The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements

Abstract

BackgroundThe substantially large bread wheat genome, organized into highly similar three sub-genomes, renders genomic research challenging. The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary relationships, provides tools for map-based cloning, and serves as a framework for reference sequencing efforts. In this study, we constructed the first comprehensive physical map of wheat chromosome arm 5DS, thereby exploring its gene space organization and evolution.ResultsThe physical map of 5DS was comprised of 164 contigs, of which 45 were organized into 21 supercontigs, covering 176 Mb with an N50 value of 2,173 kb. Fifty-eight of the contigs were larger than 1 Mb, with the largest contig spanning 6,649 kb. A total of 1,864 molecular markers were assigned to the map at a density of 10.5 markers/Mb, anchoring 100 of the 120 contigs (>5 clones) that constitute ~95 % of the cumulative length of the map. Ordering of 80 contigs along the deletion bins of chromosome arm 5DS revealed small-scale breaks in syntenic blocks. Analysis of the gene space of 5DS suggested an increasing gradient of genes organized in islands towards the telomere, with the highest gene density of 5.17 genes/Mb in the 0.67-0.78 deletion bin, 1.4 to 1.6 times that of all other bins.ConclusionsHere, we provide a chromosome-specific view into the organization and evolution of the D genome of bread wheat, in comparison to one of its ancestors, revealing recent genome rearrangements. The high-quality physical map constructed in this study paves the way for the assembly of a reference sequence, from which breeding efforts will greatly benefit.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1641-y) contains supplementary material, which is available to authorized users.

Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies

“…Thanks to the inclusion of the short contigs, we achieved one of the highest chromosome-arm coverages (94%) among all wheat physical maps published to date. In comparison with other physical maps assembled by FPC, our full assembly's N50 value (555 kb) is higher than that obtained for 3DS (445 kb) [20], 1AL (460 kb) [13] or 5A (296 kb and 252 kb for 5AS and 5AL) [19] but lower than the N50 value for 1BS (1033 kb) [14] or 5DS (1141 kb) [18]. Excluding contigs < 6 clones, the N50 of the 7DS assembly increased up to 616 kb, which brings the value closer to that obtained for 3 B (783 kb) [10].…”

“…Several projects [12,14,19,20] also exploited syntenybased approaches and anchored physical map assemblies to so called genome zippers [42], which predict a virtual gene order on the basis of synteny with three grass genomes (rice, brachypodium and sorghum). The limitation of this approach can be a relatively high proportion of genes (or non-recognized pseudogenes) in non-syntenic positions [12] and also low quality or different origin of genetic map used to build the zipper [18].…”

“…Chromosomal BAC libraries were then constructed from all wheat chromosome arms of cv. Chinese Spring [11] (http://olomouc.ueb.cas.cz/dna-libraries/cereals) and laid the basis for constructing chromosomal physical maps for the whole wheat genome [10,[12][13][14][15][16][17][18][19][20] (www.wheatgenome.org). They proved a favorable resource for map-based gene cloning [21] as well as generating a whole-chromosome sequence [22].…”

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A

“…Although this was unexpected observation, such inconsistencies in measurements of chromosomal deletions were reported previously (Qi et al, 2003; Dilbirligi et al, 2004; Sourdille et al, 2004; Philippe et al, 2013; Belova et al, 2014; Akpinar et al, 2015). In this study, a single bin 4AL – 0.66–0.73 previously defined by three lines 4AL-05 (LPGKU1147), 4AL-07 (LPGKU1149), and 4AL-11 (LPGKU1152) was split to three bins containing 43, 72, and 88 SNP loci, respectively ( Figure 1 ; Supplementary Table S2).…”

Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

“…The MTP clones of the CS-dt-5DS BAC library (42) were screened at Sabanci University (Turkey) with three pairs of primers for VRN-D4 listed in SI Appendix, Table S8. The selected BAC and 11 overlapping BACs belonging to two overlapping contigs (SI Appendix, Table S2) were sequenced using a combination of Illumina and 454 sequencing (SI Appendix, Method S2).…”