Kumar, A., Seetan, R., Mergoum, M., Tiwari, V.K., Iqbal, M.J., Wang, Y., Al-Azzam, O., Šimková, H., Luo, M.C., Dvorak, J., Gu, Y.Q., Denton, A., Kilian, A., Lazo, G.R., Kianian, S.F.
BMC GENOMICS
16:
800,
2015
Klíčová slova:
Aegilops tauschii, Deletion, Physical mapping, Radiation hybrid mapping, Sequence assembly, Wheat
Abstrakt:
Background: The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high
resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for
whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development
of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome
compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence
(retention) vs. absence (deletion) marker assay.
Methods: In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high
resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the
AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 biparental
populations, 2) a RH map of the D-genome of reference hexaploid wheat ’Chinese Spring’, and 3) two
SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome
sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical
map and draft sequence of the D-genome of Ae. tauschii.
Results: A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with
a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds
to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR)
or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to
chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps
and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609
mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of
42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored
earlier to the D-genome.
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