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Microsatellite DNA markers and uses thereof

Echt, C.S., Nelson, C.D.
United States Department of Agriculture patents 2004 no.US 6,733, 965 B2
microsatellite repeats, genetic markers, gene frequency, genetic polymorphism, tree breeding, forest trees, Pinus taeda, nucleotide sequences, patents, USDA, United States
Microsatellite, simple sequence repeat (SSR), markers have much potential for enhancing genome mapping and genotype identification research in forest genetics and tree breeding, SSR markers were developed by isolating and sequencing 1539 loblolly pine SSR clones for 11 SSR motifs. After screening out redundancy among the sequences, 566 oligonucleotide PCR primer pairs flanking the SSRs were synthesized and evaluated for their ability to amplify genomic DNA from loblolly pine. The three SSR motifs that yielded the highest proportion of informative markers from sequenced clones were (AC)n, (AAAT)n, and (AAAC)n. Eighteen polymorphic tri- and tetranucleotide SSR loci were genotyped in 20 loblolly pine trees using automated fluorescent marker analysis. The average number of alleles per locus observed was 6.4, and the average polymorphism information content (PIC) was 0.547. Subsets of the 566 primer pairs were evaluated for their ability to amplify DNA from six other pine species, and 54 primer pairs amplified markers that were polymorphic among the species. The present invention also concerns the methods of using the identified SSR loci as genetic markers.