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Characterization of variable EST SSR markers for Norway spruce (Picea abies L.)

DOI: 10.1186/1756-0500-4-401

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Abstract:

SSR sequences were identified by analyzing 14,022 publicly available EST sequences. Tri-nucleotide repeat motifs were most abundant in the data set followed by penta- and hexa-nucleotide repeats. Specific primer pairs were designed for sixty loci. Among these, 27 displayed polymorphism in a testing population of 16 P. abies individuals sampled across Austria and in an additional screening population of 96 P. abies individuals from two geographically distinct Austrian populations. Allele numbers per locus ranged from two to 17 with observed heterozygosity ranging from 0.075 to 0.99.We have characterized variable EST SSR markers for Norway spruce detected in expressed genes. Due to their moderate to high degree of variability in the two tested screening populations, these newly developed SSR markers are well suited for the analysis of stress related functional variation present in Norway spruce populations.Natural populations of Picea abies L. (Norway spruce) are found from north-western Europe outside permafrost areas down to northern Greece, westwards to the Massif Central (France) and east to the Ural Mountains. Picea abies is growing above 400-500 m and ascends close to 2000 m in the Alps. Studies on genetic variation based on allozymes have shown that Picea abies genetic differentiation among populations is rather low over its whole distribution range [1,2]. Previous studies on the genetic structure of P. abies using organelle markers showed pronounced differentiation between north-east boreal origins and areas in the central European mountains [3,4], supporting the hypothesis of two distinct main glacial refugia as postulated from pollen data [5].Initial reports on the occurrence of SSRs in conifers such as Pinus radiata [6], Pinus sylvestris [7] or Picea abies [8] have shown that marker development for such complex genomes is difficult. Frequently several DNA fragments in addition to the expected ones are amplified when using primers flanking putative SSR regio

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