Location: Crop Improvement and Genetics ResearchTitle: Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes
|KUMAR, AJAY - North Dakota State University|
|SEETAN, RAED - North Dakota State University|
|MERGOUM, MOHAMED - North Dakota State University|
|TIWARI, VIJAY - Kansas State University|
|IQBAL, MUHAMMAD - North Dakota State University|
|WANG, YI - University Of California|
|AL-ASSAM, OMAR - University Of Minnesota|
|SIMKOVA, HANA - Institute Of Experimental Botany|
|LUO, MING-CHENG - University Of California|
|DVORAK, JAN - University Of California|
|DENTON, ANN - North Dakota State University|
|KILIAN, ANDRZEJ - Diversity Arrays Technology|
|KIANIAN, SHAHRYAR - University Of Minnesota|
Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/9/2015
Publication Date: 10/16/2015
Citation: Kumar, A., Seetan, R., Mergoum, M., Tiwari, V., Iqbal, M.J., Wang, Y., Al-Assam, O., Simkova, H., Luo, M., Dvorak, J., Gu, Y.Q., Denton, A.M., Kilian, A., Lazo, G.R., Kianian, S.F. 2015. Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes. BMC Genomics. 16:800.
Interpretive Summary: Wheat accounts for approximately 30% of the global cereal consumption. However, the large size and complexity of the wheat genome presents a major hurdle in identification of genes controlling agriculturally important traits. For example, conventional breeding for crop improvement is often based on genetic recombination events. However, many important regions of the genome are not accessible through genetic breeding due to extremely low recombination rates in these regions. In this study, a new mapping population was generated based on using radiation to physically break chromosomes (radiation-hybrid mapping technology). Hundreds of molecular markers were assayed to determine whether or not they were present on the broken and healed wheat chromosomes that were recovered after crossing the irradiated wheat plants to healthy wheat. A Radiation-Hybrid (RH) map for the wheat D genome was developed that can complement the genetic map by providing genome information in the low recombination regions. The utility of incorporating RH mapping data into sequence assembly of large and complex plant genomes was evaluated. The results showed that RH mapping is a useful resource that can facilitate mapping and cloning of genes from low-recombination regions for improvement of crop traits.
Technical Abstract: The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high-resolution genome maps saturated with ordered markers to assist in anchoring and orienting BAC contigs/ sequence scaffolds for whole genome sequence assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps because it offers much higher and more uniform marker resolution across the length of a chromosome compared to genetic mapping, and does not require genetic polymorphism per se, as it is based on the presence (retention) vs. absence (deletion) of the markers. In this study, a 178 line RH panel was used to develop the first high resolution RH maps of the whole D-genome of Ae. tauschii accession AL8/78. 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 9.8Mb. The average mapping resolution across the whole 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 2,481 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 sequence scaffolds, 116 of which had not been anchored previously to the D-genome. These results suggest that high and uniform resolution in RH maps can contribute enormously to achieve complete sequence assembly of large and complex plant genomes.