• Title, Summary, Keyword: Somatic Cell Hybrid Panel

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Current Status of Comparative Mapping in Livestock

  • Lee, J.H.;Moran, C.;Park, C.S.
    • Asian-Australasian Journal of Animal Sciences
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    • v.16 no.10
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    • pp.1411-1420
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    • 2003
  • Comparative maps, representing chromosomal locations of homologous genes in different species, are useful sources of information for identifying candidate disease genes and genes determining complex traits. They facilitate gene mapping and linkage prediction in other species, and provide information on genome organization and evolution. Here, the current gene mapping and comparative mapping status of the major livestock species are presented. Two techniques were widely used in comparative mapping: FISH (Fluorescence In Situ Hybridization) and PCR-based mapping using somatic cell hybrid (SCH) or radiation hybrid (RH) panels. New techniques, using, for example, ESTs (Expressed Sequence Tags) or CASTS (Comparatively Anchored Sequence Tagged Sites), also have been developed as useful tools for analyzing comparative genome organization in livestock species, further enabling accurate transfer of valuable information from one species to another.

The gene encoding guanidinoacetate methyltransferase (GAMT) maps to mouse chromosome 10 near the locus of hesitant mutation affecting male fertility

  • Chae, Young-Jin;Chung, Chan-Ee;Kim, Byung-Jin;Lee, Mun-Han;Lee, Hang
    • Proceedings of the Korean Society of Developmental Biology Conference
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    • pp.50-51
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    • 1998
  • guanidinoacetate methyltransferase (GAMT) catalyzes the last step of creatine biosynthesis in mammals. Creatine plays an important role in cellular energy metabolism in variety of tissues including brain and male reproductive tract. Congenital deficiency of the enzyme leads to a neurologic disorder in humans. We used an interspecific backcross DNA panel to map Gamt to the central region of mouse Chromosome (Chr) 10 near the locus of hesitant mutation affecting male fertility. We assigned the human GAMT gene to Chr 19 by PCR analysis of a human/rodent somatic hybrid cell line DNA panel, and further localized the human gene to Chr 19 at band p13.3 by PCR analysis of a human radiation hybrid DNA panel. Human chr 19p13.3 is homologous to the central part of mouse Chr 10 where mouse Gamt is located. Furthermore, this part of mouse Chr 10 contains mutant loci the phenotype of which is similar to the GAMT deficiency in human.

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Chromosomal Localization and Mutation Detection of the Porcine APM1 Gene Encoding Adiponectin (Adiponectin을 암호화하는 돼지 APM1 유전자의 염색체상 위치파악과 돌연변이 탐색)

  • Park, E.W.;Kim, J.H.;Seo, B.Y.;Jung, K.C.;Yu, S.L.;Cho, I.C.;Lee, J.G.;Oh, S.J.;Jeon, J.T.;Lee, J.H.
    • Journal of Animal Science and Technology
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    • v.46 no.4
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    • pp.537-546
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    • 2004
  • Adiponectin is adipocyte complement-related protein which is highly specialized to play important roles in metabolic and honnonal processes. This protein, called GBP-28, AdipoQ, and Acrp30, is encoded by the adipose most abundant gene transcript 1 (APM1) which locates on human chromosome 3q27 and mouse chromosome 16. In order to determine chromosomal localization of the porcine APM1, we carried out PCR analysis using somatic cell hybrid panel as well as porcine whole genome radiation hybrid (RH) panel. The result showed that the porcine APM1 located on chromosome 13q41 or 13q46-49. These locations were further investigated with the two point analysis of RH panel, revealed the most significant linked marker (LOD score 20.29) being SIAT1 (8 cRs away), where the fat-related QTL located. From the SSCP analysis of APM1 using 8 pig breeds, two distinct SSCP types were detected from K~ native and Korean wild pigs. The determined sequences in Korean native and Korean wild pigs showed that two nucleotide positions (T672C and C705G) were substituted. The primary sequence of the porcine APM1 has 79 to 87% identity with those of human, mouse, and bovine APM1. The domain structures of the porcine APM1 such as signal sequence, hypervariable region, collagenous region. and globular domain are also similar to those of mammalian genes.

