Microsatellite analysis of maternal half-sib families of Quercus robur, pendunculate oak. II. Inferring the number of pollen donors from the offspring

We present an approach to infer the number of pollen donors directly from genotype data of open-pollinated progeny of Quercus robur (pedunculate oak), a highly outcrossing tree species. The approach is based on closely linked, highly polymorphic codominant microsatellite markers. Initially the close linkages between three previously mapped microsatellite loci were confirmed by studies of linkage disequilibrium (LD). Then an approach to track the pollen donors contributing to maternal half-sib families (open-pollinated families) was developed by analysing haplotype arrays of closely linked microsatellite markers transmitted from the fathers to the progeny. Simulated data of five linked microsatellite loci segregating in eight open-pollinated families were used to study the relationship between the number of paternal chromosomes detected by this "haplotype approach" and the number of diploid fathers contributing to the families. The results showed that the number of diploid pollen donors can be expressed as an exponential function of the number of paternal chromosomes inferred from the progeny. The 95% confidence interval of this regression function is used to determine the minimum number of fathers contributing to a genotyped open-pollinated family of Quercus robur. Finally this open-pollinated family is used to demonstrate the resolution obtained with the "haplotype approach". Six independent microsatellite loci were used to study relatedness among all pairs of pollen gametes that share a haplotype of three linked markers. The results suggest that the majority of such gametes are identical by descent from the same father. The "haplotype approach" presented here can be used to monitor the number of contributing pollen donors in commercial seedlot samples from oak or any other outcrossing tree species for which closely linked, highly polymorphic, codominant genetic markers are available.