Characterization of microsatellites in wild and sweet cherry (Prunus avium L.) — markers for individual identification and reproductive processes

Abstract

Nuclear microsatellites were characterized in Prunus avium and validated as markers for individual and cultivar identification, as well as for studies of pollen- and seed-mediated gene flow. We used 20 primer pairs from a simple sequence repeat (SSR) library of Prunus persica and identified 7 loci harboring polymorphic microsatellite sequences in P. avium. In a natural population of 75 wild cherry trees, the number of alleles per locus ranged from 4 to 9 and expected heterozygosity from 0.39 to 0.77. The variability of the SSR markers allowed an unambiguous identification of individual trees and potential root suckers. Additionally, we analyzed 13 sweet cherry cultivars and differentiated 12 of them. An exclusion probability of 0.984 was calculated, which indicates that the seven loci are suitable markers for paternity analysis. The woody endocarp was successfully used for resolution of all microsatellite loci and exhibited the same multilocus genotype as the mother tree, as shown in a single seed progeny. Hence, SSR fingerprinting of the purely maternal endocarp was also successful in this Prunus species, allowing the identification of the mother tree of the dispersed seeds. The linkage of microsatellite loci with PCR-amplified alleles of the self-incompatibility locus was tested in two full-sib families of sweet cherry cultivars. From low recombination frequencies, we inferred that two loci are linked with the S locus. The present study provides markers that will significantly facilitate studies of spatial genetic variation and gene flow in wild cherry, as well as breeding programs in sweet cherry.

Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers

“…There were 4 alleles identified in the peach sequenced UDP96-019 locus developed by Cipriani et al (1999), whereas there were 6 alleles identified at this locus in the plum accessions. While 6 alleles were detected in the peach sequenced (Cipriani et al, 1999) UDP96-005 SSR locus in their study on 84 wild cherry genotypes (Schueler et al, 2003), in the current study, the locus produced 6 alleles. There were 11 alleles (H O = 0.516) detected in the UDAp-404 locus used in the current study for the genetic analyses of the plum accessions, and the number of alleles was higher compared to the study by Messina et al (2004) (who developed this locus) on apricot genotypes (6 alleles, H O = 0.44).…”

Fine-scale spatial genetic dynamics over the life cycle of the tropical tree Prunus africana

“…The standard protocol was modified by using 40 ml of NaOH and 95 ml of Tris buffer for each sample. Samples were genotyped at six microsatellite loci that were originally developed for Prunus avium and Prunus persica: UDP97-403 (Cipriani et al, 1999), P12A02 (Sosinski et al, 2000), BPPCT-002 (Dirlewanger et al, 2002), UDP96-005 and UDP98-410 (Schueler et al, 2003), and EMPaS06 (Vaughan and Russell, 2004). …”

Molecular and quantitative signatures of biparental inbreeding depression in the self-incompatible tree species Prunus avium

“…The DNA was quantified on a NanoDrop system (Thermo Fisher Scientific, Schwerte, Germany) and diluted to a standardized DNA concentration of 10 ng ml À1 . We amplified eight microsatellite loci (Testolin et al, 2000;Dirlewanger et al, 2002;Schueler et al, 2003), using the combinations and conditions described in , with the only difference being the labelling from primers UDP98_411 (FAM), UDP98_412 (FAM) and BPPCT_040 (HEX). Fragments were analysed on a Megabace genetic analyser (Amersham Biosciences, Buckinghamshire, UK) using the Megabace ET 400-R size standard (GE Healthcare, Munich, Germany).…”