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...
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| Format: | Article |
| Language: | English |
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Korea Genome Organization
2018-03-01
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| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-1-10.pdf |
| _version_ | 1811294591362531328 |
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| author | Aditi Sharma Jong-Eun Park Byungho Park Mi-Na Park Seung-Hee Roh Woo-Young Jung Seung-Hwan Lee Han-Ha Chai Gul-Won Chang Yong-Min Cho Dajeong Lim |
| author_facet | Aditi Sharma Jong-Eun Park Byungho Park Mi-Na Park Seung-Hee Roh Woo-Young Jung Seung-Hwan Lee Han-Ha Chai Gul-Won Chang Yong-Min Cho Dajeong Lim |
| author_sort | Aditi Sharma |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T05:19:41Z |
| format | Article |
| id | doaj.art-e1881c9cf80443bea1bb943cbaa8c59f |
| institution | Directory Open Access Journal |
| issn | 2234-0742 |
| language | English |
| last_indexed | 2024-04-13T05:19:41Z |
| publishDate | 2018-03-01 |
| publisher | Korea Genome Organization |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj.art-e1881c9cf80443bea1bb943cbaa8c59f2022-12-22T03:00:47ZengKorea Genome OrganizationGenomics & Informatics2234-07422018-03-01161101310.5808/GI.2018.16.1.10505Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of KoreaAditi Sharma0Jong-Eun Park1Byungho Park2Mi-Na Park3Seung-Hee Roh4Woo-Young Jung5Seung-Hwan Lee6Han-Ha Chai7Gul-Won Chang8Yong-Min Cho9Dajeong Lim10 Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea Hanwoo Genetic Improvement Center of the Nonghyup Agribusiness Group Inc., Seosan 31948, Korea Hanwoo Genetic Improvement Center of the Nonghyup Agribusiness Group Inc., Seosan 31948, Korea Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, KoreaUntil 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.http://genominfo.org/upload/pdf/gi-2018-16-1-10.pdfcattlegenotype predictionHanwooparentage verification |
| spellingShingle | Aditi Sharma Jong-Eun Park Byungho Park Mi-Na Park Seung-Hee Roh Woo-Young Jung Seung-Hwan Lee Han-Ha Chai Gul-Won Chang Yong-Min Cho Dajeong Lim Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea Genomics & Informatics cattle genotype prediction Hanwoo parentage verification |
| title | Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea |
| title_full | Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea |
| title_fullStr | Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea |
| title_full_unstemmed | Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea |
| title_short | Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea |
| title_sort | accuracy of imputation of microsatellite markers from bovinesnp50 and bovinehd beadchip in hanwoo population of korea |
| topic | cattle genotype prediction Hanwoo parentage verification |
| url | http://genominfo.org/upload/pdf/gi-2018-16-1-10.pdf |
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