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Jin S, Won JI, Kim HJ, Park B, Kim SW, Kim UH, Kang SS, Lee HJ, Moon SJ, Park MS, Sim YT, Jang SS, Kim NY. Polymorphism analysis of tri- and tetranucleotide repeat microsatellite markers in Hanwoo cattle. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:717-725. [PMID: 39165748 PMCID: PMC11331372 DOI: 10.5187/jast.2024.e10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/21/2023] [Accepted: 01/23/2024] [Indexed: 08/22/2024]
Abstract
The Hanwoo traceability system currently utilizes 11 dinucleotide repeat microsatellite (MS) markers. However, dinucleotide repeat markers are known to have a high incidence of polymerase chain reaction (PCR) artifacts, such as stutter bands, which can complicate the accurate reading of alleles. In this study, we examined the polymorphisms of the 11 dinucleotide repeat MS markers currently employed in traceability systems. Additionally, we explored four trinucleotide repeat MS markers and one tetranucleotide repeat MS marker in a sample of 1,106 Hanwoo cattle. We also assessed the potential utility of the tri- and tetranucleotide repeat MS markers. The polymorphic information content (PIC) of the five tri- and tetranucleotide repeat markers ranged from 0.663 to 0.767 (mean: 0.722), sufficiently polymorphic and slightly higher than the mean (0.716) of the current 11 dinucleotide repeat markers. Using all 16 markers, the mean PIC was 0.718. The estimated probability of identity (PI) was 3.13 × 10-12 using the 11 dinucleotide repeat markers, 7.03 × 10-6 using the five tri- and tetranucleotide repeat markers, and 2.39 × 10-17 using all 16 markers; the respective PIhalf-sibs values were 2.69 × 10-9, 1.29 × 10-4, and 3.42 × 10-13; and the respective PIsibs values were 3.89 × 10-5, 9.6 × 10-3, and 3.69 × 10-7. The probability of exclusion1 (PE1) was 0.999864 for the 11 dinucleotide repeat markers, 0.981141 for five of the tri- and tetranucleotide repeat markers, and > 0.99 for all 16 markers; the respective PE2 values were 0.994632, 0.901369, and > 0.99; and the respective PE3 values were 0.998702, > 0.99, and > 0.99. The five investigated tri- and tetranucleotide repeat MS markers can be used in combination with the 11 existing MS markers to improve the accuracy of individual identification and paternity testing in Hanwoo.
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Affiliation(s)
- Shil Jin
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Jeong Il Won
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Hyoun Ju Kim
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Byoungho Park
- Animal Breeding & Genetics
Division, National Institute of Animal Science, Cheonan 31000,
Korea
| | - Sung Woo Kim
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Ui Hyung Kim
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Sung-Sik Kang
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Hyun-Jeong Lee
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Sung Jin Moon
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Myung Sun Park
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Yong Teak Sim
- miDNA Genome Research
institute, Kunsan 54156, Korea
| | - Sun Sik Jang
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Nam Young Kim
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
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Ardani P, Rezaei HR, Kaboli M. Individual Identification of Panthera pardus saxicolor Using Non-Invasive Sampling and Molecular Techniques in Iran: A Case Study in Parvar Protected Area. MAMMAL STUDY 2022. [DOI: 10.3106/ms2021-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Panteha Ardani
- Department of Environmental Science, Faculty of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid R. Rezaei
- Department of Fisheries and Environmental Science, Faculty of Environmental Science, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Mohammad Kaboli
- Department of Environmental Science, Faculty of Natural Resources, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
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Hill E, Linacre A, Toop S, Murphy N, Strugnell JM. Development of an STR panel for a non-native population of an endangered species. Mol Biol Rep 2021; 49:839-845. [PMID: 34739689 DOI: 10.1007/s11033-021-06905-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The establishment of non-native populations of threatened and legally protected species can have many implications for the areas where these species have been introduced. Non-native populations of threatened species have the potential to be exploited and therefore the subject of legal protection, while conversely, if they have become invasive in their introduced range, there is the likelihood that population control will be carried out to reduce abundance and negative impacts associated with introduced species. From both a legal and invasive species monitoring standpoint, it is important to know how many individuals are present. METHODS AND RESULTS Short tandem repeats (STRs) were developed for the hog deer, an endangered species that was introduced following European settlement to Victoria, Australia using Illumina MiSeq sequencing technology. These markers were combined with previous STRs characterised for hog deer to create a 29-plex identification system. A total of 224 samples were genotyped across the population in Victoria, and further analyses of null allele frequencies, deviation from Hardy-Weinberg equilibrium, and the removal of monomorphic or low amplifying markers resulted in a final marker panel of 15 loci. Despite low values for number of alleles at each locus (2-4), probability of identity showed sufficient discrimination power, with an average probability of identity at 2.94 × 10-6, and a probability of sibling identity of 8.9 × 10-4 across all sites. CONCLUSIONS It is feasible to create an informative DNA profiling system that can distinguish between individuals for applications in both wildlife forensic and population control research.
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Affiliation(s)
- Erin Hill
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Adrian Linacre
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042, Australia
| | - Simon Toop
- Game Management Authority, Melbourne, VIC, 3000, Australia
| | - Nicholas Murphy
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,Research Centre for Future Landscapes, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
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Cmejlova J, Rejlova M, Paprstein F, Cmejla R. A new one-tube reaction kit for the SSR genotyping of apple (Malus × domestica Borkh.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110768. [PMID: 33487353 DOI: 10.1016/j.plantsci.2020.110768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Though apple genotyping is mainly used for scientific and breeding purposes, it can also be adopted by national authorities to control the authenticity of apple cultivars. To facilitate the introduction of routine apple genotyping into practice, a new apple simple sequence repeat (SSR) genotyping kit was developed (called the Ap17 in. SSR Genotyping Kit). The kit combines 17 SSR markers including those recommended by the Working Group of the European Cooperative Programme for Plant Genetic Resources (ECPGR), covering all apple linkage groups in a one-tube reaction format, using a fragment analysis method to simplify the genotyping procedure. The kit was successfully tested using 880 unique diploid apple germplasm accessions; the kit can also readily discriminate triploid and tetraploid samples. The total probability of identity for the kit and the sample collection used was calculated to be 1.73 × 10-22. Tables for converting results to enable genotype comparisons between currently-used genotyping systems and the Ap17 in. kit are provided. The kit is ideally suited for validation in laboratories genotyping a large number of apple samples, saving time, costs, and labor, while minimizing technical and human errors.
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Affiliation(s)
- Jana Cmejlova
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic
| | - Martina Rejlova
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic
| | - Frantisek Paprstein
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic
| | - Radek Cmejla
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic.
