Journal Article

First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach

Cozzo, Mario, Giangregorio, Patrizia, Randi, Ettore, Boattini, Alessio, Mucci, Nadia, Ciucci, Paolo, Scarpulla, Erminia, Davoli, Francesca

2021

Overview

Background The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panels by different research groups studying the same population can cause problems and bias in data analysis. A priority issue in conservation genetics is the comparability of data produced by different labs with different methods. Here, we compared data from previous and ongoing studies to identify a panel of microsatellite loci efficient for the long-term monitoring of Apennine brown bears ( Ursus arctos marsicanus ), aiming at reducing genotyping uncertainty and allowing reliable individual identifications overtimes. Results We examined all microsatellite markers used up to now and identified 19 candidate loci. We evaluated the efficacy of 13 of the most commonly used loci analyzing 194 DNA samples belonging to 113 distinct bears selected from the Italian national biobank. We compared data from 4 different marker subsets on the basis of genotyping errors, allelic patterns, observed and expected heterozygosity, discriminatory powers, number of mismatching pairs, and probability of identity. The optimal marker set was selected evaluating the low molecular weight, the high discriminatory power, and the low occurrence of genotyping errors of each primer. We calibrated allele calls and verified matches among genotypes obtained in previous studies using the complete set of 13 STRs (Short Tandem Repeats), analyzing six invasive DNA samples from distinct individuals. Differences in allele-sizing between labs were consistent, showing a substantial overlap of the individual genotyping. Conclusions The proposed marker set comprises 11 Ursus specific markers with the addition of cxx20, the canid-locus less prone to genotyping errors, in order to prevent underestimation (maximizing the discriminatory power) and overestimation (minimizing the genotyping errors) of the number of Apennine brown bears. The selected markers allow saving time and costs with the amplification in multiplex of all loci thanks to the same annealing temperature. Our work optimizes the available resources by identifying a shared panel and a uniform methodology capable of improving comparisons between past and future studies.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Alleles / Animal behavior / Animal Genetics and Genomics / Animal populations / Animals / Bears / Biological diversity / Biomedical and Life Sciences / Brown bear / Conservation genetics / Cost analysis / Cross-species amplification / Data analysis / Deoxyribonucleic acid / Discriminatory power / DNA / Estimates / Evaluation / Genetic aspects / Genetic diversity / Genetic markers / Genetics / Genomics / Genotype / Genotypes / Genotyping / Heterozygosity / Identification / Identification and classification / Individual identification / Interlaboratory comparison / Invasive species / Italy / Life Sciences / Loci / Low molecular weights / Marker panels / Methodology / Methodology Article / Methods / Microarrays / Microbial Genetics and Genomics / Microsatellite Repeats / Microsatellites / Microsatellites (Genetics) / Molecular weight / Natural history / Non-human and non-rodent vertebrate genomics / Optimization / Plant Genetics and Genomics / Population genetics / Protection and preservation / Proteomics / Reproducibility / Short tandem repeats / Ursidae - genetics / Ursus arctos marsicanus / Zoological research