Abstract
A wide inventory of molecular markers is nowadays available for individual fingerprinting. Microsatellites, or simple sequence repeats (SSRs), play a relevant role due to their relatively ease of use, their abundance in the plant genomes, and their co-dominant nature, together with the availability of primer sequences in many important agricultural crops. Microsatellites with long-core motifs are more easily scored and were adopted long ago in human genetics but they were developed only in few crops, and Prunus species are not among them. In the present work the peach whole-genome sequence was used to select 216 SSRs containing long-core motifs with tri-, tetra- and penta-nucleotide repeats. Microsatellite primer pairs were designed and tested for polymorphism in the five diploid Prunus species of economic relevance (almond, apricot, Japanese plum, peach and sweet cherry). A set of 26 microsatellite markers covering all the eight chromosomes, was also selected and used in the molecular characterization, population genetics and structure analyses of a representative sample of the five diploid Prunus species, assessing their transportability and effectiveness. The combined probability of identity between two random individuals for the whole set of 26 SSRs was quite low, ranging from 2.30 × 10−7 in peach to 9.48 × 10−10 in almond, confirming the usefulness of the proposed set for fingerprinting analyses in Prunus species.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-1098-0) contains supplementary material, which is available to authorized users.
Highlights
IntroductionComparative mapping studies showed that the genomes of the diploid Prunus species are essentially colinear and syntenic (Dettori et al 2001; Dirlewanger et al 2004; Verde et al 2005; Dondini et al 2007; Jung et al 2009) and DNA fingerprinting of accessions belonging to these species consistently revealed a high transportability of molecular markers (Cipriani et al 1999; Dirlewanger et al 2002; Vendramin et al 2007)
The Prunus genus includes several diploid species of economic relevance
Comparative mapping studies showed that the genomes of the diploid Prunus species are essentially colinear and syntenic (Dettori et al 2001; Dirlewanger et al 2004; Verde et al 2005; Dondini et al 2007; Jung et al 2009) and DNA fingerprinting of accessions belonging to these species consistently revealed a high transportability of molecular markers (Cipriani et al 1999; Dirlewanger et al 2002; Vendramin et al 2007)
Summary
Comparative mapping studies showed that the genomes of the diploid Prunus species are essentially colinear and syntenic (Dettori et al 2001; Dirlewanger et al 2004; Verde et al 2005; Dondini et al 2007; Jung et al 2009) and DNA fingerprinting of accessions belonging to these species consistently revealed a high transportability of molecular markers (Cipriani et al 1999; Dirlewanger et al 2002; Vendramin et al 2007). SSR markers (simple sequence repeats), or microsatellites, consist of tandemly repeated DNA sequences with a core unit of 1–6 base pairs (bp). They offer a number of positive features for the genetic profiling of individuals including wide distribution in plant genomes, prevalent single-locus tagging in diploid species, multi-allelic co-dominant patterns, simple use and availability of several primer sequences in many important agricultural crops (Schlötterer 2004). The high variability of microsatellites is mainly due to a different number of repeats in the region of the repeated motif and to short insertion/deletion events (Decroocq et al 2003).
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