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Seo JH, Park KD, Lee HK, Kong HS. Genetic diversity of Halla horses using microsatellite markers. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2016; 58:40. [PMID: 27891245 PMCID: PMC5114825 DOI: 10.1186/s40781-016-0120-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/17/2016] [Indexed: 12/04/2022]
Abstract
BACKGROUND Currently about 26,000 horses are breeding in Korea and 57.2% (14,776 horses) of them are breeding in Jeju island. According to the statistics published in 2010, the horses breeding in Jeju island are subdivided into Jeju horse (6.1%), Thoroughbred (18.8%) and Halla horse (75.1%). Halla horses are defined as a crossbreed between Jeju and Thoroughbred horses and are used for horse racing, horse riding and horse meat production. However, little research has been conducted on Halla horses because of the perception of crossbreed and people's weighted interest toward Jeju horses. METHOD Using 17 Microsatellite (MS) Markers recommended by International Society for Animal Genetics (ISAG), genomic DNAs were extracted from the hair roots of 3,880 Halla horses breeding in Korea and genetic diversity was identified by genotyping after PCR was performed. RESULTS AND CONCLUSION In average, 10.41 alleles (from 6 alleles in HTG7 to 17 alleles in ASB17) were identified after the analysis using 17 MS Markers. The mean value of Hobs was 0.749 with a range from 0.612(HMS1) to 0.857(ASB2). Also, it was found that Hexp and PIC values were lowest in HMS1 (0.607 and 0.548, respectively), and highest in LEX3(0.859 and 0.843, respectively), and the mean value of Hexp was 0.760 and that of PIC was 0.728. 17 MS markers used in this studies were considered as appropriate markers for the polymorphism analysis of Halla horses. The frequency for the appearance of identical individuals was 5.90 × 10-20 when assumed as random mating population and when assumed as half-sib and full-sib population, frequencies were 4.08 × 10-15 and 3.56 × 10-8, respectively. Based on these results, the 17 MS markers can be used adequately for the Individual Identification and Parentage Verification of Halla horses. Remarkably, allele M and Q of ASB23 marker, G of HMS2 marker, H and L of HTG6 marker, L of HTG7 marker, E of LEX3 marker were the specific alleles unique to Halla horses.
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Affiliation(s)
- Joo-Hee Seo
- Genomic Informatics Center, Hankyong National University, Anseong, 17579 Korea
- Department of Genomic Informatics, Graduate School of Future Convergence Technology, Hankyong National University, Anseong, 456-749 Korea
| | | | - Hak-Kyo Lee
- ChonBuk National University, Jeonju, 54896 Korea
| | - Hong-Sik Kong
- Genomic Informatics Center, Hankyong National University, Anseong, 17579 Korea
- Department of Genomic Informatics, Graduate School of Future Convergence Technology, Hankyong National University, Anseong, 456-749 Korea
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Seo D, Bhuiyan MSA, Sultana H, Heo JM, Lee JH. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:471-8. [PMID: 26949947 PMCID: PMC4782081 DOI: 10.5713/ajas.15.0915] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/24/2015] [Accepted: 01/14/2016] [Indexed: 02/04/2023]
Abstract
Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.
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Affiliation(s)
- Dongwon Seo
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Shamsul Alam Bhuiyan
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Hasina Sultana
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jung Min Heo
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jun Heon Lee
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
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Winiarski KJ, McGarigal K. Effects of Photo and Genotype-Based Misidentification Error on Estimates of Survival, Detection and State Transition using Multistate Survival Models. PLoS One 2016; 11:e0145640. [PMID: 26751208 PMCID: PMC4709094 DOI: 10.1371/journal.pone.0145640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 12/07/2015] [Indexed: 11/19/2022] Open
Abstract
We simulated multistate capture histories (CHs) by varying state survival (ϕ), detection (p) and transition (ψ), number of total capture occasions and releases per capture occasion and then modified these scenarios to mimic false rejection error (FRE), a common misidentification error, resulting from the failure to match samples of the same individual. We then fit a multistate model and estimated accuracy, bias and precision of state-specific ϕ, p and ψ to better understand the effects of FRE on different simulation scenarios. As expected, ϕ, and p, decreased in accuracy with FRE, with lower accuracy when CHs were simulated under a shorter-term study and a lower number of releases per capture occasion (lower sample size). Accuracy of ψ estimates were robust to FRE except in those CH scenarios simulated using low sample size. The effect of FRE on bias was not consistent among parameters and differed by CH scenario. As expected, ϕ was negatively biased with increased FRE (except for the low ϕ low p CH scenario simulated with a low sample size), but we found that the magnitude of bias differed by scenario (high p CH scenarios were more negatively biased). State transition was relatively unbiased, except for the low p CH scenarios simulated with a low sample size, which were positively biased with FRE, and high p CH scenarios simulated with a low sample size. The effect of FRE on precision was not consistent among parameters and differed by scenario and sample size. Precision of ϕ decreased with FRE and was lowest with the low ϕ low p CH scenarios. Precision of p estimates also decreased with FRE under all scenarios, except the low ϕ high p CH scenarios. However, precision of ψ increased with FRE, except for those CH scenarios simulated with a low sample size. Our results demonstrate how FRE leads to loss of accuracy in parameter estimates in a multistate model with the exception of ψ when estimated using an adequate sample size.
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Affiliation(s)
- Kristopher J. Winiarski
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, United States of America
- Northeast Climate Science Center, University of Massachusetts, Amherst, Massachusetts, United States of America
- * E-mail:
| | - Kevin McGarigal
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, United States of America
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Napolitano C, Díaz D, Sanderson J, Johnson WE, Ritland K, Ritland CE, Poulin E. Reduced Genetic Diversity and Increased Dispersal in Guigna (Leopardus guigna) in Chilean Fragmented Landscapes. J Hered 2015; 106 Suppl 1:522-36. [PMID: 26245787 DOI: 10.1093/jhered/esv025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Landscape fragmentation is often a major cause of species extinction as it can affect a wide variety of ecological processes. The impact of fragmentation varies among species depending on many factors, including their life-history traits and dispersal abilities. Felids are one of the groups most threatened by fragmented landscapes because of their large home ranges, territorial behavior, and low population densities. Here, we model the impacts of habitat fragmentation on patterns of genetic diversity in the guigna (Leopardus guigna), a small felid that is closely associated with the heavily human-impacted temperate rainforests of southern South America. We assessed genetic variation in 1798 base pairs of mitochondrial DNA sequences, 15 microsatellite loci, and 2 sex chromosome genes and estimated genetic diversity, kinship, inbreeding, and dispersal in 38 individuals from landscapes with differing degrees of fragmentation on Chiloé Island in southern Chile. Increased fragmentation was associated with reduced genetic diversity, but not with increased kinship or inbreeding. However, in fragmented landscapes, there was a weaker negative correlation between pairwise kinship and geographic distance, suggesting increased dispersal distances. These results highlight the importance of biological corridors to maximize connectivity in fragmented landscapes and contribute to our understanding of the broader genetic consequences of habitat fragmentation, especially for forest-specialist carnivores.
