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A model for equine breed identification using microsatellites and posterior probability testing
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Fifteen new horse Microsatellite loci were identified by screening a size-fractionated plasrnid library with a (GT) 15 probe. Positive clones were sequenced and oligonucleotide primer pairs complementary to flanking region DNA were synthesized. Polymerase chain reaction (PCR) assays were performed on DNA from three breed groups of unrelated horses (E. caballus) and from an Arabian half-sib family. PCR amplification was also attempted for homologous loci in Grant's zebra, E. burchelli granti. PCR products were analyzed by polyacrylantide gel electrophoresis followed by autoradiography. Segregation analysis of the 19 n-microsatellite loci did not indicate linkage (Z > 3.0) between any of the loci. Microsatellite allele distributions in the unrelated breed groups of E. caballus were compared for calculation of population differentiation and genetic distance using three different distance estimates, Ds, Dps and Ddm. The draft-origin breed group showed the greatest allelic diversity with an average of 4.8947 alleles per locus and an average heterozygosity of 0.5642. An average of 4.0526 and 3.4737 alleles per locus and an average heterozygosity of 0.5426 and 0.5295 were observed in Arabians and Thoroughbreds, respectively. Genetic differentiation among the breeds of horses tested ranged from 0.0029 to 0.4171 with an average Fst 0. 1 126 over all loci. Although each genetic distance measure reflected similar cladistic relationships, the magnitude of divergence varied considerably with the distance measure that was used. Ds estimates were most conservative (0. 130 to 0.268), Dps estimates were intermediate (0.334 to 0.476) and Ddm estimates were greatest (0.480 to 2.050). Genetic distance measures were also applied to pairwise comparisons between the individual breed groups of E caballus and E burchelli granti. Each distance measure showed greater horse-zebra distances than any intra-specific comparison under the same measure. A model for horse breed classification was designed based on the microsatellite allele distributions observed in Arabians and Thoroughbreds. The model utilized a posterior probability algorithm across a multi-locus genotype to generate the relative likelihood that an individual was either pure Arabian (ARAB), a pure Thoroughbred (THOR) or a first generation ARAB-THOR hybrid. Thirty-four test horse genotypes were analyzed and of these, 76.47% were correctly classified, 20.59% were indistinguishable and 2.94% were incorrectly classified.
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Chastain, Pepper Alise (1996). A model for equine breed identification using microsatellites and posterior probability testing. Master's thesis, Texas A&M University. Available electronically from
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