title: Establishing a DNA identification system for pigs (Sus scrofa) using a multiplex STR amplification.
abstract: In this study we establish a novel STR multiplex using 13 tetra-nucleotide STRs and the amelogenin marker for the forensic identification of pigs. The genotypes and allele frequency were generated based on 341 samples from 11 pig breeds in Taiwan. Genetic variation was tested including Na, Ne, Ho, He, F-statistics, PIC, Pm and PE for each STR locus and for each breed. Based upon the 341 samples in this study, the CPm and CPEtrio of the 13 STR loci were 1.31 E-11 and 0.9996 respectively. The CPItrio based on ten family sets ranged from 4.012 E+4 to 4.332 E+6 for paternity test. Validation of the multiplex included: determining the sensitivity of the test, where reproducible full DNA profiles were obtained using an initial template of between 0.25 and 1 ng; a comprehensive range of tissue types generated the same genotype; and the specificity was confirmed as no DNA full profile was generated for any species other than Sus scrofa. Based on the phylogenetic analysis, the European domestic breeds clustered separately from the Asian breeds, as expected, and their hybrids formed unique clades respectively between the clades of Asian and European breeds. Eleven test samples, acting as unknown samples, matched all expected breeds. We demonstrate that this novel 14-plex PCR system is valuable in pig individualization, parentage testing, breed assessment, phylogenetic study and forensic applications.
authors: Department of Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 40227, Taiwan, ROC; Taichung City Government Police Department, 588 Wenxin Road Section 2, Xitun District, Taichung City 40758, Taiwan, ROC.
authors: Yu-Chih
authors: YC
authors: Lin
authors: Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan 33334, Taiwan, ROC.
authors: Hsing-Mei
authors: HM
authors: Hsieh
authors: Department of Forensic Medicine, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei 10051, Taiwan, ROC.
authors: James Chun-I
authors: JC
authors: Lee
authors: New Taipei City Police Department, 32 Fuzhong Road, Banqiao District, New Taipei City 22005, Taiwan, ROC.
authors: Chung-Ting
authors: CT
authors: Hsiao
authors: Livestock Research Institute, Council of Agriculture, 112, Muchang, Xinhua District, Tainan City 71246, Taiwan, ROC; Department of Life Sciences, Cheng Kung University, 1 University Road, Tainan City 701, Taiwan, ROC.
authors: Der-Yuh
authors: DY
authors: Lin
authors: School of Biological Sciences, Flinders University, Adelaide 5001, Australia.
authors: Adrian
authors: A
authors: Linacre
authors: Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan 33334, Taiwan, ROC. Electronic address: lctsai@mail.cpu.edu.tw.
authors: Li-Chin
authors: LC
authors: Tsai
mesh_terms: D053523:Amelogenin / Q000235:genetics; D000818:Animals; D016172:DNA Fingerprinting / Q000379:methods*; D005787:Gene Frequency; D005819:Genetic Markers; D005838:Genotype; D018895:Microsatellite Repeats; D060885:Multiplex Polymerase Chain Reaction; D010802:Phylogeny; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D034421:Sus scrofa / Q000235:genetics*
chemical_list: D053523:Amelogenin; D005819:Genetic Markers
keywords: Parentage testing; Pig DNA identification; Pig individualization; STR multiplex; Sus scrofa