Journal of Animal Science and Technology

Korean Society of Animal Sciences and Technology (한국축산학회)
권호 표지
DOI QR코드

DOI QR Code

Analysis of Genetic Characteristics and Probability of Individual Discrimination in Korean Indigenous Chicken Brands by Microsatellite Marker

MS 마커를 이용한 토종닭 브랜드의 유전적 특성 및 개체 식별력 분석

  • Suh, Sangwon (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Cho, Chang-Yeon (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Kim, Jae-Hwan (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Choi, Seong-Bok (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Kim, Young-Sin (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Kim, Hyun (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Seong, Hwan-Hoo (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Lim, Hyun-Tae (Department of Animal Science, Collage of Agriculture and Life Sciences, Gyeongsang National University) ;
  • Cho, Jae-Hyeon (Institute of Life Science, College of Veterinary Medicine, Gyeongsang National University) ;
  • Ko, Yeoung-Gyu (Animal Genetic Resources Station, National Institute of Animal Science, RDA)
  • 서상원 (농촌진흥청 국립축산과학원 가축유전자원시험장) ;
  • 조창연 (농촌진흥청 국립축산과학원 가축유전자원시험장) ;
  • 김재환 (농촌진흥청 국립축산과학원 가축유전자원시험장) ;
  • 최성복 (농촌진흥청 국립축산과학원 가축유전자원시험장) ;
  • 김영신 (농촌진흥청 국립축산과학원 가축유전자원시험장) ;
  • 김현 (농촌진흥청 국립축산과학원 가축유전자원시험장) ;
  • 성환후 (농촌진흥청 국립축산과학원 가축유전자원시험장) ;
  • 임현태 (경상대학교 농업생명과학대학 축산학과) ;
  • 조재현 (경상대학교 수의과대학 수의학과) ;
  • 고응규 (농촌진흥청 국립축산과학원 가축유전자원시험장)
  • Received : 2013.05.15
  • Accepted : 2013.06.28
  • Published : 2013.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

Microsatellite markers have been a useful genetic tool in determining diversity, relationships and individual discrimination studies of livestock. The level of genetic diversity, relationships among two Korean indigenous chicken brand populations (Woorimatdag: WR, Hanhyup3: HH) as well as two pure populations (White Leghorn: WL, Rhode Island Red: RIR) were analyzed, based on 26 MS markers. A total of 191 distinct alleles were observed across the four chicken populations, and 47 (24.6%) of these alleles were unique to only one population. The mean $H_{Exp}$ and PIC were estimated as 0.667 and 0.630. Nei's $D_A$ genetic distance and factorial correspondence analysis (FCA) showed that the four populations represented four distinct groups. However, the genetic distance between each Korean indigenous chicken brand (WR, HH) and the pure population (WL, RIR) were threefold that among the WR and HH. For the STRUCTURE analyses, the most appropriate number of clusters for modeling the data was determined to be three. The expected probabilities of identity among genotypes of random individuals (PI) were calculated as $1.17{\times}10^{-49}$ (All 26 markers) and $1.14{\times}10^{-15}$, $7.33{\times}10^{-20}$ (9, 12 with the highest PI value, respectively). The results indicated that the brand chicken breed traceability system employing the own highest PI value 9 to 12 markers, and might be applicable to individual identification of Korean indigenous chicken brand.

