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Molecular Marker Genotypes and Measuring their Relationship with Caspian Horses

ARDESHIR NEJATI-JAVAREMI1, GHODRAT RAHIMI2, ZOHREH HEIDARI1, ABDOLJALIL GHIADI3, DAVOOD KIANZAD4, KLAUS OLEK5

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Molecular Marker Genotypes and Measuring their Relationship with Caspian Horses

ARDESHIR NEJATI-JAVAREMI1, GHODRAT RAHIMI2, ZOHREH HEIDARI1, ABDOLJALIL GHIADI3, DAVOOD KIANZAD4, KLAUS OLEK5



1Department of Animal Science, University of Tehran, Karaj, Iran. 2Department of Animal Science, Agricultural Science University of Mazandaran, Sari, Iran. 3Turkmen Horse Breeding & Consulting Co (THBC), Raz and Jargalan, Boujnord, North Khorasan, Iran. 4National Animal Breeding Center of Iran, Karaj, Iran. 5Biopsytec GmbH, Berlin, Germany.


A total of 565 individuals from Turkmen horse breed of Iran and 20 Caspian horses were genotyped using 12 microsatellite markers as suggested by ISAG standards for individual identification and paternity tests. For 235 individuals whole blood samples were collected in EDTA treated tubes. For the remaining 350 individuals, hair samples were used to extract the genomic DNA. Genomic DNA samples were isolated in Biopsytec GmbH in Germany. Multiplex PCR reactions were carried out in a total volume of 30 μL, containing 0.17 mM dNTP-mix, 2.5 mM MgCl2, 2 U Thermo-start DNA polymerase and 100 ng of genomic DNA. The following markers were used: HMS6; HTG4; AHT4; VHL20; HTG6; HTG7; HMS3; HMS6 in the 8-plex PCR and HTG10; HMS2; ASB2; AHT5 in the 4-plex PCR. For each PCR reaction one primer was 5' end labeled with commercially fluorescent labels TAMRA, FAM and HEX. The PCR fragments were denatured, separated on an ABI 377 sequencer and analyzed with Genescan software. A total of 113 alleles (averaging 9.4±1.8) for Turkmen horse and 79 alleles (averaging 6.6±1.7) for Caspian horses were detected across the 12 microsatellite loci analyzed. The observed and expected homozygosities for all loci for both breeds are reported. Total allelic relationship was used to analyze marker genotypes. Genetic distances of each individual with the sampled population were measured. Average inbreeding for Turkmen horse was estimated at 1.09 while this figure was -6.34 for Caspians, meaning extra heterozygosity for the sampled individuals.

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