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cSNP Identification and Genotyping from C4B and BAT2 Assigned to the SLA Class III Region

돼지 SLA class III 영역 내 C4B 및 BAT2의 cSNP 동정 및 이를 이용한 유전자형 분석

  • Kim, J.H. (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) ;
  • Seo, B.Y. (Division of Applied Life Science(BK21) Graduate School of Gyeongsang National University) ;
  • Lee, S.H. (Gyeongnam animal science and technology, Gyeongsang National University) ;
  • Lee, J.B. (Division of Applied Life Science(BK21) Graduate School of Gyeongsang National University) ;
  • Yoo, C.K. (Division of Agriculture and Life, Gyeongsang National University) ;
  • Jung, E.J. (Division of Agriculture and Life, Gyeongsang National University) ;
  • Jeon, J.T. (Division of Applied Life Science(BK21) Graduate School of Gyeongsang National University)
  • 김재환 (경상대학교 대학원 응용생명과학부(BK21)) ;
  • 임현태 (경상대학교 대학원 응용생명과학부(BK21)) ;
  • 서보영 (경상대학교 대학원 응용생명과학부(BK21)) ;
  • 이상호 (경상대학교 학교기업 GAST) ;
  • 이재봉 (경상대학교 대학원 응용생명과학부(BK21)) ;
  • 유채경 (경상대학교 농생명학부) ;
  • 정은지 (경상대학교 농생명학부) ;
  • 전진태 (경상대학교 대학원 응용생명과학부(BK21))
  • Published : 2007.10.31

Abstract

C4B and BAT2, assigned to the SLA class III region, were recently reported on relation with human diseases. The primers for RT-PCR and RACE-PCR for CDS analysis of these genes of pig were designed by aligning the CDSs of humans and mice from GenBank. After we amplified and sequenced with these primers and cDNAs, the full-length CDSs of pig were determined. The CDS lengths of C4B and BAT2 were shown as 5226 bp and 6501 bp. In addition, the identities of nucleotide sequences with human and mouse were 76% to 87%, and the identities of amino acids were 72% to 90%. After we carried out the alignment with determined CDSs in this study and pig genomic sequences from GenBank, the primers for cSNP detection in genome were designed in intron regions that flanked one or more exons. Then, we amplified and directly sequenced with genomic DNAs of six pig breeds. Four cSNPs from C4B and three 3 cSNPs from BAT2 were identified. In addition, amino acid substitution occurred in six cSNP positions except for C4248T of C4B. By the Multiplex-ARMS method, we genotyped seven cSNPs with DNA samples used for direct sequencing. We verified that this result was the same as that analyzed using direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS on two randomly selected DNA samples. The genotype of each sample showed the same result from both methods. Therefore, seven cSNPs were identified from C4B and BAT2 and could be used as the basic data for haplotype analysis of SLA class III region. Moreover, the Multiplex-ARMS method should be powerful for genotyping of genes assigned to the whole SLA region for the xenograft study.

Keywords

C4B;BAT2;cSNP;Multiplex-ARMS;Direct sequencing;Genotyping;SLA

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