Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags
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Traditionally, simple sequence repeat (SSR) markers have been developed from libraries of genomic DNA. However, the large, repetitive nature of conifer genomes makes development of robust, single-copy SSR markers from genomic DNA difficult. Expressed sequence tags (ESTs), or sequences of messenger RNA, offer the opportunity to exploit single, low-copy, conserved sequence motifs for SSR development. From a 20,275-unigene spruce EST set, we identified 44 candidate EST-SSR markers. Of these, 25 amplified and were polymorphic in white, Sitka, and black spruce; 20 amplified in all 23 spruce species tested; the remaining five amplified in all except one species. In addition, 101 previously described spruce SSRs (mostly developed from genomic DNA), were tested. Of these, 17 amplified across white, Sitka, and black spruce. The 25 EST-SSRs had approximately 9% less heterozygosity than the 17 genomic-derived SSRs (mean H=0.65 vs 0.72), but appeared to have less null alleles, as evidenced by much lower apparent inbreeding (mean F=0.046 vs 0.126). These robust SSRs are of particular use in comparative studies, and as the EST-SSRs are within the expressed portion of the genome, they are more likely to be associated with a particular gene of interest, improving their utility for quantitative trait loci mapping and allowing detection of selective sweeps at specific genes.
KeywordsSimple Sequence Repeat Marker British Columbia Simple Sequence Repeat Prime Pair Simple Sequence Repeat Motif Genomic Simple Sequence Repeat Marker
Genome Canada and the Province of British Columbia, through the Genome BC Forestry Genome Project, funded this research. We acknowledge the support of the Vancouver Genome Sciences Centre for EST sequencing and database development. We thank Dr. Sally Aitken (University of British Columbia) for the white spruce collections, Washington Gapare (University of British Columbia) for the Sitka spruce collections, and Dr. Om Rajora (Dalhousie University) for the black spruce collections. Dr. Barry Jaquish of the B.C. Ministry of Forests Kalamalka research station provided the spruce species collection.
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