MS 마커는 가축의 유전적 다양성, 유연관계 및 품종식별의 연구에 있어서 매우 유용하다. 본 연구는 26개의 MS 마커를 이용하여 토종닭 브랜드 2집단(우리맛닭, 한협3호)과 토착종 순계 2집단(화이트 레그혼, 로드 아일랜드 레드)을 대상으로 집단내 및 집단간의 유전적 다양성, 계통유전학적 관계, 유전적 균일성 등을 검증하여 고유 유전자원으로서의 가치 구명 및 개체식별력이 높은 마커를 선별하여 토종닭 브랜드 계육의 생산이력시스템에 활용 가능한 기초자료를 제시하고자 실시 하였다. 대립 유전자형 분석결과 총 191개 중 47개(24.6%)가 집단 특이 대립 유전자였으며, 다형성지수의 평균은 $H_{Exp}$=0.667, PIC=0.630으로 산출 되었다. 공시된 320수 개체에 대한 요인대응분석(FCA) 결과 4개의 군집을 형성하였지만 2개 토종닭 브랜드 집단은 타 집단에 비해 매우 가까운 거리에 위치하고 있었으며, 집단간의 $D_A$ 유전거리 결과 또한 이와 동일했다. 각 집단에 대한 유전적 균일도는 모든 집단에서 94% 이상으로 높았다. 이상의 결과는 2개 토종닭 브랜드 집단은 유전적으로 유사하지만 토종닭 순계 집단과는 유전적인 차이가 크며, 순계 2집단 또한 유전적으로 확연히 분리됨을 증명 할 수 있다. 26개 MS마커 사용시 동일개체 출현확률(PI)은 $1.17{\times}10^{-49}$였다. 2011년 기준으로 닭 사육수수 149,511,309수를 고려해 PI 값이 높은 마커 9~12개 정도를 선별 및 분석에 이용 한다면 동일개체 출현확률(PI)이 $1.14{\times}10^{-15}$에서 $7.33{\times}10^{-20}$이므로 개체식별 및 친자 감별이 가능할 것으로 사료된다. 향후 경제적 효율성을 고려하여 MS 마커 및 mtDNA의 SNP를 기반으로 multiplexing PCR 시스템을 확립을 위한 연구가 이행된다면 토종닭 브랜드육의 생산이력시스템에 적용이 가능할 것으로 판단된다.

