Genetic Structure of Korean Native Pig Using Microsatellite Markers

Kim, Kyung Seok,Choi, Chang Bon 한국유전학회 2002 Genes & Genomics Vol.24 No.1

Six microsatellite loci on 67 random individuals have been analyzed to characterize the genetic variability and structure of Korean native pig (the Black pig). In addition, the data were compared with those of the two regional pigs (26 Chinese Yanbian pig and ten Japanese Kagoshima pig) and of the three cosmopolitan pigs (ten Duroc, ten Yorkshire and ten Landrace). Allele diversity, observed and expected heterozygosity, polymorphism information content (PIC), two different estimators (F_ST and G_ST) of gene differentiation, number of migrants per generation (Nm) and Nei's DA genetic distance were evaluated. Based on both expected heterozygosity and PIC, the lowest genetic diversity was exhibited in Korean native pig (H_E = 0.529, PIC = 0.451), and the highest in Chinese Yanbian pig (H_E = 0.739, PIC = 0.703). The pairwise F_ST and Nm values indicated great levels of gene differentiation between Korean native pig and the other pigs, the mean F_ST value being 0.270. Nei's DA genetic distance between each pair of six pig populations showed a similar tendency to the results of the pairwise F_ST estimates. From both analyses, Korean native pig exhibits a closer relationship to Chinese Yanbian pig than to the other pigs. UPGMA tree of individuals displays that the samples of the Korean native pig form a distinct clustering from those of the other pigs. Taken together, it is concluded that Korean native pig has a low level of genetic diversity and has been genetically subdivided from the commercial non-Korean pigs.

Discovery of cSNPs in Pig Using Full-length Enriched cDNA Libraries of the Korean Native Pig as a Source of Genetic Diversity

Dirisala, Vijaya R.,Kim, Ju-Hyun,Park, Kwang-Ha,Lee, Hoon-Taek,Park, Chan-Kyu Korean Society for Biotechnology and Bioengineerin 2007 Biotechnology and Bioprocess Engineering Vol.12 No.4

Clones from full-length enriched cDNA libraries serve as valuable resources for functional genomic studies. We analyzed 3,210 chromatograms obtained from sequencing the 5'-ends of brainstem, liver, neocortex, and spleen clones derived from full-length enriched cDNA libraries of Korean native pigs. In addition, 50,000 pig EST sequence trace files were obtained from Genbank and combined with our sequencing information for SNP identification in silica. For the SNP analysis, neocortex, and liver libraries were newly constructed, whereas the sequencing results from brainstem and spleen libraries were from previously constructed libraries. The putative SNPs from the in silica analysis were confirmed by genomic PCR from a group of 20 pigs of four different breeds. Using this approach, 86% of cSNPs identified in silico were confirmed and the SNP detection frequency was 1 SNP per 338 bp. Interestingly, we found a valine deletion at amino acid position 126 of the neuronal and endocrine protein gene in the Korean native pig. We confirmed that this deletion was caused by alternative splicing at the NAGNAG acceptors. Our study shows that large-scale EST sequencing of Korean native pigs can be effectively employed for natural polymorphism-based pig genome analysis.

재래돼지(Korea Native Pigs) 특이 genetic marker와 육질 연관성 분석

김철욱,여정수,조광근,진상근,오명곤,박준규,권은정,홍연희,김지현,이보경,박다혜,김재우,이지홍 한국동물자원과학회 2001 한국축산학회지 Vol.43 No.6