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Affiliation(s)
- Constanza Napolitano
- From the Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Napolitano and Poulin); Departamento de Ciencias Ambientales y Recursos Naturales, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile (Díaz); Small Wild Cat Conservation Foundation, Campbell, CA (Sanderson); Smithsonian Conservation Biology Institute, Front Royal, VA (Johnson); and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada (K. Ritland and CE. Ritland).
| | - Diego Díaz
- From the Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Napolitano and Poulin); Departamento de Ciencias Ambientales y Recursos Naturales, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile (Díaz); Small Wild Cat Conservation Foundation, Campbell, CA (Sanderson); Smithsonian Conservation Biology Institute, Front Royal, VA (Johnson); and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada (K. Ritland and CE. Ritland)
| | - Jim Sanderson
- From the Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Napolitano and Poulin); Departamento de Ciencias Ambientales y Recursos Naturales, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile (Díaz); Small Wild Cat Conservation Foundation, Campbell, CA (Sanderson); Smithsonian Conservation Biology Institute, Front Royal, VA (Johnson); and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada (K. Ritland and CE. Ritland)
| | - Warren E Johnson
- From the Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Napolitano and Poulin); Departamento de Ciencias Ambientales y Recursos Naturales, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile (Díaz); Small Wild Cat Conservation Foundation, Campbell, CA (Sanderson); Smithsonian Conservation Biology Institute, Front Royal, VA (Johnson); and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada (K. Ritland and CE. Ritland)
| | - Kermit Ritland
- From the Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Napolitano and Poulin); Departamento de Ciencias Ambientales y Recursos Naturales, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile (Díaz); Small Wild Cat Conservation Foundation, Campbell, CA (Sanderson); Smithsonian Conservation Biology Institute, Front Royal, VA (Johnson); and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada (K. Ritland and CE. Ritland)
| | - Carol E Ritland
- From the Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Napolitano and Poulin); Departamento de Ciencias Ambientales y Recursos Naturales, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile (Díaz); Small Wild Cat Conservation Foundation, Campbell, CA (Sanderson); Smithsonian Conservation Biology Institute, Front Royal, VA (Johnson); and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada (K. Ritland and CE. Ritland)
| | - Elie Poulin
- From the Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Napolitano and Poulin); Departamento de Ciencias Ambientales y Recursos Naturales, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile (Díaz); Small Wild Cat Conservation Foundation, Campbell, CA (Sanderson); Smithsonian Conservation Biology Institute, Front Royal, VA (Johnson); and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada (K. Ritland and CE. Ritland)
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Concordance study between the ParaDNA ® Intelligence Test, a Rapid DNA profiling assay, and a conventional STR typing kit (AmpFlSTR ® SGM Plus ® ). Forensic Sci Int Genet 2015; 16:48-51. [DOI: 10.1016/j.fsigen.2014.12.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/13/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
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Choi NR, Seo DW, Jemaa SB, Sultana H, Heo KN, Jo C, Lee JH. Discrimination of the commercial Korean native chicken population using microsatellite markers. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2015; 57:5. [PMID: 26290725 PMCID: PMC4540261 DOI: 10.1186/s40781-015-0044-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/20/2015] [Indexed: 12/03/2022]
Abstract
Background Korean native chicken (KNC) is a well-known breed due to its superior meat taste. This breed, however, owing to a low growth rate, has a high market price. In order to overcome this disadvantage, the National Institute of Animal Science (NIAS) in Korea developed a commercial KNC breed, named Woorimatdag version 2 (WM2), an upgraded version of the Woorimatdag (WM1) breed and the WM2 was created by crossing the KNC with meat type breeds. This study aims to discriminate between WM2 and other chicken breeds using microsatellite (MS) markers. Methods A total of 302 individuals from eight Korean chicken populations were examined. The genetic diversity and population structure analysis were investigated using Cervus, API-CALC, STRUCTURE, PowerMarker programs. Results Based on heterozygosity and polymorphic information content (PIC) values, 30 MS markers were initially selected from 150 markers. The identified average number of alleles (Na), expected heterozygosity, and PIC values for the WM2 samples were 7.17, 0.741, and 0.682, respectively. Additionally, the paternity of individuals was assigned with a success rate of greater than 99% using 12 markers, the best minimum number of markers. The 12 selected markers contained heterozygosity and PIC values above 0.7 and probability of identity values around zero. Using these markers, the determined probability of identity (PI), PIhalf-sibs, and PIsibs values were 3.23E-33, 5.03E-22, and 8.61E-08, respectively. Conclusions WM2 is well differentiated with respect to other chicken breeds based on estimated genetic distances. The results presented here will contribute to the identification of commercial WM2 chicken in the market. Electronic supplementary material The online version of this article (doi:10.1186/s40781-015-0044-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nu Ri Choi
- Department of Animal Science and Biotechnology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 305-764 Republic of Korea
| | - Dong Won Seo
- Department of Animal Science and Biotechnology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 305-764 Republic of Korea
| | - Slim Ben Jemaa
- Department of Animal Science and Biotechnology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 305-764 Republic of Korea ; INRA-Tunisie, Laboratoire des Productions Animales et Fourragères, Rue Hédi Karray, 2049 Ariana Tunisia
| | - Hasina Sultana
- Department of Animal Science and Biotechnology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 305-764 Republic of Korea
| | - Kang Nyeong Heo
- Poultry Science Division, National Institute of Animal Science, RDA, Cheonan, 331-801 Republic of Korea
| | - Cheorun Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Science, Seoul National University, Seoul, 151-921 Republic of Korea
| | - Jun Heon Lee
- Department of Animal Science and Biotechnology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 305-764 Republic of Korea
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Drechsler A, Helling T, Steinfartz S. Genetic fingerprinting proves cross-correlated automatic photo-identification of individuals as highly efficient in large capture-mark-recapture studies. Ecol Evol 2014; 5:141-51. [PMID: 25628871 PMCID: PMC4298441 DOI: 10.1002/ece3.1340] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/06/2022] Open
Abstract
Capture-mark-recapture (CMR) approaches are the backbone of many studies in population ecology to gain insight on the life cycle, migration, habitat use, and demography of target species. The reliable and repeatable recognition of an individual throughout its lifetime is the basic requirement of a CMR study. Although invasive techniques are available to mark individuals permanently, noninvasive methods for individual recognition mainly rest on photographic identification of external body markings, which are unique at the individual level. The re-identification of an individual based on comparing shape patterns of photographs by eye is commonly used. Automated processes for photographic re-identification have been recently established, but their performance in large datasets (i.e., > 1000 individuals) has rarely been tested thoroughly. Here, we evaluated the performance of the program AMPHIDENT, an automatic algorithm to identify individuals on the basis of ventral spot patterns in the great crested newt (Triturus cristatus) versus the genotypic fingerprint of individuals based on highly polymorphic microsatellite loci using GENECAP. Between 2008 and 2010, we captured, sampled and photographed adult newts and calculated for 1648 samples/photographs recapture rates for both approaches. Recapture rates differed slightly with 8.34% for GENECAP and 9.83% for AMPHIDENT. With an estimated rate of 2% false rejections (FRR) and 0.00% false acceptances (FAR), AMPHIDENT proved to be a highly reliable algorithm for CMR studies of large datasets. We conclude that the application of automatic recognition software of individual photographs can be a rather powerful and reliable tool in noninvasive CMR studies for a large number of individuals. Because the cross-correlation of standardized shape patterns is generally applicable to any pattern that provides enough information, this algorithm is capable of becoming a single application with broad use in CMR studies for many species.
