The SSR Null Allele Problem, and Its Consequences in Pedigree Reconstruction and Population Genetic Studies in Viticulture

Abstract

Null alleles are alleles that are recessive to codominant markers without any effect on the phenotype. In SSR assays, there are several reasons for the lack of amplification at a locus: the primer does not bind well, longer fragments do not amplify due to imperfections in the PCR reaction, or the amount of DNA in the sample is insufficient. In microsatellite studies, null alleles are mostly used in pedigree analysis and population genetics calculations such as diversity estimation. Null alleles in pedigree analysis can cause rejection of the true parent; if not recognized while in population genetics they distort the results in underestimating diversity. In this review, the effects caused by null-alleles in viticultural research and its possible solutions were summarized.