An SSR-Based Genetic Linkage Map of the Model Grass Brachypodium distachyon

Authors: Garvin, David; MCKENZIE, NEIL - John Innes Center; Vogel, John; MOCKLER, TODD - Oregon State University; Blankenheim, Zachary; WRIGHT, JON - John Innes Center; HUO, NAXIN - University Of California; CHEEMA, JITENDER - John Innes Center; DICKS, JO - John Innes Center; Hayden, Daniel; Gu, Yong; Tobias, Christian; CHANG, JEFF - Oregon State University; CHU, ASHLEY - Oregon State University; TRICK, MARTIN - John Innes Center; MICHAEL, TODD - Rutgers University; BEVAN, MICHAEL - John Innes Center; SNAPE, JOHN - John Innes Center

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/24/2009
Publication Date: 1/1/2010
Citation: Garvin, D.F., Mckenzie, N., Vogel, J.P., Mockler, T.C., Blankenheim, Z., Wright, J., Huo, N., Cheema, J.J., Dicks, J., Hayden, D.M., Gu, Y.Q., Tobias, C.M., Chang, J.H., Chu, A., Trick, M., Michael, T.P., Bevan, M.W., Snape, J.W. 2010. An SSR-Based Genetic Linkage Map of the Model Grass Brachypodium distachyon. Genome. 53(1):1-13.

Interpretive Summary: Domesticated cool season grass crops such as wheat play a major role in the global food system. It would be desirable to search out genes in wheat that are agriculturally important, but the large size and complex gene organization of wheat chromosomes make it challenging to do so. The weedy grass species Brachypodium distachyon (Brachypodium) possesses the same general set of genes as wheat, but the way that they are organized is far more simple, with all of the genes in Brachypodium occupying the same space as just one of wheat's 42 chromosome arms. This feature of Brachypodium lends itself to using the species as a surrogate model system to rapidly identify and characterize genes of importance to wheat and then translating this knowledge back to wheat improvement. This study reports the first genetic linkage map of Brachypodium. It is estimated that this linkage map may cover as much as 75% of the combined length of the Brachypodium chromosomes. Interestingly, the order of the molecular markers in Brachypodium is in many cases similar to the order of the same markers in rice. The molecular markers in the Brachypodium linkage map will serve as chromosome landmarks that researchers can use to navigate to genes controlling disease resistance, yield, and other traits. Results of this study will accelerate gene discovery efforts in wheat and in doing so will provide new opportunities to improve wheat production.

Technical Abstract: The grass species Brachypodium distachyon (Brachypodium) has been adopted as a model system for grasses. While many genome resources are being developed, genetic resources will be essential to make full use of this model. Here, we describe the first molecular map of diploid Brachypodium. The genetic linkage map was developed from 183 F2 individuals derived from a cross between the inbred diploid Brachypodium lines Bd3-1 and Bd21. The map was populated with simple sequence repeat polymorphism (SSR) loci designed de novo from existing Brachypodium EST and BAC end sequences, and with conserved orthologous sequence (COS) markers from other grass species. The map consists of 139 marker loci distributed across 20 linkage groups, with a combined length of 1386 cM. Five of the linkage groups approach or exceed 100 cM in length, with the largest consisting of 20 markers spanning 231 cM, while the other 15 linkage groups range in size from 67 cM to 3.9 cM. Comparisons of inferred colinearity between the Brachypodium linkage groups and the rice genome sequence reveals a significant degree of macrosynteny between the two genomes. The genetic linkage map and molecular markers described here for Brachypodium will provide a framework for expanding the genetic linkage map of Brachypodium and for molecular genetic analyses and other applications in this new model plant system.