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Affiliation(s)
- Axel Drechsler
- Department of Behavioural Biology, Unit of Molecular Ecology and Behaviour, University of Bielefeld Morgenbreede 45, D-33619, Bielefeld, Germany
| | - Tobias Helling
- Department of Behavioural Biology, Unit of Molecular Ecology and Behaviour, University of Bielefeld Morgenbreede 45, D-33619, Bielefeld, Germany
| | - Sebastian Steinfartz
- Department of Behavioural Biology, Unit of Molecular Ecology and Behaviour, University of Bielefeld Morgenbreede 45, D-33619, Bielefeld, Germany ; Zoological Institute, Department of Evolutionary Biology, Unit Molecular Ecology, Technische Universität Braunschweig, Mendelssohnstr. 4 38106, Braunschweig, Germany
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12
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Pomilla C, Amaral AR, Collins T, Minton G, Findlay K, Leslie MS, Ponnampalam L, Baldwin R, Rosenbaum H. The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea. PLoS One 2014; 9:e114162. [PMID: 25470144 PMCID: PMC4254934 DOI: 10.1371/journal.pone.0114162] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 11/04/2014] [Indexed: 11/18/2022] Open
Abstract
A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.
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Affiliation(s)
- Cristina Pomilla
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Ana R. Amaral
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Centro de Biologia Ambiental, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, Bronx, New York, United States of America
- Environment Society of Oman, Ruwi, Sultanate of Oman
| | - Gianna Minton
- Environment Society of Oman, Ruwi, Sultanate of Oman
- World Wide Fund for Nature, Gabon, Libreville, Gabon
| | - Ken Findlay
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Matthew S. Leslie
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Ocean Giants Program, Wildlife Conservation Society, Bronx, New York, United States of America
| | - Louisa Ponnampalam
- Environment Society of Oman, Ruwi, Sultanate of Oman
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Howard Rosenbaum
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Ocean Giants Program, Wildlife Conservation Society, Bronx, New York, United States of America
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13
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Oh JD, Song KD, Seo JH, Kim DK, Kim SH, Seo KS, Lim HT, Lee JB, Park HC, Ryu YC, Kang MS, Cho S, Kim ES, Choe HS, Kong HS, Lee HK. Genetic traceability of black pig meats using microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:926-31. [PMID: 25050032 PMCID: PMC4093566 DOI: 10.5713/ajas.2013.13829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/27/2014] [Accepted: 04/10/2014] [Indexed: 11/27/2022]
Abstract
Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and −0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10−14 in population J, 3.17×10−9 in population B, and 1.03×10−12 in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers.
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Affiliation(s)
- Jae-Don Oh
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Ki-Duk Song
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Joo-Hee Seo
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Duk-Kyung Kim
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Sung-Hoon Kim
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Kang-Seok Seo
- Department of Animal Science and Technology, Sunchon National University, Sunchon 540-742, Korea
| | - Hyun-Tae Lim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Jae-Bong Lee
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | | | - Youn-Chul Ryu
- Major of Animal Science and Biotechnology, Jeju National University, Jeju 690-756, Korea
| | - Min-Soo Kang
- Major of Animal Science and Biotechnology, Jeju National University, Jeju 690-756, Korea
| | | | - Eui-Soo Kim
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea ; Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Ho-Sung Choe
- Department of Animal Biotechnology, Chonbuk National University, Jeonju 561-756, Korea
| | - Hong-Sik Kong
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Hak-Kyo Lee
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
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Szabolcsi Z, Egyed B, Zenke P, Padar Z, Borsy A, Steger V, Pasztor E, Csanyi S, Buzas Z, Orosz L. Constructing STR multiplexes for individual identification of Hungarian red deer. J Forensic Sci 2014; 59:1090-9. [PMID: 24512288 DOI: 10.1111/1556-4029.12403] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 04/02/2013] [Accepted: 04/06/2013] [Indexed: 11/28/2022]
Abstract
Red deer is the most valuable game of the fauna in Hungary, and there is a strong need for genetic identification of individuals. For this purpose, 10 tetranucleotide STR markers were developed and amplified in two 5-plex systems. The study presented here includes the flanking region sequence analysis and the allele nomenclature of the 10 loci as well as the PCR optimization of the DeerPlex I and II. LD pairwise tests and cross-species similarity analyses showed the 10 loci to be independently inherited. Considerable levels of genetic differences between two subpopulations were recorded, and F(ST) was 0.034 using AMOVA. The average probability of identity (PI(ave)) was at the value of 2.6736 × 10(-15). This low value for PI(ave) nearly eliminates false identification. An illegal hunting case solved by DeerPlex is described herein. The calculated likelihood ratio (LR) illustrates the potential of the 10 red deer microsatellite markers for forensic investigations.
