Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea

Until now microsatellite (MS) have been a popular choice of markers for parentage verification. Recently many countries have moved or are in process of moving from MS markers to single nucleotide polymorphism (SNP) markers for parentage testing. FAO-ISAG has also come up with a panel of 200 SNPs to replace the use of MS markers in parentage verification. However, in many countries most of the animals were genotyped by MS markers till now and the sudden shift to SNP markers will render the data of those animals useless. As National Institute of Animal Science in South Korea plans to move from standard ISAG recommended MS markers to SNPs, it faces the dilemma of exclusion of old animals that were genotyped by MS markers. Thus to facilitate this shift from MS to SNPs, such that the existing animals with MS data could still be used for parentage verification, this study was performed. In the current study we performed imputation of MS markers from the SNPs in the 500-kb region of the MS marker on either side. This method will provide an easy option for the labs to combine the data from the old and the current set of animals. It will be a cost efficient replacement of genotyping with the additional markers. We used 1,480 Hanwoo animals with both the MS data and SNP data to impute in the validation animals. We also compared the imputation accuracy between BovineSNP50 and BovineHD BeadChip. In our study the genotype concordance of 40% and 43% was observed in the BovineSNP50 and BovineHD BeadChip respectively.

DNA testing for parentage verification in a conservation nucleus of Pantaneiro horse

We investigated the genealogy of the in situ conservation nucleus of the Pantaneiro horse using DNA microsatellites by evaluating 101 horses, the group consisting of 71 adult horses (3 stallions, 40 male and 31 mares) and 27 foals (14 colts and 13 fillies). Genomic DNA was extracted from hair roots and genotyped using 12 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, HMS3 HMS6, HMS7, HTG4, HTG10, LEX33 and VHL20). The number of alleles per locus varied from 6 to 13, with a mean of 7.8 and the expected heterozygosity ranged from 0.544 to 0.734 (mean 0.644). The VLH20, ASB2, HTG10, ASB23 markers had a high (> 0.8) polymorphism information content and the total exclusion probability of the 12 microsatellite loci was 0.99. The genealogical study of the Pantaneiro horse using genetic markers was efficient in detecting mistakes during paternity and maternity designation and is an important tool which can be used together with traditional systems of animal identification. The use of genetic markers is recommended in the systematic control of the genealogical registrations and conservation plans to improve genetic aspects of the Pantaneiro horse.

Parentage testing of Thoroughbred horse in Korea using microsatellite DNA typing

The present study was to construct a parentage testing system for Thoroughbred (TB) horse. A total number of 1,285 TB horse samples including 962 foals for parentage testing, 9 sires and 314 dams for individual identification were genotyped. Genomic DNA was extracted from 5 hair roots and genotyped by using 14 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3 and VHL20). This method consisted of multiplexing PCR procedure and showed reasonable amplification of all PCR products. Genotypes were determined by genetic analyzer. The number of alleles per locus varied from 3 to 9 with a mean value of 6.36 in TB horse. The expected heterozygosity was ranged from 0.548 to 0.831 (mean 0.699), and the total exclusion probability of 14 microstellite loci was 0.9998. Of the 14 markers, ASB2, ASB17, ASB23, HMS7 and HTG10 loci have relatively high PIC value (> 0.7). Of the 962 foals, 960 foals were qualified by compatibility according to the Mendelism. These results suggest that the DNA typing method has high potential for parentage verification and individual identification of TB horses.