Abstract
Simple sequence repeats (SSRs) are among the most useful DNA markers in plant science. The aim of this study was to compare the features and usefulness of genomic SSR (gSSR) and EST-SSRs in European plum (Prunus domestica L.), an economically important, hexaploid stone fruit crop globally cultivated to produce fleshy fruits and derived foodstuff. The analysis of an ample set of morphologically diverse varieties indicated that gSSRs and EST-SSRs provide different estimates of some of the locus-based indicators of diversity. Moreover, the two classes of SSRs gave different, weakly correlated, estimations of distance-based parameters with gSSRs being more powerful for discriminating purposes. The two SSR classes provide complementary information in European plum, making the contribution of EST-SSRs useful not only as non-neutral markers. The differences between SSR classes are discussed considering the neutral and non-neutral evolution, and the polyploidy and asexual propagation of the cultivated tree varieties.
Highlights
European plum (Prunus domestica L.) is an economically important stone fruit crop, globally cultivated in temperate areas for its fleshy fruits
In order to provide information useful for the analysis of genetic diversity and for association studies in P. domestica, we investigated the differences between ESTSSRs and genomic SSR (gSSR) in revealing genetic diversity considering a common large set of European plum varieties
The Simpson’s index of diversity (1–D) was high and displayed little variation across loci (CV = 5.74%), while a higher variation across loci was present for the evenness (CV = 15.6%), a parameter that measures the distribution of genotype abundance in a population
Summary
European plum (Prunus domestica L.) is an economically important stone fruit crop, globally cultivated in temperate areas for its fleshy fruits. These are mainly marketed fresh, canned or dried (Neumüller 2011). Considerable progress in describing and classifying the ample diversity of the European plum has been achieved with the introduction of DNA molecular markers (Decroocq et al 2004; Dirlewanger et al 2002; Li et al 2010; Shimada et al 1999). These analyses confirmed that the European plum clade of P. domestica has a high level of diversity (Zhebentyayeva et al 2019). DNA markers have been used in plum for different purposes, such as map-based cloning (Claverie et al 2004), population structure analysis (Horvath et al 2011), phylogenetic relationships (Liu et al 2007; Reales et al 2010), landraces examination (Manco et al 2019; Sehic et al 2015), and discrimination of clones (Gharbi et al 2014)
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