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Affiliation(s)
- Zoltan Szabolcsi
- Department of Genetics, Eötvös Loránd University, Pázmány Péter s. 1/c, 1117, Budapest, Hungary; Institute of Molecular Genetics, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100, Gödöllő, Hungary; Department of Genetics, Institute for Forensic Sciences, Mosonyi u. 9, 1087, Budapest, Hungary
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15
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Banks SC, Lindenmayer DB. Inbreeding avoidance, patch isolation and matrix permeability influence dispersal and settlement choices by male agile antechinus in a fragmented landscape. J Anim Ecol 2013; 83:515-24. [PMID: 23991826 DOI: 10.1111/1365-2656.12128] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 07/16/2013] [Indexed: 11/30/2022]
Abstract
Animal dispersal is highly non-random and has important implications for the dynamics of populations in fragmented habitat. We identified interpatch dispersal events from genetic tagging, parentage analyses and assignment tests and modelled the factors associated with apparent emigration and post-dispersal settlement choices by individual male agile antechinus (Antechinus agilis, a marsupial carnivore of south-east Australian forests). Emigration decisions were best modelled with on data patch isolation and inbreeding risk. The choice of dispersal destination by males was influenced by inbreeding risk, female abundance, patch size, patch quality and matrix permeability (variation in land cover). Males were less likely to settle in patches without highly unrelated females. Our findings highlight the importance of individual-level dispersal data for understanding how multiple processes drive non-randomness in dispersal in modified landscapes. Fragmented landscapes present novel environmental, demographic and genetic contexts in which dispersal decisions are made, so the major factors affecting dispersal decisions in fragmented habitat may differ considerably from unfragmented landscapes. We show that the spatial scale of genetic neighbourhoods can be large in fragmented habitat, such that dispersing males can potentially settle in the presence of genetically similar females after moving considerable distances, thereby necessitating both a choice to emigrate and a choice of where to settle to avoid inbreeding.
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Affiliation(s)
- Sam C Banks
- The Fenner School of Environment and Society, The Australian National University.,Australian Research Council Centre of Excellence for Environmental Decisions, National Environmental Research Program Environmental Decisions Hub, Australia
| | - David B Lindenmayer
- The Fenner School of Environment and Society, The Australian National University.,Australian Research Council Centre of Excellence for Environmental Decisions, National Environmental Research Program Environmental Decisions Hub, Australia
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16
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Suh S, Cho CY, Kim JH, Choi SB, Kim YS, Kim H, Seong HH, Lim HT, Cho JH, Ko YG. Analysis of Genetic Characteristics and Probability of Individual Discrimination in Korean Indigenous Chicken Brands by Microsatellite Marker. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2013. [DOI: 10.5187/jast.2013.55.3.185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Choi NR, Hoque MR, Seo DW, Sultana H, Park HB, Lim HT, Heo KN, Kang BS, Jo C, Lee JH. ISAG-recommended Microsatellite Marker Analysis Among Five Korean Native Chicken Lines. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2012. [DOI: 10.5187/jast.2012.54.6.401] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Andreassen R, Schregel J, Kopatz A, Tobiassen C, Knappskog PM, Hagen SB, Kleven O, Schneider M, Kojola I, Aspi J, Rykov A, Tirronen KF, Danilov PI, Eiken HG. A forensic DNA profiling system for Northern European brown bears (Ursus arctos). Forensic Sci Int Genet 2012; 6:798-809. [PMID: 22483764 DOI: 10.1016/j.fsigen.2012.03.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/10/2012] [Accepted: 03/11/2012] [Indexed: 11/29/2022]
Abstract
A set of 13 dinucleotide STR loci (G1A, G10B, G1D, G10L, MU05, MU09, MU10, MU15, MU23, MU26, MU50, MU51, MU59) were selected as candidate markers for a DNA forensic profiling system for Northern European brown bear (Ursus arctos). We present results from validation of the markers with respect to their sensitivity, species specificity and performance (precision, heterozygote balance and stutter ratios). All STRs were amplified with 0.6ng template input, and there were no false bear genotypes in the cross-species amplification tests. The validation experiments showed that stutter ratios and heterozygote balance was more pronounced than in the tetranucleotide loci used in human forensics. The elevated ratios of stutter and heterozygote balance at the loci validated indicate that these dinucleotide STRs are not well suited for interpretation of individual genotypes in mixtures. Based on the results from the experimental validations we discuss the challenges related to genotyping dinucleotide STRs in single source samples. Sequence studies of common alleles showed that, in general, the size variation of alleles corresponded with the variation in number of repeats. The samples characterized by sequence analysis may serve as standard DNA samples for inter laboratory calibration. A total of 479 individuals from eight Northern European brown bear populations were analyzed in the 13 candidate STRs. Locus MU26 was excluded as a putative forensic marker after revealing large deviations from expected heterozygosity likely to be caused by null-alleles at this locus. The remaining STRs did not reveal significant deviations from Hardy-Weinberg equilibrium expectations except for loci G10B and MU10 that showed significant deviations in one population each, respectively. There were 9 pairwise locus comparisons that showed significant deviation from linkage equilibrium in one or two out of the eight populations. Substantial genetic differentiation was detected in some of the pairwise population comparisons and the average estimate of population substructure (F(ST)) was 0.09. The average estimate of inbreeding (F(IS)) was 0.005. Accounting for population substructure and inbreeding the total average probability of identity in each of the eight populations was lower than 1.1×10(-9) and the total average probability of sibling identity was lower than 1.3×10(-4). The magnitude of these measurements indicates that if applying these twelve STRs in a DNA profiling system this would provide individual specific evidence.
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Affiliation(s)
- R Andreassen
- Faculty of Health Sciences, Oslo and Akershus University College, Oslo, Norway.
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Unger SD, Burgmeier NG, Williams RN. Genetic markers reveal high PIT tag retention rates in giant salamanders (Cryptobranchus alleganiensis). AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/156853812x641712] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Estimation of population size using mark-recapture (MRR) methods are based on the fundamental assumption that individuals retain their marks throughout the course of study. Passive Integrated Transponder (PIT) tags are useful as a cost effective, reliable marking method in many amphibian and reptile species. Few studies however, use secondary methods to evaluate tag retention rates. Failure to do so can lead to biased population estimates, erroneous conclusions, and thus poor management decisions. Surprisingly, estimates of PIT tag retention are currently lacking for the majority of amphibian species, many of which are experiencing population declines. Herein, we use genetic tagging to assess the retention of PIT tags of the eastern hellbender (Cryptobranchus alleganiensis alleganiensis). We captured and tagged 78 individuals across 35 sites. Recapture rate was 24% and genetic tagging revealed 100% tag retention across all recaptured individuals.