본 연구는 재래돼지 특이적인 marker를 개발하고 이들 marker와 육질과의 연관성을 규명하기 위하여 실시하였다. 실험동물로 재래돼지와 랜드레이스 각각 30두씩 총 60두를 사용하였으며, 품종 특이 marker를 찾기 위하여 4번과 7번 염색체에 존재하는 총 60개의 microsatellite를 이용하여 PCR (polymerase chain reaction)을 수행하였다. PCR 증폭은 형광물질 Fam과 Hex, Ned로 표지된 한쌍의 microsatellite primer를 이용하였으며, 형광물질로 표식된 PCR 산물은 Genetic Analyzer ABI 310으로 전기영동하여 대립 유전자를 규명하고 통계 분석하였다. 대립 유전자에 대한 통계 분석 결과 총 60개의 microsatellite중 27개가 다양한 유전적 다형현상을 보이는 대립 유전자가 증폭되었으며 (p<0.05), 특히 SW1364와 SW445, SW1369, SWR773 microsatellite의 증폭 산물에서 재래돼지와 랜드레이스 두 품종간을 구분할 수 있는 품종 특이적인 대립 유전자를 확인하였다 (p<0.01). 또한 육질에 영향을 미치는 유전적 marker를 얻기 위해 60두 전체에 대한 육색, 지방색, 지방산 조성, 콜레스테롤 함량, 연도와 경도에 대한 육질 분석을 실시하여 육질 형질과 marker와의 연관성을 분석한 결과 육질 형질에 영향을 미치는 28개 marker를 확인하였으며, 육색과 지방색에 연관된 4개, 조직감과 연관된 10개의 marker를 확인하였다. 이렇게 선발된 marker들은 고급육 생산을 위한 돼지의 유전적 개량을 위하여 유용하게 이용될 수 있다. This study was conducted to develop Korean native pig-specific DNA markers and analyze its relativity with meat quality using 30 of Korean native pigs and Landraces, respectively. To find species-specific DNA markers, we selected and tested a total of 60 microsatellite markers on the 4 and 7 chromosome using polymerase chain reaction (PCR). PCR amplification was carried out by microsatellite primer pairs labeled with fluorescent Fam, Hex and Ned. The fluorescent labeled PCR products were electrophoresed with Genetic Analyzer ABI 310 followed by the allelic and statistical analysis. According to the allelic frequency annalysis, of the 60 microsatellite markers 27 were preduced with a variety of genetic polymorphic alleles (p<0.05). Especially, alleles of SW1364, SW445, SW1369 and SWR773 microsatellite markers were identified to be species-specific markers between two breeds (p<0.01). To analyze the meat quality we determined the meat color, fat color, fat composition, cholesterol contents and hardness, and compared these characteristics with the alleles of 36 species-specific markers in all pigs. Of the 60 microsatellite markers 28 were found to be related with meat quality; 18 for meat and fat color, 7 for fatty acid, 4 for cholesterol contents and 10 for shear force and hardness. These selected markers will be useful in the genetic improvement of pigs for an excellent meat quality.

한국 재래돼지 브랜드 돈육 원산지 검증을 위한 유전자 감식 기법 활용 연구

최봉암 ( Choi Bong-am ),이학교 ( Lee Hak-kyo ),전광주 ( Jeon Gwang-joo ),오재돈 ( Oh Jean-don ),최일신 ( Choi Il-sin ),박미현 ( Park Mi-hyun ),공홍식 ( Kong Hong-sik ),정일정 ( Jung Il-jung ),김태헌 ( Kim Tae-hun ),윤두학 ( Yoon D 한국유기농업학회 2004 韓國有機農業學會誌 Vol.12 No.2

Identification of animals has been used with an ear tag with dummy code and blood typing has been used for paternity and individual identification in live animals. Various genetic markers are different for breeds of pig and hence, it is necessary to identity the discrete genetic marker in korean native pig. A total of 240 pigs were used to find korean native pig population specific markers that expressed in population of korean native pigs. To identify the individual traceability, 20 animals were randomly chosen and tested for a whole process from being live to slaughter stages. The candidate genetic marker used in the study were 18 DNA microsatellites which were identified in pig genome. The number of alleles of those DNA microsatellites ranged form a minimum of 3 to maximum of 6. The heterozygote frequency ranged from 0.44 to 0.69. Effective number of alleles for each DNA microsatellotes were 2 to 4. By choosing 6 candidate genetic markers among all, the traceability of individual identification was estimated as accurate as 99.99%(p>0.0014), nearly.

유전자 지문을 이용한 한국재래돼지의 유전분석

여정수,김재우,장태경,박영애,이지흥,육심교,이석태 영남대학교 자원문제연구소 2000 資源問題硏究 Vol.19 No.-

In the results of genetic analysis of Korean native pig(Pohang, Jirae and Kyungbuk) and foreign pig breeds(Yorkshire, Duroc, Hampshire and Landrace) using DNA fingerprintings with YNZ22/HeaⅢ, Korean native pig had long genetic distance from foreign pig breeds, and especially Pohang Korean native pig had the highest in genetic similarity within breed, band frequency, mean probability, allele frequency, homozygosity and inbreeding coefficient. The population of Pohang Korean native pig was found to have the high value for breeding of Korean native pig.

