Skip to main content
ARS Home » Midwest Area » West Lafayette, Indiana » Crop Production and Pest Control Research » Research » Publications at this Location » Publication #189204
Title: EST-DERIVED SSR MARKERS FROM DEFINED REGIONS OF THE WHEAT GENOME TO IDENTIFY LOPHOPYRUM ELONGATUM SPECIFIC LOCI

Author
item MULLAN, D - U. WESTERN AUSTRALIA
item PLATTETER, AMANDA - UNIV. OF ADELAIDE
item TREAKLE, N - U. WESTERN AUSTRALIA
item APPELS, R - DEPT. OF AGRICULTURE
item COLMER, T - U. WESTERN AUSTRALIA
item Anderson, Joseph
item FRANCKI, M - DEPT. OF AGRICULTURE

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/25/2005
Publication Date: 12/1/2005
Citation: Mullan, D.J., Platteter, A., Treakle, N.L., Appels, R., Colmer, T.D., Anderson, J.M., Francki, M.D. 2005. Est-derived ssr markers from defined regions of the wheat genome to identify lophopyrum elongatum specific loci. Genome.48:811-822.

Interpretive Summary: Lophopyrum elongatum, a close relative of wheat has been shown to be resistant to various pests and diseases and has adaptive mechanisms to drought, waterlogging and salinity stress. Exploiting this genetic resource has become an objective within many wheat improvement programs and involves the introgression of small portions of L. elongatum chromosome segments into wheat. Previously inefficient, expensive and time consuming molecular techniques were used to identify small segments of Lophopyrum chromatin in wheat lines. The main aim of this study was to use mapped wheat expressed-sequence-tags as the basis for developing Simple Sequence Repeat (SSRs) PCR-based DNA markers capable of efficiently detecting L. elongatum loci in wheat during the breeding process. Using this approach, 22 markers were identified that are located at specific chromosome locations in Lophopyrum elongatum. These markers, and additional ones found by ourselves and other scientists using our methods, will substantially increase the efficiency of screening large breeding populations for elite wheat lines that contain small Lophopyrum DNA segments that carry desirable traits. This material and information will be used by USDA, university and private company scientists such as wheat breeders and plant pathologists in the USA and around the world to develop wheat lines containing Lophopryum-derived traits.

Technical Abstract: Lophopyrum elongatum, a close relative of wheat, provides a source of novel genes for wheat improvement. Molecular markers were developed to monitor the introgression of L. elongatum chromosome segments into hexaploid wheat. Existing simple sequence repeats (SSRs) derived from genomic libraries were initially screened for detecting polymorphic L. elongatum loci, but only 6 of the 163 markers tested were 6 successful. To increase detection of L. elongatum specific loci, 165 SSRs were identified from wheat expressed sequence tags (ESTs), where their chromosomal positions in wheat were known from deletion bin mapping. Detailed sequence analysis identified 41 SSRs within this group as potentially superior in their ability to detect L. elongatum loci. BLASTN alignments were used to position primers within regions of the ESTs that have sequence conservation with at least one similar EST from another cereal species. The targeting of primers in this manner enabled 14 L. elongatum polymorphic markers from 41 wheat ESTs to be identified, whereas only 2 from 124 primers designed in random positions flanking SSRs detected polymorphic L. elongatum loci. Addition and ditelosomic lines were used to assign all 22 markers to specific chromosome locations in L. elongatum. Approximately half (9) of these SSR markers were assigned to homoeologous chromosome locations based on their similar position in hexaploid wheat. The remaining mapped to non-homoeologous L. elongatum chromosomes indicating a degree of chromosome rearrangements, paralogous sequences and/or sequence variation between the two species. The EST-SSR markers were also used to screen other wheatgrass species indicating further chromosome rearrangements and/or sequence variation between wheatgrass genomes. This study details methodologies for the generation of SSRs for detection of polymorphic L. elongatum loci.