Molecular Characterization, Chromosomal Localizations, Expression Profile, and Association Analysis of the Porcine PECI Gene with Carcass Traits

  • Gao, H.;Fan, B.;Zhu, M.J.;Liu, Bang
    • Asian-Australasian Journal of Animal Sciences
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    • v.23 no.1
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    • pp.7-12
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    • 2010
  • The full-length cDNA of the porcine peroxisomal ${\Delta}^3$,${\Delta}^2$-enoyl-CoA isomerase (PECI) gene encodes a monofunctional peroxisomal ${\Delta}^3$,${\Delta}^2$-enoyl-CoA isomerase. Cloning and sequencing of the porcine PECI cDNA revealed the presence of an 1185-base pair open reading frame predicted to encode a 394-amino acid protein by the 5'rapid amplification of cDNA ends (5'RACE) and EST sequences. The porcine PECI gene was expressed in seven tissues (heart, liver, spleen, lung, kidney, skeletal muscle, fat) which was revealed by reverse transcriptase-polymerase chain reaction (RT-PCR). The porcine PECI was mapped to SSC71/2 p11-13 using the somatic cell hybrid panel (SCHP) and the radiation hybrid panel (RH) (LOD score 12.84). The data showed that PECI was closely linked to marker S0383. A C/T single nucleotide polymorphism in PECI exon 10 (3'UTR) was detected as a PvuII PCR-RFLP. Association analysis in our experimental pig population showed that different genotypes of PECI gene were significantly associated with the Average Backfat thickness (ABF) (p<0.05) and Buttock backfat thickness (p<0.01).

Mapping, Tissue Distribution and Polymorphism Study of the Porcine SOCS2 and SOCS3 Genes

  • Li, X.Y.;Liu, B.;Fan, B.;Yu, M.;Zhu, M.J.;Xiong, T.A.;Li, K.
    • Asian-Australasian Journal of Animal Sciences
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    • v.19 no.2
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    • pp.165-170
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    • 2006
  • Using the somatic cell hybrid panel (SCHP) and radiation hybrid (IMpRH) panel, porcine SOCS2 gene was mapped at SSC5 (1/2) q21-q24 and closely linked with SW1383 marker (47 cR in distance), while SOCS3 gene was assigned to SSC12p11-(2/3p13) and closely linked with SW2490 (43 cR). The reverse transcriptase-polymerase chain reaction (RT-PCR) was performed to detect the expression of these two genes in the different tissues and the results showed that both SOCS2 and SOCS3 genes were widely expressed in tissues investigated (heart, liver, spleen, lung, kidney skeletal muscle, fat and brain), although some tissues showed lower gene expression. Moreover, SOCS2 and SOCS3 genes had different expression levels at different stages, in different tissues and in different breeds. A G/A substitution, which can be recognized by restriction enzyme of Cfr421, was observed in 5' untranslated region (5'-UTR) of SOCS2 gene. The allele frequencies was investigated by PCR-restriction fragment length polymorphism (PCR-RFLP) method and it showed that the allele frequency among Dahuabai, Erhualian, Yushan, Qingping, Large white and Landrace tested were different. Association analysis in a cross experimental populations revealed no significant association between the SOCS2 gene polymorphism and the economic traits investigated. The full-length coding regions (CDs) of porcine SOCS3 gene was obtained by RT-PCR.

