Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

0451393 - ÚEB 2016 RIV US eng J - Journal Article
Kumar, A. - Seetan, R. - Mergoum, M. - Tiwari, V.K. - Iqbal, M. - Wang, Y. - Al-Azzam, O. - Šimková, Hana - Luo, M.C. - Dvorak, J. - Gu, Y.Q. - Denton, A. - Kilian, A. - Lazo, G.R. - Kianian, S.F.
Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes.
BMC Genomics. Roč. 16, OCT 16 (2015), s. 800. ISSN 1471-2164. E-ISSN 1471-2164
R&D Projects: GA ČR(CZ) GAP501/12/2554
Institutional support: RVO:61389030
Keywords : Aegilops tauschii * Deletion * Physical mapping
Subject RIV: EB - Genetics ; Molecular Biology
Impact factor: 3.867, year: 2015

The large and complex genome of bread wheat (Triticum aestivum L., similar to 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. 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. This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.
Permanent Link: http://hdl.handle.net/11104/0252568