Markers Nomenclature and Type I and II Errors Control in Cattle Parentage Exclusion Expertise with Microsatellite Markers

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Abstract

Erroneous pedigree records reduce the quality of breeding work with cattle; therefore, parentage exclusion expertise has become an integral part of breeding work. For many years on the territory of the Russian Federation, the expertise was carried out using immunogenetic markers, but the improvement of technologies and tightening of regulatory requirements has led to the process of replacement of immunogenetics by microsatellite markers. At present there is no domestic protocol clearly regulating the procedure of cattle parentage exclusion expertise using microsatellite loci, which makes laboratory work more difficult. In particular, the requirements for the number and nomenclature of genetic markers which are used in the genetic expertise are only available for cattle, embryos and semen products being transported across the Eurasian Economic Union. There are no regulations for errors I (false positives) and II (false negatives) types control, which must be taken into account when forming expert judgements. In this paper we will review the approaches to addressing these issues proposed by the International Society for Animal Genetics (ISAG), the International Committee for Animal Recording (ICAR), the Collegium of the Eurasian Economic Commission, as well as domestic regulatory documents governing the production of forensic medical tests related to parentage exclusion expertise. Based on the results of the review, a nomenclature of microsatellite markers and a parentage exclusion protocol will be proposed, in which errors I and II type control are carried out. Special attention will be paid to the description of the sources of II type error and the necessity of its control.

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About the authors

M. V. Modorov

Ural Federal Agrarian Scientific Research Center, Ural Branch, Russian Academy of Sciences

Author for correspondence.
Email: mmodorov@gmail.com
Russian Federation, Yekaterinburg, 620142

I. V. Tkachenko

Ural Federal Agrarian Scientific Research Center, Ural Branch, Russian Academy of Sciences

Email: mmodorov@gmail.com
Russian Federation, Yekaterinburg, 620142

A. A. Kleshcheva

Ural Federal Agrarian Scientific Research Center, Ural Branch, Russian Academy of Sciences

Email: mmodorov@gmail.com
Russian Federation, Yekaterinburg, 620142

M. Yu. Sevost'yanov

Ural Federal Agrarian Scientific Research Center, Ural Branch, Russian Academy of Sciences

Email: mmodorov@gmail.com
Russian Federation, Yekaterinburg, 620142

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2. Fig. 1. Hypothetical example of type II errors (false negative conclusion about the origin of the offspring from the declared parents) associated with the presence of mutations in the DNA sequence complementary to the primer sequence. In the first test, when determining the genotype of the bull (♂), cow (♀) and offspring (F1), reagent kit “a” was used, which includes a primer, at the site of complementary binding of which to the DNA matrix a mutation occurred in the bull (shown by the arrow). As a result of the mutation, a fragment of 66 bp is not amplified (null allele). The bull's genotype, designated by the number of motifs in the fragment, will be read as “10 / 10” (homozygote), although in fact its genotype is “8 / 10” (heterozygote). The cow's genotype using this reagent kit is read without errors “4 / 12”. The offspring inherits the bull's allele "8" and the cow's allele "4". When decoding the offspring's genotype with the same reagent set, the genotype "4/4" is read, since the "8" allele is not amplified due to a mutation at the site of complementary binding of the primer to the DNA matrix (variant F1a). The resulting data allow us to conclude that the bull and offspring do not have common alleles at this locus. Another laboratory used the genetic passports of the parents, and analyzed the offspring's genotype using another reagent set "b". In reagent set "b" for analyzing this locus, the developers included other primers complementary to other sequences of the matrix DNA, as a result of which both alleles "4" and "8" (F1ᵇ) are read in the offspring. However, in this situation, a conclusion will be made about the absence of common alleles at this locus in the bull and the offspring.

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3. Fig. 2. Results of fragment analysis performed using the COrDIS Cattle reagent kit. a – alleged mother (dizygotic twin with chimeric blood cells); b – tested offspring (singleton pregnancy). For each fragment of the offspring, it is possible to select a fragment present in the alleged mother, but at many loci the offspring inherited an allele whose fragment height in the mother was relatively low (such alleles are shown by red arrows).

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