The SSR Null Allele Problem, and Its Consequences in Pedigree Reconstruction and Population Genetic Studies in Viticulture
Gizella Jahnke,
József Smidla,
Tamás Deák,
Róbert Oláh,
Barna Árpád Szőke,
Diána Ágnes Nyitrainé Sárdy
Affiliations
Gizella Jahnke
Badacsony Research Station, Institute for Viticulture and Oenology, Hungarian University for Agriculture and Life Sciences, Római út 181, H-8261 Badacsonytomaj, Hungary
József Smidla
Institute of Informatics and Mathematics, Faculty of Wood Engineering and Creative Industries, University of Sopron, Bajcsy-Zsilinszky Str. 9, H-9400 Sopron, Hungary
Tamás Deák
Department of Viticulture, Institute for Viticulture and Oenology, Buda Campus, Hungarian University for Agriculture and Life Sciences, Villányi Str. 29-43, H-1118 Budapest, Hungary
Róbert Oláh
Kecskemét Research Station, Institute for Viticulture and Oenology, Hungarian University for Agriculture and Life Sciences, Katona Zsigmond Str. 5, H-6000 Kecskemét, Hungary
Barna Árpád Szőke
Badacsony Research Station, Institute for Viticulture and Oenology, Hungarian University for Agriculture and Life Sciences, Római út 181, H-8261 Badacsonytomaj, Hungary
Diána Ágnes Nyitrainé Sárdy
Department of Oenology, Institute for Viticulture and Oenology, Buda Campus, Hungarian University of Agriculture and Life Sciences, Villányi Str. 29-43, H-1118 Budapest, Hungary
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.
