Skip to main content
ARS Home » Research » Publications at this Location » Publication #168149
Title: DEVELOPMENT AND MAPPING OF MICROSATELLITE (SSR) MARKERS IN WHEAT

Author
item SONG, Q - UNIVERSITY OF MARYLAND
item SHI, J - CHINA
item SINGH, S - KANSAS STATE UNIVERSITY
item Fickus, Edward
item COSTA, J - UNIVERSITY OF MARYLAND
item LEWIS, J - MICHIGAN STATE UNIVERSITY
item GILL, B - KANSAS STATE UNIVERSITY
item WARD, R - MICHIGAN STATE UNIVERSITY
item Cregan, Perry

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/25/2005
Publication Date: 1/25/2005
Citation: Song, Q.J., Shi, J.R., Singh, S., Fickus, E.W., Costa, J.M., Lewis, J., Gill, B.S., Ward, R., Cregan, P.B. 2005. Development and mapping of microsatellite (ssr) markers in wheat. Theoretical and Applied Genetics 110: 550-560.

Interpretive Summary: DNA markers serve as genetic landmarks and are interspersed among the 50,000 or more genes throughout the 21 chromosome pairs of the wheat genome. If a marker is located near a gene of interest, the marker can be used to select for the desired form of the gene. For example, the plant breeder can use a DNA marker to identify plants that carry the form of the gene that gives resistance to a disease rather than the form that leads to susceptibility. It was the objective of this work to report the development of 540 new simple sequence repeat (SSR) DNA markers in wheat and to report the position of 347 of these markers on the genetic maps of the 21 wheat chromosomes so as to make these DNA markers useful to the wheat research community. The new version of the SSR-based wheat chromosome maps will improve the ability to define the genome position of quantitative trait loci (QTL) that control wheat traits of interest. Furthermore, the markers on the new genome map will be of use in 'marker assisted selection' to identify wheat breeding lines that possess improved characteristics. The new and augmented version of the wheat genome map will be of particular use to wheat geneticists and wheat breeders.

Technical Abstract: Microsatellite DNA markers are consistently found to be more informative than other classes of markers in hexaploid wheat. The objectives of this research were to develop new primers flanking wheat microsatellites, and to position the associated loci on the wheat genome map by genetic linkage mapping in the ITMI W7984 x 'Opata85' RIL population and/or by physical mapping with cytogenetic stocks. We observed that the efficiency of marker development could be increased in wheat by creation of libraries from sheared rather than enzyme digested DNA fragments for microsatellite screening, by focusing on microsatellites with the [ATT/TAA]n motif, and by the addition of an untemplated G-C clamp to the 5'-end of primers. A total of 540 microsatellite-flanking primer pairs were developed, tested, and annotated from random genomic libraries. Primer pairs and associated loci were assigned identifiers prefixed with 'Xbarc' or 'BARC', respectively. 'BARC' is the acronym for the USDA-ARS Beltsville Agricultural Research Center. A subset of 315 primer sets was used to map 347 loci. One hundred twenty five loci were localized by physical mapping alone. Of the 222 loci mapped with the ITMI population, 126 were also physically mapped. Considering all mapped loci, 126, 125, and 96 mapped to the A, B, and D genomes, respectively. Twenty-three of the new loci were positioned in gaps larger than 10 cM in the map based on pre-existing markers, and fourteen mapped to the ends of chromosomes. The length of the linkage map was extended by 80.7 cM. Map positions were consistent for 111 of the 126 loci positioned by both genetic and physical mapping. The majority of the 15 discrepancies between genetic and physical mapping involved chromosome group 5.