Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

BMC Genomics

Research Article

Anne Denton¹  Omar Al-Azzam²  Ajay Kumar³  Penny MA Kianian³  Shahryar F Kianian³  Monika Michalak de Jiménez³  Muhammad J Iqbal³  Farhad Ghavami³  Kristin Simons³  Filippo M Bassi³  Jan Dvorak⁴  Ming-Cheng Luo⁴  Steven S Xu⁵  Yong Q Gu⁶  Gerard R Lazo⁶  Thomas Drader⁶  Yi Wang⁶ 

[1] Department of Computer Sciences, North Dakota State University, 58105, Fargo, ND, USA;Department of Computer Sciences, North Dakota State University, 58105, Fargo, ND, USA;Math, Science and Technology Department, University of Minnesota, 56716, Crookston, MN, USA;Department of Plant Sciences, North Dakota State University, 58108, Fargo, ND, USA;Department of Plant Sciences, University of California, 95616, Davis, CA, USA;USDA-ARS, Northern Crop Science Laboratory, 58102, Fargo, ND, USA;USDA-ARS, Western Regional Research Center, 94710, Albany, CA, USA;

关键词: Aegilops tauschii;    Genetically effective cell number;    Physical mapping;    Radiation hybrid mapping;    Repeat DNA junction marker;    Wheat;   

DOI  :  10.1186/1471-2164-13-597

 received in 2012-08-30, accepted in 2012-10-31,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundDevelopment of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported.ResultsRadiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker scaffolds of the D-genome.ConclusionsThe RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome.

【 授权许可】

Unknown   
© Kumar et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.