Akpinar, B.A., Magni, F., Yuce, M., Lucas, S.J., Šimková, H., Šafář, J., Vautrin, S., Bergès, H., Cattonaro, F., Doležel. J., Budak, H.
BMC GENOMICS
16:
453,
2015
Keywords:
Triticum aestivum, 5DS, Hexaploid wheat, Physical mapping, Gene space, Grass evolution
Abstract:
Background: The 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.
Results: The 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.
Conclusions: Here, 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.
Fulltext: contact IEB authors
IEB authors: Jaroslav Doležel,
Jan Šafář,
Hana Šimková