Keywords

References

  1. Ayres, K. L. and Overall, A. D. J. 2004. API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives. Mol. Ecol. Notes 4(2):315-318. https://doi.org/10.1111/j.1471-8286.2004.00616.x
  2. Bao, W. B. Shu, J. T., Musa, H. H. and Chen, G. H. 2007. Analysis of Pairwise Genetic Distance and its Relation with Geographical Distance of 15 Chinese Chicken Breeds. Int. J. Trop. Med. 2(3):107-112.
  3. Belkhir, K., Borsa, P., Chikhi, L., Raufaste, N. and Bonhomme, F. (2004). GENETIX 4.05, Logiciel Sous Windows TM Pour la Genetique des Populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000, Universite de Montpellier II, Montpellier
  4. Botstein, D., White, R. L., Skolnik, M. and Davis, R. W. 1980. Construction of a Genetic Linkage Map in Man Using Restriction Fragment Length Polymorphisms Am. J. Hum. Genet. 32(3): 314-331.
  5. Chen, G., Bao, W., Shu, J., Ji, C., Wang, C., Eding, H., Muchadeyi, F. and Weigend, S. 2008. Assessment of Population Structure and Genetic Diversity of 15 Chinese Indigenous Chicken Breeds Using Microsatellite Markers. Asian-Aust. J. Anim. Sci. 21(3): 331-339. https://doi.org/10.5713/ajas.2008.70125
  6. Choi, N. R., Hoque, M. R., Seo, D. W., Sultana, H., Park, H. B., Lim, H. T., Heo, K. Y., Kang, B. S., Cho, C. and Lee, J. H. 2012. ISAG-recommended Microsatellite Marker Analysis Among Five Korean Native Chicken Lines. J. Anim. Sci. & Technol. 54(6):401-409. https://doi.org/10.5187/JAST.2012.54.6.401
  7. Cuc, N. T. K., Muchadeyi, F. C., Baulain, U., Eding, H., Weigend, S. and Wollny, C. B. A. 2006. An assessment of genetic diversity of Vietnamese H'mong chickens. Int. J. Poult. Sci. 5(10):912-920. https://doi.org/10.3923/ijps.2006.912.920
  8. Cuc, N. T. K., Simianer, H., Groeneveld, L. F. and Weigend, S. 2011. Multiple Maternal Lineages of Vietnamese Local Chickens Inferred by Mitochondrial DNA D-loop Sequences. Asian-Aust. J. Anim. Sci. 24(2):155-161. https://doi.org/10.5713/ajas.2011.10155
  9. Dancause, K. N., Vilar, M. G., Steffy, R. and Lum, J. K. 2011. Characterizing Genetic Diversity of Contemporary Pacific Chickens Using Mitochondrial DNA Analyses. PLoS ONE. 6(2):e16843. https://doi.org/10.1371/journal.pone.0016843
  10. Ding, F. X., Zhang, G. X., Wang, J. Y., Li, Y., Zhang L, J., Wei, Y., Wang, H. H., Zhang, L. and Hou, Q. R. 2010. Genetic Diversity of a Chicnease Native Chicken Breed, Bian Chicken, Based on Twenty-nine Microsatellite Markers. Asian-Aust. J. Anim. Sci. 23(2):154-161.
  11. Earl, D. A. and Holdt, B. M. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4:359-361. https://doi.org/10.1007/s12686-011-9548-7
  12. Evanno, G., Regnaut, S. and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  13. FAO. 2011. Molecular genetic characterization of animal genetic resources. FAO Animal Production and Health Guidelines. Rome. No. 9:84-85.
  14. Glaubitz, J. C. 2004. CONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol. Ecol. Notes 4(2):309-310. https://doi.org/10.1111/j.1471-8286.2004.00597.x
  15. Goraga, Z., Weigend, S. and Brockmann, G. 2012. Genetic diversity and population structure of five Ethiopian chicken ecotypes. Anim. Genet. 43(4):454-457. https://doi.org/10.1111/j.1365-2052.2011.02270.x
  16. Harumi, T., Sano, A., Minematsu, T. and Naito, M., 2011. Allele-specific typing and sequencing of the mitochondrial D-loop region in four layer breeds. Anim. Sci. J. 82:223-226. https://doi.org/10.1111/j.1740-0929.2010.00831.x
  17. Hoque, M. R., Lee, S. H., Jung, K. C., Kang, B. S., Park, M. N., Lim, H. K., Choi, K. D. and Lee, J. H. 2011. Discrimination of Korean Native Chicken Populations Using SNPs from mtDNA Polymorphisms. Asian-Aust. J. Anim. Sci. 24(12):1637-1643. https://doi.org/10.5713/ajas.2011.11144
  18. Kaya, M. and Yildiz, M. A. 2008. Genetic Diversity Among Turkish Native Chickens, Denizli and Gerze, Estimated by Microsatellite Markers. Biochem. Genet. 46:480-491. https://doi.org/10.1007/s10528-008-9164-8
  19. Lim, H. T., Seo, B. Y., Jung, E. J., Yoo, C. K., Yoon, D. H. and Jeon, J. T. 2009a. A Comparison of Discriminating Powers Between 14 Microsatellite markers and 60 SNP Markers Applicable to the Cattle Identification Test. J. Anim. Sci. & Technol. 51(5):353-360. https://doi.org/10.5187/JAST.2009.51.5.353
