A novel 13‐plex STR typing system for individual identification and parentage testing of donkeys (Equus asinus)

Abstract

Summary Background Previous studies investigating donkey parentage and genetic diversity used horse‐specific multiplex systems. However, several mis‐allele and null‐allele issues were found with some of the horse primers when used in donkeys. In 2017, the International Society for Animal Genetics (ISAG) recommended 13 dinucleotide short tandem repeats (STRs) (AHT4, ASB23, HMS2, HMS3, HMS6, HMS7, HMS18, HTG7, HTG10, TKY297, TKY312, TKY337 and TKY343) as a core panel that should be used to identify individuals and to test for parentage in donkeys. To date, no single multiplex STR typing system containing all 13 donkey STRs recommended by the ISAG has been reported. Objectives To establish a novel and donkey‐specific multiplex STR typing system containing all 13 recommended STRs. Study design Assay development and validation in field population. Methods Primers for seven of the STRs were redesigned and conditions for polymerase chain reaction (PCR) were optimised. We analysed the allele sequences, sensitivity, species‐specificity and stutter ratios of this new system. Results A 13‐plex STR typing system for donkey was established. A full profile could be generated from a single PCR reaction using as little as 5 ng of DNA template with the 13 pairs of primers labelled with fluorescent dyes. An allele ladder, containing 101 alleles from the 13 STRs, was generated. No full genotype profile was generated with these primers if DNA from humans, or 11 other commonly encountered animals, was used. Genotypes could be generated for the horse and horse‐donkey hybrids (mule and hinny). Stutter ratios and population genetic parameters were calculated based on samples from 150 donkeys. The combined probabilities of paternity exclusion for this system were 0.988907326 (CPEduo) and 0.999665018 (CPEtrio). Main limitations This system cannot detect sex. Conclusions Our results indicate that our donkey‐specific 13‐plex STR typing system is sensitive, species‐specific and robust for individual identification, paternity testing and population genetic analysis in donkeys, and has potential forensic applications.