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Affiliation(s)
- Shem D. Unger
- Department of Forestry & Natural Resources, Purdue University, 195 Marstellar Street, West Lafayette, Indiana, 47907, USA
| | - Nicholas G. Burgmeier
- Department of Forestry & Natural Resources, Purdue University, 195 Marstellar Street, West Lafayette, Indiana, 47907, USA
| | - Rod N. Williams
- Department of Forestry & Natural Resources, Purdue University, 195 Marstellar Street, West Lafayette, Indiana, 47907, USA
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20
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Luikart G, Amish SJ, Winnie J, Beja-Pereira A, Godinho R, Allendorf FW, Harris RB. High connectivity among argali sheep from Afghanistan and adjacent countries: Inferences from neutral and candidate gene microsatellites. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0195-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Lim HT, Kim BW, Yoon D, Lee SH, Yoo CK, Lee JH, Jeon JT. An allelic ladder for eleven short tandem repeat loci for use in the cattle identity test. Anim Genet 2011; 42:226-7. [PMID: 24725233 DOI: 10.1111/j.1365-2052.2010.02142.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- H-T Lim
- Division of Applied Life Science (BK21 Program), Graduate School of Gyeongsang National University, Jinju 660-701, Korea.Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Suwon 441-706, Korea.Division of Animal Science and Resources, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
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22
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Lorenzini R, Cabras P, Fanelli R, Carboni GL. Wildlife molecular forensics: identification of the Sardinian mouflon using STR profiling and the Bayesian assignment test. Forensic Sci Int Genet 2011; 5:345-9. [PMID: 21371958 DOI: 10.1016/j.fsigen.2011.01.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/24/2011] [Accepted: 01/31/2011] [Indexed: 11/20/2022]
Abstract
A forensic short tandem repeat (STR) typing test using a population database was developed to investigate an instance of poaching on the protected Sardinian mouflon. The case study involves a suspected poacher found in possession of a carcass, which he claimed was that of a sheep from his flock and had died accidentally. His claim was refuted by the molecular forensic analyses as DNA typing and the Bayesian assignment test revealed the carcass to be mouflon-derived; the genetic profile of the carcass matched also that of additional trace evidence collected by forestry officers at the scene of the kill. The matching evidence led to the poacher being charged with the illegal harvest of protected wildlife. Molecular techniques, in combination with a reference population database, and the appropriate statistical evaluation of genetic information, are fundamental to wildlife forensics. This approach allows DNA testing to be accepted in court as submissible evidence in the fight against poaching and other crimes involving wildlife.
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Affiliation(s)
- Rita Lorenzini
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana, Via Tancia 21, 02100 Rieti, Italy.
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Lim HT, Kim BW, Cho IC, Yoo CK, Park MS, Park HB, Lee JB, Lee JG, Jeon JT. An Empirical Study on Verifying the Estimated Discrimination and Parentage Test Powers of the 13 Traceability Microsatellite Markers for Commercial Pigs Produced by a Three-way Cross. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2011. [DOI: 10.5187/jast.2011.53.1.29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Bridging the gaps between non-invasive genetic sampling and population parameter estimation. EUR J WILDLIFE RES 2010. [DOI: 10.1007/s10344-010-0477-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chen JW, Uboh CE, Soma LR, Li X, Guan F, You Y, Liu Y. Identification of racehorse and sample contamination by novel 24-plex STR system. Forensic Sci Int Genet 2010; 4:158-67. [DOI: 10.1016/j.fsigen.2009.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 08/04/2009] [Accepted: 08/04/2009] [Indexed: 10/20/2022]
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26
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Unger SD, Fike JA, Sutton T, Rhodes OE, Williams RN. Isolation and development of 12 polymorphic tetranucleotide microsatellite markers for the eastern hellbender (Cryptobranchus alleganiensis alleganiensis). CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-009-9170-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Eiken H, Andreassen R, Kopatz A, Bjervamoen S, Wartiainen I, Tobiassen C, Knappskog P, Aspholm P, Smith M, Aspi J. Population data for 12 STR loci in Northern European brown bear (Ursus arctos) and application of DNA profiles for forensic casework. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Lim HT, Seo BY, Jung EJ, Yoo CK, Yoon DH, Jeon JT. A Comparison of Discriminating Powers Between 14 Microsatellite markers and 60 SNP Markers Applicable to the Cattle Identification Test. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2009. [DOI: 10.5187/jast.2009.51.5.353] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Lim HT, Seo BY, Jung EJ, Yoo CK, Zhong T, Cho IC, Yoon DH, Lee JG, Jeon JT. Establishment of a Microsatellite Marker Set for Individual, Pork Brand and Product Origin Identification in Pigs. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2009. [DOI: 10.5187/jast.2009.51.3.201] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Herreman JK, Blundell GM, McDonald DB, Ben-David M. Asymmetrical male-mediated gene flow between harbor seal (Phoca vitulina) populations in Alaska. CAN J ZOOL 2009. [DOI: 10.1139/z09-033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Harbor seals ( Phoca vitulina richardii (Gray, 1864)) in Alaska are currently treated as three distinct management stocks. Previous genetic analyses using mitochondrial DNA suggested that these stocks are differentiated genetically. We studied populations in Glacier Bay (GB; Southeast Alaska Stock), where harbor seals are declining, and Prince William Sound (PWS; Gulf of Alaska Stock), where the population has recently stabilized. Using six pairs of hypervariable microsatellite primers, we determined that these populations are a single panmictic unit with estimated migration rates of 22 animals/generation (PWS to GB) and 63 animals/generation (GB to PWS). The asymmetrical gene flow between GB and PWS is likely driven in part by a recent increase in competitors and predators of seals in GB. In contrast with males, emigration of females from PWS to GB (8.3 seals/generation) is higher than emigration of females from GB to PWS (3.3 seals/generation), likely because females use glacial ice as pupping habitat. Despite the high gene flow, the number of migrants per year (0.02% of the Gulf of Alaska population) is likely too low to influence the demographics of harbor seals in PWS, and the two populations may best be managed as separate stocks.
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Affiliation(s)
- J. K. Herreman
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
- Alaska Department of Fish and Game, Division of Wildlife Conservation, P.O. Box 110024, Juneau, AK 99811-0024, USA
| | - G. M. Blundell
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
- Alaska Department of Fish and Game, Division of Wildlife Conservation, P.O. Box 110024, Juneau, AK 99811-0024, USA
| | - D. B. McDonald
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
- Alaska Department of Fish and Game, Division of Wildlife Conservation, P.O. Box 110024, Juneau, AK 99811-0024, USA
| | - M. Ben-David
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
- Alaska Department of Fish and Game, Division of Wildlife Conservation, P.O. Box 110024, Juneau, AK 99811-0024, USA
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GUZINSKI JARO, BULL CMICHAEL, DONNELLAN STEPHENC, GARDNER MICHAELG. Molecular genetic data provide support for a model of transmission dynamics in an Australian reptile tick,Bothriocroton hydrosauri. Mol Ecol 2009; 18:227-34. [DOI: 10.1111/j.1365-294x.2008.04023.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Williams RN, Bos DH, Gopurenko D, Dewoody JA. Amphibian malformations and inbreeding. Biol Lett 2008; 4:549-52. [PMID: 18593670 PMCID: PMC2610075 DOI: 10.1098/rsbl.2008.0233] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 06/03/2008] [Accepted: 06/10/2008] [Indexed: 11/12/2022] Open
Abstract
Inbreeding may lead to morphological malformations in a wide variety of taxa. We used genetic markers to evaluate whether malformed urodeles were more inbred and/or had less genetic diversity than normal salamanders. We captured 687 adult and 1,259 larval tiger salamanders (Ambystoma tigrinum tigrinum), assessed each individual for gross malformations, and surveyed genetic variation among malformed and normal individuals using both cytoplasmic and nuclear markers. The most common malformations in both adults and larvae were brachydactyly, ectrodactyly and polyphalangy. The overall frequency of adults with malformations was 0.078 compared to 0.081 in larval samples. Genetic diversity was high in both normal and malformed salamanders, and there were no significant difference in measures of inbreeding (f and F), allele frequencies, mean individual heterozygosity or mean internal relatedness. Environmental contaminants or other extrinsic factors may lead to genome alternations that ultimately cause malformations, but our data indicate that inbreeding is not a causal mechanism.
