Determination of consensus genotypes by microsatellites for museum accessions of cattle (Вos taurus)

DNA analysis of ancient and historical samples, including specimens stored in museum and craniological collections, is an invaluable source of genetic information for reconstructing the origin of local breeds of livestock. Given the high degree of DNA degradation in most of these samples, studies are usually conducted on the mitochondrial genome, since it is present in hundreds or even thousands of copies in a single cell. However, in some cases, the study of mitochondrial DNA (mtDNA) does not allow us to fully trace the demographic history of animal species and breeds, especially when crossbreeding is used in breeding work. An informative tool for analyzing these types of demographic events is the study of microsatellites, or short tandem repeats (STRs). However, in microsatellite genotyping for DNA extracted from museum specimens imposes an increased risk of amplification errors. The aim of our work was to improve the algorithm for determining consensus STR marker genotypes for samples containing highly degraded DNA and to evaluate the effectiveness of the algorithm suggested for cattle craniological museum samples. The material were museum exhibits of cattle skulls dated from the end of the 19th to the first half of the 20th century and stored in the craniological collection of the Liskun Museum of Animal Husbandry (RSAU - Timiryazev Moscow Agricultural Academy). For genotyping, a multiplex panel was used which included 11 microsatellite loci recommended by the International Society of Animal Genetics (ISAG), according to protocols adopted at the Ernst Federal Research Center for Animal Husbandry. The success of amplification for each locus in the sample was assessed by calculating genotyping quality indices (QI). The most frequently occurring genotypes were coded as 1, and the genotypes that differed from those coded as 1 due to allelic drop-out (ADO) or false alleles (FA) were defined as 0. Next, the proportion was calculated of genotypes with the value 1 to the total number of repetitions. The threshold value for QI was set at 0.75. The genotypes that showed a frequency of occurrence above the threshold value for each locus were included in the consensus genotype. The algorithm was tested on 144 museum samples of black-and-white, Turano-Mongolian, pale-and-white and brown cattle. A complete profile (11 microsatellite loci) was obtained for 60.42 % of accessions. The quality of genotyping at most loci (9 out of 11 loci examined) was above 0.950, ranging from 0.951±0.011 at the TGLA122 locus to 0.995±0.003 at the BM2113 locus. An assessment of genotyping efficiency showed that the TGLA53 and BM1818 loci had the lowest genotyping success (74.86 % and 61.45 %, respectively). A positive correlation at the trend level ( r 2 = 0.53, p = 0.09) between the size of alleles at the locus and the proportion of genotyping errors was revealed. Since studying the allele pool of populations is impossible without obtaining correct genotypes, our proposed algorithm, which ensures the probability of correct genotyping p function show_eabstract() { $('#eabstract1').hide(); $('#eabstract2').show(); $('#eabstract_expand').hide(); }