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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #309717

Research Project: Enhancing Plant Genome Function Maps Through Genomic, Genetic, Computational and Collaborative Research

Location: Plant, Soil and Nutrition Research

Title: A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

Author
item LOU, MC - University Of California
item Gu, Yong
item YOU, FM - University Of California
item DEAL, KR - University Of California
item MA, Y. - University Of California
item HU, Y. - University Of California
item HUO, NAXIN - University Of California
item WANG, Y. - University Of California
item WANG, J. - University Of California
item CHEN, S. - University Of California
item JORGENSEN, CM - University Of California
item ZHANG, Y. - University Of California
item MCGUIRE, PE - University Of California
item PASTERNAK, S. - Cold Spring Harbor Laboratory
item STEIN, JC - Cold Spring Harbor Laboratory
item Ware, Doreen
item KRAMER, M. - Cold Spring Harbor Laboratory
item MCCOMBIE, W. - Cold Spring Harbor Laboratory
item KIANIAN, S. - North Dakota State University
item MARTIS, M. - Helmholtz Centre
item MAYER, K. - Helmholtz Centre
item SEHGAL, K. - Kansas State University
item LI, W. - Kansas State University
item GILL, B. - Kansas State University
item BEVAN, M. - John Innes Center
item SIMKOVA, H. - Institute Of Experimental Botany
item DOLEZEL, J. - Institute Of Experimental Botany
item WEINING, S. - Northwest Agriculture And Forestry University
item Lazo, Gerard
item Anderson, Olin
item DVORAK, J. - University Of California

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2013
Publication Date: 5/7/2013
Publication URL: http://DOI: 10.1073/psas.1219082110
Citation: Lou, M., Gu, Y.Q., You, F., Deal, K., Ma, Y., Hu, Y., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C., Zhang, Y., Mcguire, P., Pasternak, S., Stein, J., Ware, D., Kramer, M., Mccombie, W., Kianian, S., Martis, M., Mayer, K., Sehgal, K., Li, W., Gill, B., Bevan, M., Simkova, H., Dolezel, J., Weining, S., Lazo, G.R., Anderson, O.D., Dvorak, J. 2013. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences. 110(19):7940-7945.

Interpretive Summary: This publication reports on the creation and analysis of an integrated genetic and physical map of the plant Aegilops tauschii. This species is the diploid ancestor of the D-type genome found in hexaploid bread wheat (bread wheat). Due to its extraordinary size, analysis of the wheat genome presents many challenges. Completion of the anchored physical map of Ae. tauschii provides an important resource for wheat breeders and for the discovery of genes that contribute to agronomic traits. This research publication also provides insights into the evolution of wheat genomes.

Technical Abstract: The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.