Empirical selection of informative microsatellite markers within co-ancestry pig populations is required for improving the individual assignment efficiency

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

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

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 (F ST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values (F IS) 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 missassigned 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.

Original languageEnglish
Pages (from-to)616-627
Number of pages12
JournalAsian-Australasian Journal of Animal Sciences
Volume27
Issue number5
DOIs
Publication statusPublished - 2014 May

Fingerprint

Microsatellite Repeats
ancestry
Animals
Swine
microsatellite repeats
breeds
swine
Genetic Databases
heterozygosity
Population
Genetic Markers
swine breeds
Duroc
Testing
Inbreeding
genetic variation
landraces
Loss of Heterozygosity
Laboratory Animals
Taiwan

Keywords

  • Assignment test
  • Microsatellite markers
  • Pigs

ASJC Scopus subject areas

  • Food Science
  • Animal Science and Zoology
  • Engineering(all)

Cite this

Empirical selection of informative microsatellite markers within co-ancestry pig populations is required for improving the individual assignment efficiency. / Li, Y. H.; Chu, H. P.; Jiang, Y. N.; Lin, C. Y.; Li, S. H.; Li, K. T.; Weng, G. J.; Cheng, C. C.; Lu, D. J.; Ju, Y. T.

In: Asian-Australasian Journal of Animal Sciences, Vol. 27, No. 5, 05.2014, p. 616-627.

Research output: Contribution to journalArticle

Li, Y. H. ; Chu, H. P. ; Jiang, Y. N. ; Lin, C. Y. ; Li, S. H. ; Li, K. T. ; Weng, G. J. ; Cheng, C. C. ; Lu, D. J. ; Ju, Y. T. / Empirical selection of informative microsatellite markers within co-ancestry pig populations is required for improving the individual assignment efficiency. In: Asian-Australasian Journal of Animal Sciences. 2014 ; Vol. 27, No. 5. pp. 616-627.
@article{4d37abf7997141328ce6d214d954d6cf,
title = "Empirical selection of informative microsatellite markers within co-ancestry pig populations is required for improving the individual assignment efficiency",
abstract = "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 (F ST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values (F IS) 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 missassigned 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.",
keywords = "Assignment test, Microsatellite markers, Pigs",
author = "Li, {Y. H.} and Chu, {H. P.} and Jiang, {Y. N.} and Lin, {C. Y.} and Li, {S. H.} and Li, {K. T.} and Weng, {G. J.} and Cheng, {C. C.} and Lu, {D. J.} and Ju, {Y. T.}",
year = "2014",
month = "5",
doi = "10.5713/ajas.2013.13365",
language = "English",
volume = "27",
pages = "616--627",
journal = "Asian-Australasian Journal of Animal Sciences",
issn = "1011-2367",
publisher = "Asian-Australasian Association of Animal Production Societies",
number = "5",

}

TY - JOUR

T1 - Empirical selection of informative microsatellite markers within co-ancestry pig populations is required for improving the individual assignment efficiency

AU - Li, Y. H.

AU - Chu, H. P.

AU - Jiang, Y. N.

AU - Lin, C. Y.

AU - Li, S. H.

AU - Li, K. T.

AU - Weng, G. J.

AU - Cheng, C. C.

AU - Lu, D. J.

AU - Ju, Y. T.

PY - 2014/5

Y1 - 2014/5

N2 - 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 (F ST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values (F IS) 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 missassigned 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.

AB - 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 (F ST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values (F IS) 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 missassigned 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.

KW - Assignment test

KW - Microsatellite markers

KW - Pigs

UR - http://www.scopus.com/inward/record.url?scp=84899550183&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84899550183&partnerID=8YFLogxK

U2 - 10.5713/ajas.2013.13365

DO - 10.5713/ajas.2013.13365

M3 - Article

AN - SCOPUS:84899550183

VL - 27

SP - 616

EP - 627

JO - Asian-Australasian Journal of Animal Sciences

JF - Asian-Australasian Journal of Animal Sciences

SN - 1011-2367

IS - 5

ER -