Sequence Characterization, Expression Profile, Chromosomal Localization and Polymorphism of the Porcine SMPX Gene

  • Guan, H.P.;Fan, B.;Li, K.;Zhu, M.J.;Yerle, M.;Liu, Bang
    • Asian-Australasian Journal of Animal Sciences
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    • v.19 no.7
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    • pp.931-937
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    • 2006
  • The full-length cDNA of the porcine SMPX gene was obtained by the rapid amplification of cDNA ends (RACE). The nucleotide sequences and the predicted protein sequences share high sequence identity with both human and mouse. The promoter of SMPX was sequenced and then analyzed to find the promoter binding sites. The reverse transcriptase-polymerase chain reaction (RT-PCR) revealed that SMPX has a high level of expression in heart and skeletal muscle, a very low expression in lung and spleen and no expression in liver, kidney, fat and brain. Moreover, SMPX has a differential expression level in skeletal muscle, the expression in 65-day embryos being higher than other stages. The porcine SMPX was mapped to SSCXp24 by using a somatic cell hybrid panel (SCHP) and was found closely linked to SW1903 using the radiation hybrid panel IMpRH. An A/G single nucleotide polymorphism (PCR-RFLP) in the 3'-untranslated region (3'-UTR) was detected in eight breeds. The analysis of allele frequency distribution showed that introduced pig breeds (Duroc and Large White) have a higher frequency of allele A while in the Chinese indigenous pig breeds (Qingping pig, Lantang pig, YushanBlack pig, Large Black-White pig, Small Meishan) have a higher frequencies of allele G. The association analysis using an experimental population (188 pigs), which included two cross-bred groups and three pure-blood groups, suggested that the SNP genotype was associated with intramuscular fat content.

The Porcine FoxO1, FoxO3a and FoxO4 Genes: Cloning, Mapping, Expression and Association Analysis with Meat Production Traits

  • Yu, Jing;Zhou, Quan-Yong;Zhu, Meng-Jin;Li, Chang-Chun;Liu, Bang;Fan, Bin;Zhao, Shu-Hong
    • Asian-Australasian Journal of Animal Sciences
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    • v.20 no.5
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    • pp.627-632
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    • 2007
  • FoxO1, FoxO3a and FoxO4 belong to the FoxO gene family, which play important roles in the PI3K/PKB pathway. In this study, we cloned the porcine FoxO1, FoxO3a and FoxO4 sequences and assigned them to SSC11p11-15, SSC1p13 and SSC xq13 using somatic cell hybrid panel (SCHP) and radiation hybrid panel (IMpRH). RT-PCR results showed that these three genes are expressed in multiple tissues. Sequencing of PCR products from different breeds identified a synonymous T/C polymorphism in exon 2 of FoxO3a. This FoxO3a single nucleotide polymorphism (SNP) can be detected by AvaII restriction enzyme. The allele frequencies of this SNP were investigated in Dahuabai, Meishan, Tongcheng, Yushan, Large White, and Duroc pigs. Association of the genotypes with growth and carcass traits showed that different genotypes of FoxO3a were associated with carcass length and backfat thickness between 6th and 7th ribs (BTR) and drip loss (p<0.05).

Cloning and Initial Analysis of Porcine MPDU1 Gene

  • Yang, J.;Yu, M.;Liu, B.;Fan, B.;Zhu, M.;Xiong, T.;Li, Kui
    • Asian-Australasian Journal of Animal Sciences
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    • v.18 no.9
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    • pp.1237-1241
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    • 2005
  • Mannose-P-dolichol utilization defect 1 (MPDU1) gene is required for utilization of the mannose donor MPD in synthesis of both lipid-linked oligosaccharides (LLOs) and glycosylphosphatidylinositols (GPI) which are important for functions such as protein folding and membrane anchoring. The full length cDNA of the porcine MPDU1 was determined by in silico cloning and rapid amplification of cDNA ends (RACE). The deduced amino acid showed 91% identity to the corresponding human sequence with five predicted transmembrane regions. RT-PCR was performed to detect its expression pattern in five tissues and results showed that it is expressed ubiquitously among the tissues checked. A single nucleotide substitution resulting in the amino acid change (137 Tyr-137 His) was detected within exon 5. Allele frequencies in six pig breeds showed distinctive differences between those Chinese indigenous pigs breeds and European pigs. Using the pig/rodent somatic cell hybrid panel (SCHP), we mapped the porcine MPDU1 gene to SSC12, which is consistent with the comparative mapping result as conservative syntenic groups presented between human chromosome 17 and pig chromosome 12.