: grasses, line up and form a circle. Curr Biol. 1995;5:737–739. PubMed

Murray M, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980;8:4321–4326. PubMed PMC

Naranjo T, Roca A, Goicoechea P, Giraldez R. Arm homoeology of wheat and rye chromosomes. Genome. 1987;29:873–882.

Nelson JC, et al. Molecular mapping of wheat: major genes and rearrangements in homoeologous groups 4, 5, and 7. Genetics. 1995;141:721. PubMed PMC

Ozkan H, Levy AA, Feldman M. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops–Triticum) group. Plant Cell. 2001;13:1735–1747. PubMed PMC

Paux E, et al. A physical map of the 1-gigabase bread wheat chromosome 3B. Science. 2008;322:101–104. PubMed

Qi L, et al. A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics. 2004;168:701–712. PubMed PMC

Qi L, Friebe B, Gill BS. Complex genome rearrangements reveal evolutionary dynamics of pericentromeric regions in the Triticeae. Genome. 2006;49:1628–1639. PubMed

Rustenholz C, 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. PubMed PMC

Salse J, et al. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell. 2008;20:11–24. PubMed PMC

Sears ER. Agric Exp Stn Res Bull. Vol. 572. University of Missouri; 1954. The aneuploids of common wheat; pp. 1–58.

Sears ER, Riley R, Lewis K. Nullisomictetrasomic combinations in hexaploid wheat. In: Riley R, Lewis KR, editors. Chromosome manipulation and plant genetics. London: Oliver and Boyd; 1966. pp. 29–45.

Sears ER, Sears L. The telocentric chromosomes of common wheat. In: Ramanujam S, editor. Proceedings of the 5th International Wheat Genet Symposium. New Delhi: Indian Society of Genetics and Plant Breeding; 1978. pp. 389–407.

Song K, Lu P, Tang K, Osborn TC. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc Natl Acad Sci U S A. 1995;92:7719–7723. PubMed PMC

Valárik M, et al. High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J. 2004;37:940–950. PubMed

Vogel JP, et al. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010;463:763–768. PubMed

Wicker T, et al. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell. 2011;23:1706–1718. PubMed PMC

Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat

Putative interchromosomal rearrangements in the hexaploid wheat (Triticum aestivum L.) genotype 'Chinese Spring' revealed by gene locations on homoeologous chromosomes