A framework for the development of STR genotyping in domestic animal species: characterization and population study of 12 canine X-chromosome loci

TY - JOUR

T1 - A framework for the development of STR genotyping in domestic animal species

T2 - characterization and population study of 12 canine X-chromosome loci

AU - van Asch, Barbara

AU - Pinheiro, Raquel

AU - Pereira, Rui

AU - Alves, Cíntia

AU - Pereira, Vania

AU - Pereira, Filipe

AU - Gusmão, Leonor

AU - Amorim, António

PY - 2010/1

Y1 - 2010/1

N2 - This study reports the methodology used to search, select and characterize STR loci on the canine X chromosome using publicly available genome resources and following the current guidelines for human and non-human forensic testing. After several rounds of selection, 12 X-STR markers were optimized for simultaneous co-amplification in a single PCR, and genetic profiles were determined in a sample of 103 unrelated dogs. Mendelian inheritance was verified and mutation rates were assessed using family groups. Alleles that varied in size were sequenced to create a standardized nomenclature proposal based on the number of repeats. All loci conformed to Hardy-Weinberg expectations. The resulting panel showed high forensic efficiency, presenting high values of power of discrimination (in males and females) and mean exclusion chance, both in trios involving female offspring and in duos composed of dam and male offspring. Its use may complement the information obtained by autosomal STR analysis and contribute to the resolution of complex cases of kinship in dogs. The presented methodology for the de novo construction of an STR multiplex may also provide a helpful framework for analogous work in other animal species. As an increasing number of reference genomes become available, convenient tools for individual identification and parentage testing based on STR loci selected from autosomes or sex chromosomes' sequences may be created following this strategy.

AB - This study reports the methodology used to search, select and characterize STR loci on the canine X chromosome using publicly available genome resources and following the current guidelines for human and non-human forensic testing. After several rounds of selection, 12 X-STR markers were optimized for simultaneous co-amplification in a single PCR, and genetic profiles were determined in a sample of 103 unrelated dogs. Mendelian inheritance was verified and mutation rates were assessed using family groups. Alleles that varied in size were sequenced to create a standardized nomenclature proposal based on the number of repeats. All loci conformed to Hardy-Weinberg expectations. The resulting panel showed high forensic efficiency, presenting high values of power of discrimination (in males and females) and mean exclusion chance, both in trios involving female offspring and in duos composed of dam and male offspring. Its use may complement the information obtained by autosomal STR analysis and contribute to the resolution of complex cases of kinship in dogs. The presented methodology for the de novo construction of an STR multiplex may also provide a helpful framework for analogous work in other animal species. As an increasing number of reference genomes become available, convenient tools for individual identification and parentage testing based on STR loci selected from autosomes or sex chromosomes' sequences may be created following this strategy.

KW - Animals

KW - Chromosome Mapping

KW - Dogs

KW - Female

KW - Gene Frequency

KW - Genetic Loci

KW - Genetic Variation

KW - Genomic Instability

KW - Genotype

KW - Linkage Disequilibrium

KW - Male

KW - Microsatellite Repeats

KW - Polymerase Chain Reaction

KW - X Chromosome

U2 - 10.1002/elps.200900389

DO - 10.1002/elps.200900389

M3 - Journal article

C2 - 20024924

SN - 0173-0835

VL - 31

SP - 303

EP - 308

JO - Electrophoresis

JF - Electrophoresis

IS - 2

ER -