Location: Forage and Range ResearchTitle: Development and Annotation of Perennial Triticeae ESTs and SSR Markers) Author
Submitted to: Genome
Publication Type: Peer reviewed journal
Publication Acceptance Date: 6/9/2008
Publication Date: 8/9/2008
Citation: Bushman, B.S., Larson, S.R., Mott, I.W., Cliften, P.F., Wang, R.R.-C., Chatterton, N.J., Hernandez, A.G., Ali, S., Kim, R.W., Thimmapuram, J., Gong, G., Liu, L., Mikel, M.A. Development and Annotation of Perennial Triticeae ESTs and SSR Markers. Genome 51:779-788. 2008. Interpretive Summary: Although annual Triticeae cereals such as wheat and barley have substantial genomic tools available, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of DNA sequence information available for perennial Triticeae species, we developed Expressed Sequence Tag (EST) libraries for three important Triticeae genera. From the EST libraries, we developed Simple Sequence Repeat molecular markers, tested them for species represented in each library, and genetically mapped a subset on an existing Leymus genetic map. We anticipate these resources will be useful for researchers of Triticeae grasses, researchers of comparative genomics and evolution in grasses, and ecologists and rangeland botanists.
Technical Abstract: The Triticeae tribe contains hundreds of species of both annual and perennial types. Although annual Triticeae cereals such as wheat and barley have substantial genomic tools available, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three EST libraries were developed and annotated for Pseudoroegneria spicata, a mixture of both Elymus wawawaiensis and E. lanceolatus, and a Leymus cinereus x L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8,780 for P. spicata, 11,281 for Leymus, and 7,212 for the Elymus libraries. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b*(1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database (http://titan.biotec.uiuc.edu/Triticeae/).