ARS | Publication request: Cross Species Utility and Comparative Genomic Use of SSR Markers Derived From Perennial Triticeae

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 15, 2008
Publication Date: January 16, 2008
Citation: Bushman, B.S., Larson, S.R., Mott, I.W., Wang, R., Liu, L., Thinipuran, J., Hernandez, A., Kim, R.W., Mikel, M.A. 2008. Cross Species Utility and Comparative Genomic Use of SSR Markers Derived From Perennial Triticeae. Plant and Animal Genome Conference.

Technical Abstract: Comparative in silico mapping allows inference of candidate genes in more recalcitrant grass species based on the map position of orthologous genes in model grasses. The Triticeae tribe of grasses contains over 400 species in 14 genera; with annual species including important cereals such as wheat, barley, and rye - and perennial species including important forage wheatgrasses and ryegrasses. We sequenced 30,000 ESTs from perennial Triticeae plants in the Pseudoroegneria, Elymus, and Leymus genera. The final unigene sets were compared by BLAST searches to NCBI Festuca ESTs (65% of ESTs with hits), NCBI Poaceae ESTs (84% of ESTs with hits,) and individual annual Triticeae ESTs (approx. 85% of ESTs with hits). The ESTs were also aligned to physically mapped rice genes based on homology, and approximately 3400 SSR markers were identified, many with map positions that can be inferred based on rice alignments. From the Leymus library, markers mapping to chromosome 3 were homologous to genes in rice chromosome 1. From the Pseudoroegneria library, 192 markers were tested on barley, perennial ryegrass, tall fescue, and several Triticeae grasses. The amplification success ranged from 41% (barley) to 92% (Pseudoroegneria). Thus, we have found that a substantial number of Triticeae derived ESTs and markers have merit across a suite of grasses, and can be used in comparative mapping.