DOI QR코드

DOI QR Code

Detection of Copy Number Variation of the KIT Gene in the Landrace Breed using an Quantitative Oligonucleotide Ligation Assay(qOLA)

Quantitative Oligonucleotide Ligation Assay(qOLA)를 이용한 Landrace 품종의 KIT 유전자 반복수 변이 탐지

  • Seo, B.Y. (Division of Applied Life Science(BK21), Graduate School of Gyeongsang National University) ;
  • Kim, J.H. (Division of Applied Life Science(BK21), Graduate School of Gyeongsang National University) ;
  • Nahm, D.W. (Division of Applied Life Science(BK21), Graduate School of Gyeongsang National University) ;
  • Yoo, C.K. (Division of Agriculture and Life, Gyeongsang National University) ;
  • Lee, S.H. (Gyeongnam Animal Science Technology) ;
  • Lee, J.B. (Division of Applied Life Science(BK21), Graduate School of Gyeongsang National University) ;
  • Lim, H.T. (Division of Applied Life Science(BK21), Graduate School of Gyeongsang National University) ;
  • Jung, E.J. (Division of Agriculture and Life, Gyeongsang National University) ;
  • Cho, I.C. (National Institute of Subtropical Agriculture, R. D. A.) ;
  • Heo, K.N. (National Institute of Animal Science, R. D. A.) ;
  • Jeon, J.T. (Division of Applied Life Science(BK21), Graduate School of Gyeongsang National University)
  • 서보영 (경상대학교 대학원 응용생명과학부(BK21)) ;
  • 김재환 (경상대학교 대학원 응용생명과학부(BK21)) ;
  • 남덕우 (경상대학교 대학원 응용생명과학부(BK21)) ;
  • 유채경 (경상대학교 농생명학부) ;
  • 이상호 (경남동물과학기술) ;
  • 이재봉 (경상대학교 대학원 응용생명과학부(BK21)) ;
  • 임현태 (경상대학교 대학원 응용생명과학부(BK21)) ;
  • 정은지 (경상대학교 농생명학부) ;
  • 조인철 (농촌진흥청 난지농업연구소) ;
  • 허강녕 (축산과학원 동물유전체과) ;
  • 전진태 (경상대학교 대학원 응용생명과학부(BK21))
  • Published : 2007.10.31

Abstract

Recently, copy number variations (CNV) of genes or genomic segments have been intensively studied and various analysis methods have been developed. In this study, quantitative oligonucleotide ligation assay (qOLA) was applied to investigate CNV of KIT gene in the Landrace breed. A combined assay using qOLA and pyrosequencing, 6 genotype classes, I1/I1 or I3/i (IBe), I1/I2 or I3/IP, I1/I3, I1/IP or I2/i (IBe), I2/I2and I2/IP, were identified from 44 Landrace pigs. Genotype assignment using grouping features of measurements on a scatter plot showed 100% agreement with those using a statistical assignment by PROC FASTCLUS procedure implemented in the SAS package. Two versions (3100 and 3130) of ABI sequencers gave the same genotyping results, indicating there was no influence on qOLA by different versions of instrument, however, the means of standard deviation and coefficient of variation from the qOLA on a ABI 3130 (2.33 and 4.10) was lower than those from the qOLA on a ABI 3100 (2.67 and 4.81). Effect of proteinase K treatment on the PCR product followed by qOLA was very clear because noise peaks were disappeared and the observed ration fit better to the reference ratio corresponding to each genotype.

Keywords

Copy number variation;KIT;Landrace;OLA

References

  1. Bernstein, A., Chabot, B., Dubreuil, P., Reith, A., Nocka, K., Majumder, S., Ray, P. and Besmer, P. 1990. The mouse W/c-KIT locus. Ciba Found. Symp. 148:158-172
  2. Daniel L. B., Caleb F. D., Lisa A. G. and Jeffrey, L. N. 1999. Identification of Three Novel $Ca^{2+}$ Channel ${\gamma}$ Subunit Genes Reveals Molecular Diversification by Tandem and Chromosome Duplication. Genome Res. 9:1204-1213 https://doi.org/10.1101/gr.9.12.1204
  3. Giuffra, E., Evans, G., Tornsten, A., Wales, R., Day, A., Looft, H., Plastow, G. and Andersson, L. 1999. The Belt mutation in pigs is an allele at the Dominant white(I/KIT) locus. Mamm. Genome 10(12):1132-1136 https://doi.org/10.1007/s003359901178
  4. Giuffra, E., Tornsten, A., Marklund, S., ongcam-Rudloff, E., Chardon, P., Kijas, J. M. H., Anderson, S. I., Archibald, A. L. and Andersson, L. 2002. A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT. Mamm. Genome 13:569-577 https://doi.org/10.1007/s00335-002-2184-5
  5. Jackson, I. J. 1994. Molecular and developmental genetics of mouse coat color. Annu. Rev. Genet. 28:189-217 https://doi.org/10.1146/annurev.ge.28.120194.001201
  6. James, W. T., Mary, G. S., Tyrone, J. S., Robert, W. B., Jennifer, C. M., Pamela, J. T., Jacquelyn, R. I., Valerie, V. B. M., Shih, Q. L. L., Jeffrey W. T., Gerard, G. B., Stephen, M. B. S. and Eric D. G. 2003. Pericentromeric Duplications in the Laboratory Mouse. Genome Res. 13:55-63 https://doi.org/10.1101/gr.791403
  7. Johansson, M. M., Chaudhary, R., Hellmen, E., Hoyheim, B., Chowdhary, B. and Andersson, L. 1996. Pigs with the dominant white coat color phenotype carry a duplication of the KIT gene encoding the mast/stem cell growth factor receptor. Mamm. Genome 7:822-830 https://doi.org/10.1007/s003359900244
  8. Lynch, M. and Conery, J. S. 2000. The evolutionary fate and consequence of duplicate genes. Science 10:1151-1155
  9. Marklund, S., Kijas, J., Martinez, H. R., Ronnstrand, L., Funa, K, Moller, M., Lange, D., Lilja, I. E. and Andersson, L. 1998. Molecular Basis for the Dominant White Phenotype in the Domestic Pig. Genome Res. 8:826-833 https://doi.org/10.1101/gr.8.8.826
  10. Pielberg, G., Olsson, C., Syvanen, A. C. and Andersson, L. 2002. Unexpectedly High Allelic Diversity at the KIT Locus Causing Dominant White Color in the Domestic Pig. Genetics 160:305-311
  11. Pielberg G., Day A. E., Plastow G. S. and Andersson L. 2003. A sensitive method for detecting variation in copy numbers of duplicated genes. Genome Res. 13:2171-217 https://doi.org/10.1101/gr.1188203
  12. Richard M. and David S., 1998. Pathological consequences of sequence duplications in the human genome. Genome Res. 8:1007-1021 https://doi.org/10.1101/gr.8.10.1007
  13. Walsh, P. S., Metzger, D. A., Higuchi, R. 1991. Chelex-100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506-513
  14. Eichler, E. E. 2001. Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet. 17:661-669 https://doi.org/10.1016/S0168-9525(01)02492-1
  15. Bailey, J. A., Gu, Z., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., Adams, M. D., Myers, E. W., Li, P. W. and Eichler, E. E. 2002. Recent segmental duplications in the human genome. Science 297:1003-1007 https://doi.org/10.1126/science.1072047