Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor aegilops tauschii accession AL8/78

Authors: KUMAR, AJAY - North Dakota State University; SIMONS, KRISTIN - North Dakota State University; IQBAL, MUHAMMAD - North Dakota State University; JIMENEZ, MONIKA - North Dakota State University; BASSI, PILIPPO - North Dakota State University; GHAVAM, FARHAD - North Dakota State University; AL-AZZAM, OMAR - North Dakota State University; Drader, Thomas; WANG, YI - University Of California; LUO, MING-CHENG - University Of California; Gu, Yong; DENTON, ANNE - North Dakota State University; Lazo, Gerard; Xu, Steven; DVORAK, JAN - University Of California; KIANIAN, PENNY - North Dakota State University; Kianian, Shahryar

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/31/2012
Publication Date: 11/5/2012
Citation: Kumar, A., Simons, K., Iqbal, M.J., Jimenez, M., Bassi, F.M., Ghavami, F., Al, A., Wang, Y., Luo, M., Gu, Y.Q., Denton, A., Xu, S.S., Dvorak, J., Kianian, P., Kianian, S.F. 2012. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor aegilops tauschii. Biomed Central (BMC) Genomics. 13:597.

Interpretive Summary: Polyploid bread wheat is one of the most important staple crops worldwide. However, due to its large and complex genome, genetic mapping and map-based cloning of genes controlling agronomically important traits in polyploid wheat still represents a great challenge for wheat improvement. In this work, a novel mapping technology, radiation hybrid (RH) mapping, was developed to generate a high-resolution physical map for the wheat genome. Our results showed that RH map provides higher and more uniform resolution than conventional genetic maps. The technique can be applied to other important crops with complex genomes.

Technical Abstract: Background: A high quality reference sequence can provide a complete catalog of genes of a species, the regulatory elements that control their structure and function provide the basis for understanding the role of genes in evolution and development. However, development of a high quality reference sequence is a daunting task in many important crops like wheat with extremely large (~17Gb) and highly repetitive (~90%) genomes and polyploid nature. The development of a high quality physical map is a necessary first step to obtain a complete sequence assembly of genomes. Due to the lack of recombination in certain regions of the chromosomes, genetic mapping 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 scaffold for sequence assembly in animal systems. Here the development and characterization of a radiation hybrid panel for mapping of D-genome of wheat progenitor Aegilops tauschii is reported. Results: Radiation dose was optimized for seed irradiation of a synthetic hexaploid (AABBDD) 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 were obtained, of which 592 were generated from the mature RH1 seeds, and 918 were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) from screening with SSR markers uniformly covering all the D-genome chromosomes. Three different marker systems were also compared for the detection of deletions. Using markers covering known distance, the mapping resolution of this RH panel was estimated to be <140kb. With only 16 RH lines with deletions, a preliminary RH map for chromosome 2D showed a cM/cR ratio of 1:5.2 and dissected the chromosome into 15 distinct bins. Additionally, with this small set of lines, the potential for EST mapping was also tested. A total of 399 most informative RH lines was identified for whole D-genome with a deletion frequency of ~10% and included lines with multiple chromosome breaks. Conclusion: The 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 generating wheat RH lines (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for developing a complete marker scaffold for the wheat D-genome, fine mapping markers and functional characterization of genes and gene networks present on the D-genome.