Structural variations (SVs) such as copy number and presence-absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent production of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild accessions. We assessed SVs affecting genes and transposable elements (TEs) in a Triticeae diversity panel of 45 accessions from seven tetraploid and hexaploid species using high-coverage shotgun sequencing of sorted chromosome 3B DNA and dedicated bioinformatics approaches. We showed that 23% of the genes are variable within this panel, and we also identified 330 genes absent from the reference accession Chinese Spring. In addition, 60% of the TE-derived reference markers were absent in at least one accession, revealing a high level of intraspecific and interspecific variability affecting the TE space. Chromosome extremities are the regions where we observed most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses. This study provides deeper insights into the genomic variability affecting the complex Triticeae genomes at the intraspecific and interspecific levels and suggests a phylogeny with independent hybridization events leading to different hexaploid species.
- Publikační typ
- časopisecké články MeSH
Bread wheat (Triticum aestivum L.) is a staple food for a significant part of the world's population. The growing demand on its production can be satisfied by improving yield and resistance to biotic and abiotic stress. Knowledge of the genome sequence would aid in discovering genes and QTLs underlying these traits and provide a basis for genomics-assisted breeding. Physical maps and BAC clones associated with them have been valuable resources from which to generate a reference genome of bread wheat and to assist map-based gene cloning. As a part of a joint effort coordinated by the International Wheat Genome Sequencing Consortium, we have constructed a BAC-based physical map of bread wheat chromosome arm 7DS consisting of 895 contigs and covering 94% of its estimated length. By anchoring BAC contigs to one radiation hybrid map and three high resolution genetic maps, we assigned 73% of the assembly to a distinct genomic position. This map integration, interconnecting a total of 1713 markers with ordered and sequenced BAC clones from a minimal tiling path, provides a tool to speed up gene cloning in wheat. The process of physical map assembly included the integration of the 7DS physical map with a whole-genome physical map of Aegilops tauschii and a 7DS Bionano genome map, which together enabled efficient scaffolding of physical-map contigs, even in the non-recombining region of the genetic centromere. Moreover, this approach facilitated a comparison of bread wheat and its ancestor at BAC-contig level and revealed a reconstructed region in the 7DS pericentromere.
- MeSH
- Aegilops genetika MeSH
- centromera genetika MeSH
- chromozomy rostlin genetika MeSH
- fyzikální mapování chromozomů metody MeSH
- genom rostlinný MeSH
- hybridizace genetická MeSH
- klonování DNA MeSH
- pšenice genetika MeSH
- rostlinné geny MeSH
- šlechtění rostlin MeSH
- umělé bakteriální chromozomy genetika MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
The cereals are of enormous importance to mankind. Many of the major cereal species - specifically, wheat, barley, oat, rye, and maize - have large genomes. Early cytogenetics, genome analysis and genetic mapping in the cereals benefited greatly from their large chromosomes, and the allopolyploidy of wheat and oats that has allowed for the development of many precise cytogenetic stocks. In the genomics era, however, large genomes are disadvantageous. Sequencing large and complex genomes is expensive, and the assembly of genome sequence is hampered by a significant content of repetitive DNA and, in allopolyploids, by the presence of homoeologous genomes. Dissection of the genome into its component chromosomes and chromosome arms provides an elegant solution to these problems. In this review we illustrate how this can be achieved by flow cytometric sorting. We describe the development of methods for the preparation of intact chromosome suspensions from the major cereals, and their analysis and sorting using flow cytometry. We explain how difficulties in the discrimination of specific chromosomes and their arms can be overcome by exploiting extant cytogenetic stocks of polyploid wheat and oats, in particular chromosome deletion and alien addition lines. Finally, we discuss some of the applications of flow-sorted chromosomes, and present some examples demonstrating that a chromosome-based approach is advantageous for the analysis of the complex genomes of cereals, and that it can offer significant potential for the delivery of genome sequencing and gene cloning in these crops.
