Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species

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.

High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

“…Consequently, in silico high-throughput marker development approaches have almost totally replaced microsatellite-enriched library based methods. Accordingly, high-throughput development of SSR markers via mining publicly available genome assemblies has recently been reported for diverse crop plant taxa, including wheat [17], chickpea [18], cucumber [14], peach [19], melon [20], bitter melon [21], sesame [22], hazelnut [15], seven different Nicotiana species [23] and 16 different tree species [24].…”

A set of tetra-nucleotide core motif SSR markers for efficient identification of potato (<i>Solanum tuberosum</i>) cultivars

“…Long nucleotide repeats are widely adopted for genetic profiling in humans and animals (Butler et al 2004, Butler 2006, Hammond et al 1994, Hellmann et al 2006, Ruitberg et al 2001). Meanwhile, regarding plants, the use of long nucleotide repeats has been limited to the variety identification of a few crops: grape (Cipriani et al 2008, 2010), Eucalyptus (Faria et al 2011), olive (De la Rosa et al 2013), peach (Dettori et al 2015), and tea (Wang et al 2016). …”

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

“…A variety of SSR markers have been developed for Prunus. Examples include almond (Prunus dulcis) Messina et al, 2004), apricot and Japanese apricot (Prunus mume) (Lopes et al, 2002;Decroocq et al, 2003;Vilanova et al, 2006;Li et al, 2010;Wang et al, 2014), cherries (Clarke and Tobutt, 2003;, and peach (Aranzana et al, 2002;Yamamoto et al, 2002;Howad et al, 2005;Chen et al, 2014;Dettori et al, 2015). SSR markers along with other marker systems have been used in the construction of apricot genetic maps, genetic diversity assessments, and characterization of apricot germplasm collections (Lambert et al, 2007;Lalli et al, 2008;Dondini et al, 2011;Soriano et al, 2012;Rubio et al, 2014, Decroocq et al, 2014Gürcan et al, 2015).…”