Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis

TLDR

The study compares dominant AFLP markers with codominant microsatellites for parentage reconstruction and develops statistical tests to determine true parentage. Using 89 oak trees genotyped for six microsatellites and 159 AFLP loci, the authors calculated likelihood ratios—including mistyping—to identify both parents without prior relationship knowledge through simulations and tests. Both marker types achieved high exclusion probabilities, dominant markers with allele frequencies 0.1–0.4 were more informative, microsatellites overestimated external gene flow while AFLPs underestimated it, and although less efficient, dominant markers remain reliable when loci are chosen by allele frequency.

Abstract

Abstract This study compares the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of codominant multiallelic markers, such as microsatellites, in reconstructing parentage. These two types of markers were used to search for both parents of an individual without prior knowledge of their relationships, by calculating likelihood ratios based on genotypic data, including mistyping. Experimental data on 89 oak trees genotyped for six microsatellite markers and 159 polymorphic AFLP loci were used as a starting point for simulations and tests. Both sets of markers produced high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1–0.4 were more informative. Such codominant and dominant markers can be used to construct powerful statistical tests to decide whether a genotyped individual (or two individuals) can be considered as the true parent (or parent pair). Gene flow from outside the study stand (GFO), inferred from parentage analysis with microsatellites, overestimated the true GFO, whereas with AFLPs it was underestimated. As expected, dominant markers are less efficient than codominant markers for achieving this, but can still be used with good confidence, especially when loci are deliberately selected according to their allele frequencies.