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Affiliation(s)
- Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA.
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Dawnay N, Ogden R, Wetton JH, Thorpe RS, McEwing R. Genetic data from 28 STR loci for forensic individual identification and parentage analyses in 6 bird of prey species. Forensic Sci Int Genet 2008; 3:e63-9. [PMID: 19215871 DOI: 10.1016/j.fsigen.2008.07.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Revised: 06/06/2008] [Accepted: 07/01/2008] [Indexed: 11/28/2022]
Abstract
Twenty-eight STR loci were screened in wild populations of six bird of prey species providing allele frequencies and population genetic parameters necessary for the application of STRs in wildlife forensic genetic casework. Individual STR loci were validated according to forensic recommendations in specimens of golden eagle (Aquila chrysaetos), goshawk (Accipiter gentilis), merlin (Falco columbarius), peregrine falcon (Falco peregrinus), gyr falcon (Falco rusticolus) and saker falcon (Falco cherrug). Deviations from Hardy-Weinberg expectations and linkage disequilibrium between locus pairs were examined. The average probability of identity (PI(ave)) and power of exclusion (PE) suggest the profiling systems of golden eagle, goshawk, merlin and peregrine falcons are capable of providing robust and highly discriminatory forensic evidence for legal proceedings. Due to low sample numbers the allele frequency data for gyr and saker falcons is not currently capable of providing an effective probability of identity. Further work should focus on increasing the size of these data sets.
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Affiliation(s)
- Nick Dawnay
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, United Kingdom.
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Breck SW, Williams CL, Beckmann JP, Matthews SM, Lackey CW, Beecham JJ. Using Genetic Relatedness to Investigate the Development of Conflict Behavior in Black Bears. J Mammal 2008. [DOI: 10.1644/07-mamm-a-028r2.1] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Dodds KG, Amer PR, Auvray B. Using genetic markers in unpedigreed populations to detect a heritable trait. J Zhejiang Univ Sci B 2007; 8:782-6. [PMID: 17973338 DOI: 10.1631/jzus.2007.b0782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Before a breeder invests selection pressure on a trait of interest, it needs to be established whether that trait is actually heritable. Some traits may not have been measured widely in pedigreed populations, for example, a disease or deformity may become more prevalent than previously, but is still relatively rare. One approach to detect inheritance would be to screen a commercial population to obtain a sample of "affecteds" (the test group) and to also obtain a random control group. These individuals are then genotyped with a set of genetic markers and the relationships between individuals within each group estimated. If the relatedness is higher in the test group than in the control group, this provides initial evidence for the trait being heritable. A power simulation shows that this approach is feasible with moderate resources.
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Affiliation(s)
- Ken G Dodds
- Applied Biotechnologies Group, AgResearch Limited, Invermay Research Centre, Private Bag 50034, Mosgiel, New Zealand.
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Dawnay N, Ogden R, Thorpe RS, Pope LC, Dawson DA, McEwing R. A forensic STR profiling system for the Eurasian badger: a framework for developing profiling systems for wildlife species. Forensic Sci Int Genet 2007; 2:47-53. [PMID: 19083789 DOI: 10.1016/j.fsigen.2007.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 07/19/2007] [Accepted: 08/13/2007] [Indexed: 10/22/2022]
Abstract
Developing short tandem repeat (STR) profiling systems for forensic identification is complicated in animal species. Obtaining a representative number of individuals from populations, limited access to family groups and a lack of developed STR markers can make adhering to human forensic guidelines difficult. Furthermore, a lack of animal specific guidelines may explain why many wildlife forensic STR profiling systems developed to date have not appropriately addressed areas such as marker validation or the publication and analysis of population data necessary for the application of these tools to forensic science. Here we present a methodology used to develop an STR profiling system for a legally protected wildlife species, the Eurasian badger Meles meles. Ten previously isolated STR loci were selected based on their level of polymorphism, adherence to Hardy-Weinberg expectations and their fragment size. Each locus was individually validated with respect to its reproducibility, inheritance, species specificity, DNA template concentration and thermocycling parameters. The effects of chemical, substrate and environmental exposure were also investigated. All ten STR loci provided reliable and reproducible results, and optimal amplification conditions were defined. Allele frequencies from 20 representative populations in England and Wales are presented and used to calculate the level of population substructure (theta) and inbreeding (f). Accounting for these estimates, the average probability of identity (PI(ave)) was 2.18 x 10(-7). This case study can act as a framework for others attempting to develop wildlife forensic profiling systems.
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Affiliation(s)
- Nick Dawnay
- School of Biological Sciences, University of Wales, Bangor LL57 2UW, United Kingdom.
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Abstract
Humpback whales seasonally migrate long distances between tropical and polar regions. However, inter-oceanic exchange is rare and difficult to document. Using skin biopsy samples collected in the Indian Ocean and in the South Atlantic Ocean, and a genetic capture-recapture approach based on microsatellite genotyping, we were able to reveal the first direct genetic evidence of the inter-oceanic migration of a male humpback whale. This exceptional migration to wintering grounds of two different ocean basins questions traditional notions of fidelity to an ocean basin, and demonstrates how the behaviour of highly mobile species may be elucidated from combining genetics with long-term field studies. Our finding has implications for management of humpback whale populations, as well as for hypotheses concerning cultural transmission of behaviour.
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Affiliation(s)
- Cristina Pomilla
- Department of Biology, New York University, New York, NY 10003, USA.
