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

BMC Genomics

Research Article

Anne Denton¹  Omar Al-Azzam²  Raed Seetan³  Vijay K. Tiwari⁴  Mohamed Mergoum⁵  Ajay Kumar⁵  Muhammad J. Iqbal⁶  Shahryar F. Kianian⁷  Jan Dvorak⁸  Ming-Cheng Luo⁸  Andrzej Kilian⁹  Hana Šimková^1,10  Gerard R. Lazo^1,11  Yong Q. Gu^1,11  Yi Wang^1,11 

[1] Department of Computer Sciences, North Dakota State University, 58102, Fargo, ND, USA;Department of Computer Sciences, North Dakota State University, 58102, Fargo, ND, USA;Department of Computer Science and Information Technology, St. Cloud State University, 56301, St. Cloud, MN, USA;Department of Computer Sciences, North Dakota State University, 58102, Fargo, ND, USA;Department of Computer Science, Slippery Rock University, 16057, Slippery Rock, PA, USA;Department of Plant Pathology, Kansas State University, 66506-5502, Manhattan, KS, USA;Department of Plant Sciences, North Dakota State University, 58102, Fargo, ND, USA;Department of Plant Sciences, North Dakota State University, 58102, Fargo, ND, USA;Department of Plant Sciences, University of California, 95616, Davis, CA, USA;Department of Plant Sciences, North Dakota State University, 58102, Fargo, ND, USA;USDA-ARS, Cereal Disease Laboratory, University of Minnesota, 55108, St. Paul, MN, USA;Department of Plant Sciences, University of California, 95616, Davis, CA, USA;Diversity Arrays Technology Pty Limited, 1 Wilf Crane Crescent, ACT2600, Yarralumla, Australia;Faculty of Science, Palacký University, 783 71, Olomouc, Czech Republic;Institute of Experimental Botany, Šlechtitelů 31, 783-71, Olomouc, Czech Republic;USDA-ARS, Western Regional Research Center, 94710, Albany, CA, USA;

关键词: Aegilops tauschii;    Deletion;    Physical mapping;    Radiation hybrid mapping;    Sequence assembly;    Wheat;   

DOI  :  10.1186/s12864-015-2030-2

 received in 2015-03-19, accepted in 2015-10-09,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe 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.MethodsIn 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 bi-parental 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.ResultsA 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.ConclusionThis 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.

【 授权许可】

CC BY   
© Kumar et al. 2015