  20. Lim, H. T., Seo, B. Y., Jung, E. J., Yoo, C. K., Zhong, Tao., Cho, I. C., Yoon, D. H., Lee, J. G. and Jeon, J. T. 2009b. Estabilishment of a Microsatellite Marker Set for Individual, Pork Brand and Product Origin Identification in Pigs. J. Anim. Sci. & Technol. 51(3):201-206. https://doi.org/10.5187/JAST.2009.51.3.201
  21. Lim, H. T., Kim, B. W., Cho, I. C., Yoo, C. K., Park, M. S., Park, H. B., Lee, J. B., Lee, J. G. and Jeon, J. T. 2011. 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-was Cross. J. Anim. Sci. & Technol. 53(1):29-34. https://doi.org/10.5187/JAST.2011.53.1.29
  22. Mwacharo, J. M., Bjornstad, G., Mobegi, V., Nomura, K., Hanada, H., Amano, T., Jianlin, H. and Hanotte, O. 2011. Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. Mol. Phylogenet. Evol. 58(2):374-382. https://doi.org/10.1016/j.ympev.2010.11.027
  23. MIAFF. 2012. Primary statistics of food, Agriculture, Forestry and Fisheries, Korea
  24. Muchadeyi, F. C., Eding, H., Wollny, C. B., Groeneveld, E., Makuza, S. M., Shamseldin, R., Simianer, H. and Weigend, S. 2007. Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. Anim. Genet. 38(4):332-339. https://doi.org/10.1111/j.1365-2052.2007.01606.x
  25. Nei, M., Taima, F. and Tateno, Y. 1983. Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 19:153-170. https://doi.org/10.1007/BF02300753
  26. NIAS. 2008. Korean Native Chicken Certification Standard Institution Research.
  27. NIAS. 2012. Livestock Research Leading Result.
  28. Osman, S. A. M., Sekino, M., Nishihata, A., Kobayashi, Y., Takenaka, W., Kinoshita, K., Kuwayama, T., Nishibori, M., Yamamoto, Y. and Tsudzuki, M. 2006. The Genetic Variability and Relationships of Japanese and Foreign Chickens Assessed by Microsatellite DNA Profiling. Asian-Aust. J. Anim. Sci. 19(10):1369-1378. https://doi.org/10.5713/ajas.2006.1369
  29. Park, S. D. E. 2001. The Excel microsatellite toolkit (version 3.1). Animal Genomics Laboratory, University College Dublin, Ireland. http://animalgenomics.ucd.ie/sdepark/ms-toolkit/.
  30. Peakall, R. and Smouse, P. E. 2006. GenAlEx 6: genetic analysis in excel population genetic software for teaching and research. Mol. Ecol. Notes 6(1):288-295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
  31. Pritchard, J. K., Stephens, M. and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155(2):945-959.
  32. Seo, D. W., Hoque,M. R., Choi, N. R., Sultana, H., Park, H. B., Heo, K. N., Kang, B. S., Jo, C. and Lee, J. H. 2013. Discrimination of Korean Native Chicken Lines Using Fifteen Selected Microsatellite Markers. Asian-Aust. J. Anim. Sci. 26(3):316-322. https://doi.org/10.5713/ajas.2012.12469
  33. Sultana, H., Hoque, M. R.,, Seo, D. W., Kang, B. S, Heo, K. N., Cho, C. and Lee, J. H. 2012. Mitochondrial D-Loop Variations for discrimination of Commercial Korean Native Chicken Population. Korean J. Poult. Sci. 39(4):311-315. https://doi.org/10.5536/KJPS.2012.39.4.311
  34. Tadano, R., Sekino, M., Nishibori, M. and Tsudzuki, M. 2007. Microsatellite Marker Analysis for the Genetic Relationships Among Japanese Long-Tailed Chicken Breeds. Poult. Sci. 86(3):460-469. https://doi.org/10.1093/ps/86.3.460
  35. Tautz, D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17:6463-6471. https://doi.org/10.1093/nar/17.16.6463
  36. Wilkinson, S., Wiener, P., Teverson, D., Haley, C. S. and Hocking, P. M. 2012. Characterization of the genetic diversity, structure and admixture of British chicken breeds. Anim. Genet. 43(5):552-563.
  37. Zanetti, E., Dalvit, C., Marchi, Md., Zotto, R. D. and Cassandro, M. 2007. Genetic characterisation of Italian chicken breeds using a panel of twenty microsatellite markers. Poljoprivreda 13:197-200.

Cited by

  1. Genome-wide Copy Number Variation in a Korean Native Chicken Breed vol.41, pp.4, 2014, https://doi.org/10.5536/KJPS.2014.41.4.305
  2. Studies on Genetic Diversity and Phylogenetic Relationships of Korean Native Chicken using the Microsatellite Marker vol.42, pp.1, 2015, https://doi.org/10.5536/KJPS.2014.42.1.15
  3. Discrimination of the commercial Korean native chicken population using microsatellite markers vol.57, pp.1, 2015, https://doi.org/10.1186/s40781-015-0044-6
  4. DNA Markers for the Genetic Diversity in Korean Native Chicken Breeds: A Review vol.43, pp.2, 2016, https://doi.org/10.5536/KJPS.2016.43.2.63
  5. Paternity Identification Using the Multiplex PCR with Microsatellite Markers in Chicken vol.48, pp.2, 2014, https://doi.org/10.14397/jals.2014.48.2.69