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Craft KJ, Owens JD, Ashley MV. Application of plant DNA markers in forensic botany: Genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites. Forensic Sci Int 2007; 165:64-70. [PMID: 16632287 DOI: 10.1016/j.forsciint.2006.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 03/03/2006] [Accepted: 03/03/2006] [Indexed: 10/24/2022]
Abstract
As highly polymorphic DNA markers become increasingly available for a wide range of plant and animal species, there will be increasing opportunities for applications to forensic investigations. To date, however, relatively few studies have reported using DNA profiles of non-human species to place suspects at or near crime scenes. Here we describe an investigation of a double homicide of a female and her near-term fetus. Leaf material taken from a suspect's vehicle was identified to be that of sand live oak, Quercus geminata, the same tree species that occurred near a shallow grave where the victims were found. Quercus-specific DNA microsatellites were used to genotype both dried and fresh material from trees located near the burial site and from the material taken from the suspect's car. Samples from the local population of Q. geminata were also collected and genotyped in order to demonstrate that genetic variation at four microsatellite loci was sufficient to assign leaves to an individual tree with high statistical certainty. The cumulative average probability of identity for these four loci was 2.06x10(-6). DNA was successfully obtained from the dried leaf material although PCR amplification was more difficult than amplification of DNA from fresh leaves. The DNA profiles of the dried leaves from the suspect's car did not match those of the trees near the crime scene. Although this investigation did not provide evidence that could be used against the suspect, it does demonstrate the potential for plant microsatellite markers providing physical evidence that links plant materials to live plants at or near crime scenes.
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Affiliation(s)
- Kathleen J Craft
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
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Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: a pilot study. BMC Genet 2006; 7:48. [PMID: 17044939 PMCID: PMC1636336 DOI: 10.1186/1471-2156-7-48] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Accepted: 10/17/2006] [Indexed: 11/30/2022] Open
Abstract
Background Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation. Results In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India. Conclusion Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use.
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Pomilla C, Rosenbaum HC. Estimates of relatedness in groups of humpback whales (Megaptera novaeangliae) on two wintering grounds of the Southern Hemisphere. Mol Ecol 2006; 15:2541-55. [PMID: 16842425 DOI: 10.1111/j.1365-294x.2006.02943.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Group formation in humpback whales has been described in relation to different components of the migratory cycle, yet it is debated whether such groups represent real social bonding or ephemeral aggregations. Cooperative behaviours are exhibited during feeding activities, and it has been suggested that males may cooperate during competition for mates. Since most cooperative behaviours are expected to originate among kin, genetic relatedness represents a critical variable in the understanding of any social phenomenon, especially when cooperation cannot be confirmed unequivocally. Using an approach combining multi-locus microsatellite genotyping and several genetic relatedness estimators, we analyzed whale associations for two different wintering grounds in the Southern Hemisphere. The analyses included 648 whales sampled from 292 groups off the coast of Gabon and Northeast Madagascar, and screened for eleven microsatellite loci. Through simulations, we assessed the performance of three pairwise relatedness estimators. The individuals were molecularly sexed and their associations were investigated in the context of sex and group type. No significant association among relatives was found with the exception of mother-offspring pairs, supporting previous indications of extended maternal care. The analysis from the Gabon population also suggests that related males may avoid each other during competitive activities. Our results demonstrate that if cooperative behaviours occur on wintering grounds they are not favoured by kin selection.
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Affiliation(s)
- Cristina Pomilla
- New York University, Department of Biology, 100 Washington Square East, New York, NY 10003, USA.
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Peakall R, Ebert D, Cunningham R, Lindenmayer D. Mark-recapture by genetic tagging reveals restricted movements by bush rats (Rattus fuscipes) in a fragmented landscape. J Zool (1987) 2006. [DOI: 10.1111/j.1469-7998.2005.00011.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Jeon JT, Lee JH, Kim KS, Park CK, Oh SJ. Application of DNA markers in animal industries. ACTA ACUST UNITED AC 2006. [DOI: 10.1071/ea05191] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The current animal industry is both technology-intensive and globalised. Efficient molecular tools, such as DNA markers, are in demand to strengthen competitive power by maximising the improvement of livestock and obtaining the trust of customers by the verification of product origins. This review describes the present techniques applying DNA markers in the animal industry, with a focus on beef cattle and pigs. Preliminary data from an individual traceability assay for Hanwoo (Korean cattle) using 20 microsatellite markers is described. The potential uses of the assay are demonstrated for several key markers of different traits: for the porcine stress syndrome gene using the RYR mutation; for acid meat using the PRKAG3 mutation; for intramuscular fat using the FABP3 mutation and for fixing the Dominant white allele using KIT duplication. In addition, a possible strategy is suggested to discriminate between pig breeds using mutations of KIT, MC1R, ND2 and the 11-bp insertion in the D-loop of mitochondrial DNA. The industrial application of DNA techniques is limited at present, however, it is expected that DNA markers originating from trait genes, especially those of low-heritability and difficult-to-measure traits, may contribute to maximising the improvement of the major economic traits of animals in the future.
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PUECHMAILLE SEBASTIEN, MATHY GREGORY, PETIT ERIC. Characterization of 14 polymorphic microsatellite loci for the lesser horseshoe bat, Rhinolophus hipposideros (Rhinolophidae, Chiroptera). ACTA ACUST UNITED AC 2005. [DOI: 10.1111/j.1471-8286.2005.01123.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Analysis and Selection of Microsatellites Markers for Individual Traceability System in Hanwoo. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2005. [DOI: 10.5187/jast.2005.47.4.491] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Iyengar A, Babu VN, Hedges S, Venkataraman AB, Maclean N, Morin PA. Phylogeography, genetic structure, and diversity in the dhole (Cuon alpinus). Mol Ecol 2005; 14:2281-97. [PMID: 15969714 DOI: 10.1111/j.1365-294x.2005.02582.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Asiatic wild dog or dhole was once very widely distributed across Asia but now has a very fragmented range. In this first genetic study of this little-known species, we obtained information on genetic diversity, phylogeography, and social structure using both mitochondrial control region sequencing and microsatellite genotyping of noninvasive faecal samples from wild populations, as well as from museum and captive samples. A pattern largely consistent with isolation by distance across the Asian mainland was observed, with no clear subspecies distinctions. However, two major phylogeographical groupings were found across the mainland, one extending from South, Central, and North India (south of the Ganges) into Myanmar, and the other extending from India north of the Ganges into northeastern India, Myanmar, Thailand and the Malaysian Peninsula. We propose a scenario involving glaciation events that could explain this pattern. The origin of the dhole populations in Sumatra and Java is enigmatic and requires further study. Very low levels of genetic diversity were observed among wild dholes from Baluran National Park in Java, Indonesia, but in contrast, high levels were observed in Mudumalai Wildlife Sanctuary in South India.
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Affiliation(s)
- A Iyengar
- Laboratory for Conservation Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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WILBERG MICHAELJ, DREHER BRIANP. genecap: a program for analysis of multilocus genotype data for non-invasive sampling and capture-recapture population estimation. ACTA ACUST UNITED AC 2004. [DOI: 10.1111/j.1471-8286.2004.00797.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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MEIRMANS PATRICKG, VAN TIENDEREN PETERH. genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. ACTA ACUST UNITED AC 2004. [DOI: 10.1111/j.1471-8286.2004.00770.x] [Citation(s) in RCA: 1509] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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