Characterization of EST-SSRs in loblolly pine and spruce
- 228 Downloads
In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for EST-SSRs. One database was from “interior spruce” (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.
KeywordsExpressed sequence tags Microsatellites Simple sequence repeats Conifers
This research was made possible through funding by Genome Canada and the Province of British Columbia (to J.B. and K.R.) through the Genome BC Forestry Genome Project. The authors would also like to acknowledge the support of the Vancouver Genome Sciences Centre for EST sequencing and database development.
- Gupta PK, Balyan HS, Sharma PC, Ramesh B (1996) Microsatellites in plants: a new class of molecular markers. Curr Sci 70:45–54Google Scholar
- Powell W, Machray GC, Provan J (1996) Polymorphisms revealed by simple sequence repeats. Trends Plant Sci 1:215–222Google Scholar
- Rajora OP, Rahman MH, Dayanandan S, Mosseler A (2000) Isolation, characterization, inheritance and linkage of microsatellite DNA markers in white spruce (Picea glauca) and their usefulness in other spruce species. Mol Gen Genet 264:871–882Google Scholar
- Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452PubMedCrossRefGoogle Scholar
- Wright JW (1955) Species crossability in spruce in relation to distribution and taxonomy. For Sci 1:319–349Google Scholar
- ftp://ftp.ncbi.nih.gov/repository/dbEST/; NCBI’s EST database ftp site
- http://www.genetics.forestry.ubc.ca/ritland/programs.html; Kermit Ritland’s repository of population genetics/bioinformatics programs. The Java program SSRFinder version 2 can be found here