Comparison of two methods for identifying alien genotypes in clonal seed orchards and consequences of misidentification

Genetic gains in forestry are often implemented by producing improved forest seeds in seed orchards. However, unwanted alien genotypes are often accidentally introduced into seed orchards, or genotypes are planted in incorrect locations, both of which can reduce genetic gains. Such errors can be detected using markers, mainly isoenzymatic proteins and microsatellite DNA. These markers differ in their sensitivity, meaning that they can yield different assessments of seed orchard genetic material even when plant material is identical. The main objective of this paper was to compare these two verification methods and their consequences for genetic improvement. Two uneven-aged Scots pine clonal seed orchards were analysed using sets of isoenzymatic and microsatellite loci identified in other studies. The statistical analysis allowed comparison of the actual architecture of seed orchards to the planned layout. The number of clones was also compared to the effective number of clones. The results of microsatellite DNA analysis indicate that misplaced ramets are present from 12.29% to 30.89% of the time. Errors had an impact on breeding efficiency by reducing the relative effective number of clones. Isoenzyme and microsatellite methods had different discriminatory powers, which affected the results of the study.This study indicates that seed orchards can contain large numbers of incorrectly identified individuals. Microsatellite DNA analysis is recommended over isoenzyme analysis for detecting such errors, as the former is a more sensitive analytical method.