Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the microsatellites, thereby decreasing the contrast between the neutral microsatellites and the S-locus.

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.

We describe the development of a SCAR-marker linked to low extractives content of Norway Spruce (Picea abies L [Karst.]) derived from AFLPs. In these analyses 57 different primer enzyme combinations were used in a bulked segregant analysis approach comparing individuals with high and low extractives content. A total of 14 polymorphic AFLP markers were detected between the pools. Five markers were selected for further analyses to verify their linkage to extractives content based on individuals used for pool constitution. One AFLP marker, found to be significant linked to low extractives content was converted into a SCAR marker for further validation. For this marker, a monomorphic band was obtained by using sets of nested primers or restriction site specific primers (RSS) which include the AFLP-restriction recognition site. The separation of the marker from unlinked size homologous marker-alleles was realized by a SSCP-approach. Validation of the marker on different full-sib families confirmed the usability to separate the classes for low and high extractives content of Picea abies.

The identification of AFLP markers and their subsequent conversion to SCAR-markers linked to wood density of Norway Spruce (Picea abies L [Karst.]) is described for the first time. In AFLP-analyses, 102 different primer enzyme combinations were screened in a bulked segregant approach comparing individuals with high and low wood density. A total of 107 polymorphic AFLP fragments were obtained between the DNA-pools. Twenty-three markers were selected for further analyses to verify their linkage to wood density based on individuals used for pool constitution and additional unrelated clonal material. For 15 markers, a significant linkage to wood density was confirmed by a two-sided Fisher’s-exact test. Four markers were converted into SCAR markers and validated for plant material assayed for wood density by X-ray microdensitometry. For each marker a monomorphic band was obtained using sets of nested primers or restriction site-specific primers (RSS), which include the AFLP-restriction recognition sites. For two markers that are linked to high wood density, a separation from unlinked size homologous marker-alleles was realized by a PCR-restriction approach. Validation of these markers in different full-sib families confirmed their usability to separate the classes for low and high wood density of Picea abies.