Discovery of single nucleotide polymorphisms in SLA-1 cDNA from Korean native pigs and phylogenetic analysis

Nam Eun Kim,Chan Jin Woo,Ho Jun Choi,Vijaya Ramu,Sang Jun Uhm,Hoon Taek Lee,Chan Kyu Park 한국유전학회 2006 Genes & Genomics Vol.28 No.4

Identification of new alleles of MHC genes has significant meaning due to their functional importance. The characterization of SLA molecules is also important to develop suitable pig breeds as basic research models for biomedical research including xenotransplantation experiments. We cloned the complete cDNAs of the SLA-1 gene from five Korean native pigs and analyzed the DNA sequence polymorphism. From the sequence comparison with previously reported SLA-1 alleles, we found three new SLA-1 alleles. Three out of five animals were homozygous for the SLA-1 locus. The phylogenetic analysis showed that SLA-1 alleles from Korean native pigs clustered with those of miniature pigs. This study will provide valuable information on the characteristics of MHC molecules of Korean native pigs and genetic diversity of MHC molecules in pigs.

Phylogenetic analysis of the swine leukocyte antigen - 2 gene for Korean native pigs

Hoyoung Chung,Matthew McClure,Jaeyoung Kim 한국유전학회 2011 Genes & Genomics Vol.33 No.4

The objective of this study was to investigate genetic relationships of the SLA-2 gene, to characterize SLA-2 alleles, and to provide basic genetic information of Korean pigs. The swine leukocyte antigen - 2 (SLA-2) gene in the MHC classical region was cloned with spleen tissues from Korean native pigs selected from the main land (KNP) and Jeju Island (KJP). Primer sequences based on swine cDNA (GenBank accession numbers AF464049 and AF464005) were used to amplify the entire SLA-2 gene, and the amplification product including both 3’ and 5’ UTRs was sized 1,520 bp. A BAC clone was selected from miniature pigs and sequenced for the genomic region of the SLA-2 gene showing that 4,585 bp in total length consisted of exons (1,087 bp) and introns (3,498 bp). A sequence analysis confirmed 58 SNPs in coding regions, which revealed higher numbers of SNPs in KNP than other pig breeds, implicating more genetic variability in Korean pigs. Approximately 82% of the SLA-2 SNPs were located in the highly polymorphic exons 2 and 3. Newly identified sequences of the SLA-2 gene for KNP and KJP were submitted into the IPD-MHC database with new nomenclatures (SLA-2*1501,SLA-2*1601, and SLA-2*w08hy01 allele), while the representative sequences of KNP and KJP were submitted into GenBank with accession numbers (DQ992495, DQ992496,and DQ992501), respectively. The identified KNP allele (SLA-2*1501) clustered with previously defined alleles for Korean pigs (SLA-2*kn02 and SLA-2*jh01), but SLA-2*1601(KNP) and SLA-2*w08hy01 (KJP) alleles showed no significant genetic relationships with any other allele. A sequence comparison revealed that KNP has departed from KJP both genetically and phenotypically. The results of SLA-2 SNP in KNP and KJP reported here will serve as the SLA-2 reference for Korean pigs.

Characterization of DQB1 and DRB1 in Korean Native Pigs and the Identification of Three New DQB1 Alleles

Chan Jin Woo,Ju Hyun Kim,Kwang Ha Park,Yoon Shin Oh,Vijaya Dirisala,Rui Xiao,Na Meun Kim,In Chul Cho,Chan Kyu Park 한국유전학회 2007 Genes & Genomics Vol.29 No.4

There has been no prior report on allelic variations of SLA class II loci in Korean native pigs. Here, we analyzed two important SLA class II genes, DQB1 and DRB1, in Korean native pigs (n = 65). DQB1 and DRB1 were PCR amplified from genomic DNA by using locus-specific oligonucleotides, and six alleles were identified for each locus. In DQB1, all six alleles were identical to those previously reported. However, we identified three new alleles in DRB1. The level of heterozygosity for DQB1 and DRB1 was 49 and 34%, respectively. Phylogenetic analyses showed that alleles from Korean native pigs were clustered in five distinct groups for DQB1 and four for DRB1. Finally, we defined 13 DQB1-DRB1 haplotypes by combining genotyping results and pedigree information. These results provide information on the genetic diversity of Korean native pigs and SLA systems.

