Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency
The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to t...
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| Format: | Article |
| Language: | English |
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Asian-Australasian Association of Animal Production Societies
2014-05-01
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| Series: | Asian-Australasian Journal of Animal Sciences |
| Subjects: | |
| Online Access: | http://www.ajas.info/upload/pdf/ajas-27-5-616-2.pdf |
| _version_ | 1811209093758582784 |
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| author | Y. H. Li H. P. Chu Y. N. Jiang C. Y. Lin S. H. Li K. T. Li G. J. Weng C. C. Cheng D. J. Lu Y. T. Ju |
| author_facet | Y. H. Li H. P. Chu Y. N. Jiang C. Y. Lin S. H. Li K. T. Li G. J. Weng C. C. Cheng D. J. Lu Y. T. Ju |
| author_sort | Y. H. Li |
| collection | DOAJ |
| description | The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu’s inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations. |
| first_indexed | 2024-04-12T04:33:35Z |
| format | Article |
| id | doaj.art-915e55eccbd946b189a2886add051849 |
| institution | Directory Open Access Journal |
| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-04-12T04:33:35Z |
| publishDate | 2014-05-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-915e55eccbd946b189a2886add0518492022-12-22T03:47:52ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172014-05-0127561662710.5713/ajas.2013.133654857Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment EfficiencyY. H. LiH. P. Chu0Y. N. JiangC. Y. Lin1S. H. Li2K. T. Li3G. J. Weng4C. C. Cheng5D. J. Lu6Y. T. Ju Taitung Animal Propagation Station, Livestock Research Institute, Taitung, .Taiwan Taitung Animal Propagation Station, Livestock Research Institute, Taitung, .Taiwan Department of Life Science, National Taiwan Normal University, Taipei, .Taiwan Institute of History and Philology, Academia Sinica, Taipei, .Taiwan Institute of Wildlife Conservation, National Pingtung University of Science and Technology, Pintung, .Taiwan Graduate Institute of Hakka Cultural Industry, National Pingtung University of Science and Technology, Pintung, .Taiwan School of Forestry and Resource Conservation, National Taiwan University, Taipei, .TaiwanThe Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu’s inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations.http://www.ajas.info/upload/pdf/ajas-27-5-616-2.pdfMicrosatellite MarkersPigsAssignment Test |
| spellingShingle | Y. H. Li H. P. Chu Y. N. Jiang C. Y. Lin S. H. Li K. T. Li G. J. Weng C. C. Cheng D. J. Lu Y. T. Ju Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency Asian-Australasian Journal of Animal Sciences Microsatellite Markers Pigs Assignment Test |
| title | Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency |
| title_full | Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency |
| title_fullStr | Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency |
| title_full_unstemmed | Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency |
| title_short | Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency |
| title_sort | empirical selection of informative microsatellite markers within co ancestry pig populations is required for improving the individual assignment efficiency |
| topic | Microsatellite Markers Pigs Assignment Test |
| url | http://www.ajas.info/upload/pdf/ajas-27-5-616-2.pdf |
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