Abstract
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.
Highlights
A polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequencespecific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR)
We used a wide range of statistics to evaluate the performance of these molecular marker systems, including a measure of genetic polymorphism, the efficiency of polymorphism detection, and the capacity of different techniques to identify genetic relationships of accessions
The IRAP, REMAP, and sequence-specific amplification polymorphism (S-SAP) marker systems allowed the differentiation of all Prunus species analysed, as did the RAFLP, ISSR and SSR systems
Summary
RTN activity in wild almond species and IRAP analysis. To analyse genetic variations in 389 individ-. Single IRAP primers (designed based on RTN Tps12a from Pisum sativum) amplified scorable but not polymorphic banding patterns. The percentage values of IRAP polymorphic loci in population ranged from 47.6 (FEN) to 89.6 (KOT), with an average of 80.44. The characteristics of amplified loci by means of 34 REMAP primers are shown in Supplementary. Nine genotype-specific REMAP loci were identified in populations KOR, KOT, TRI, ERI, URU, ARA, HAV, PAB and SCO. Similar to that shown by IRAP and REMAP markers, the level of genetic variation was higher between populations (83%) compared to within populations (7%). Due to high genetic diversity between populations, IRAP + REMAP-based cluster analysis was carried out using complete linkage algorithms based on simple matching (SM) similarity coefficient to recognize groups among all 389 wild almond accessions
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