Reporting 678 putative cSNPs from full-length enriched cDNA sequences of the Korean native pig

Park, K.,Dirisala, V.R.,Oh, Y.,Choi, H.,Lee, K.T.,Kim, J.H.,Lee, H.T.,Seo, K.H.,Park, C. Blackwell Publishing Ltd 2009 Journal of animal breeding and genetics Vol.126 No.2

<P>Summary</P><P>Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomic studies. We have analysed 1970 high-quality chromatograms (Phred value ≥ 30) that were obtained from sequencing the 5′ ends of brainstem, liver, neocortex and spleen clones derived from full-length enriched cDNA libraries from Korean native pigs. In addition, 50 000 pig expressed sequence tag (EST) sequence trace files were obtained from Genbank and combined with our sequencing information to facilitate SNP identification <I>in silico</I>. The process generated 8118 contigs, of which 239 included minimum one sequence from Korean native pig and contained 678 putative coding single nucleotide polymorphisms (cSNPs). Of these, 33 putative cSNPs were randomly selected for confirmatory analysis and validated using 20 pigs from four different breeds (Duroc, Landrace, Yorkshire, Korean native pig). Of the 33 putative cSNPs, 20 were confirmed (61%), which was similar to the frequency reported in other studies. We also identified 15 new cSNPs from the validation process, which were not detected by our <I>in silico</I> analysis. Our study shows that analysing genetically diverse pig breeds including the Korean native pig could serve as a useful strategy for generating a large number of cSNPs.</P>

Transcriptome analysis to identify long non coding RNA (lncRNA) and characterize their functional role in back fat tissue of pig

Kumar, Himansu,Srikanth, Krishnamoorthy,Park, Woncheol,Lee, Seung-Hoon,Choi, Bong-Hwan,Kim, Hana,Kim, Yong-Min,Cho, Eun-Seok,Kim, Jin Hyoung,Lee, Jang Hee,Jung, Ji Yeon,Go, Gwang-woong,Lee, Kyung-Tai Elsevier 2019 Gene Vol.703 No.-

<P><B>Abstract</B></P> <P>Long non coding RNAs (lncRNA) have been previously found to be involved in important cellular activities like epigenetics, implantation, cell growth etc. in pigs. However, comprehensive analysis of lncRNA in back fat tissues at different developmental stages in pigs is still lacking. In this study we conducted transcriptome analysis in the back fat tissue of a F1 crossbred Korean Native Pig (KNP) × Yorkshire Pig to identify lncRNA. We investigated their role in 16 pigs at two different growth stages; stage 1 (10 weeks, n = 8) and stage 2 (26 weeks, n = 8). After quality assessment of sequencing reads, we got a total of 1,641,165 assembled transcripts out of eight paired end read from each stage. Among them, 6808 lncRNA transcripts were identified by filtering on the basis of multiple parameters like read length ≥ 200 nucleotides, exon numbers ≥2, FPKM ≥0.5, coding potential score < 0 etc. PFAM and RFAM were used to filter out all possible protein coding genes and housekeeping RNAs respectively. A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed (DE) between the two stages (|log2FC| > 2, q < 0.05). We also identified 306 genes located around 100 kb upstream and 234 genes downstream around these DE lncRNA transcripts. The expression of top eleven DE lncRNAs (COL4A6, LY7S, MYH2, OXCT1, SMPDL3A, TMEM182, TTC36, RFOOOO4, RFOOO15, RFOOO45, CADM2) had been validating by qRT-PCR. Pathway and GO terms analysis showed that, positive regulation of biosynthetic process, Wnt signaling pathway, cellular protein modification process, and positive regulation of nitrogen compound were differentially enriched. Our results suggested that, KEGG pathways such as protein digestion and absorption, Arrhythmogenic right ventricular cardiomyopathy (ARVC) to be significantly enriched in both DE lncRNAs as well as DE mRNAs and involved in back fat tissues development. It also suggests that, identified lncRNAs are involved in regulation of important adipose tissues development pathways.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Analysis of lncRNAs in back fat tissues at different developmental stages in the pigs </LI> <LI> A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed. </LI> <LI> KEGG pathway and GO analysis for functional annotation of lncRNAs </LI> <LI> Top DE transcripts were validated by qRTPCR. </LI> <LI> Relation between back fat metabolism and lncRNAs were established. </LI> </UL> </P>