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C K Tuggle

Publications and source records attributed to C K Tuggle.

At least 19 recordsLinked to original sources
PubMed2006

Integration of structural and functional genomics.

This paper introduces a special issue of Animal Genetics, which is devoted to the recent symposium held at Iowa State University entitled 'Integration of Structural and Functional Genomics'. We describe issues and needs that confront the animal genomics community, and describe how this symposium was structured to address these issues by improving communication and collaboration across species and disciplines. The session topics and oral presentations are briefly described for all invited speakers.

Animals↗
PubMed2005

Physical mapping of genes in the porcine ovarian transcriptome.

Reproductive efficiency and associated traits are of major economic importance to the swine industry and have been more difficult to improve genetically than other production traits. Integration of phenotypical data with gene mapping and expression studies provides a powerful approach for dissection of the genetic basis regulating complex traits. We developed a total of 101 polymerase chain reaction-based markers, representing 91 unique genes, for expressed sequence tags previously reported to be putatively differentially expressed in the porcine ovarian transcriptome of a swine line selected on an index of high ovulation rate and embryonic survival. These were subsequently used in physical mapping experiments with a porcine radiation hybrid and somatic cell hybrid panels. Our results increased the information content of the porcine physical map useful for comparative mapping by c. 10%. Moreover, the mapped genes are likely to be biologically relevant to the molecular mechanisms that control ovulation rate in the pig. A total of 12 differentially expressed genes were mapped to regions previously reported to contain quantitative trait loci affecting swine ovulation rate.

Animals↗
PubMed2005

Mapping of 443 porcine EST improves the comparative maps for SSC1 and SSC7 with the human genome.

Numerous mapping studies of complex traits in the pig have resulted in quantitative trait loci (QTL) intervals of 10-20 cM. To improve the chances to identify the genes located in such intervals, increased expressed sequence tags (EST)-based marker density, coupled with comparative mapping with species whose genomes have been sequenced such as human and mouse, is the most efficient tool. In this study, we mapped 443 porcine EST with a radiation hybrid (RH) panel (384 had LOD > 6.0) and a somatic cell hybrid panel. Requiring no discrepancy between two-point and multipoint RH data allowed robust assignment of 309 EST, of which most were located on porcine chromosomes (SSC) 1, 4, 7, 8 and X. Moreover, we built framework maps for two chromosomes, SSC1 and SSC7, with mapped QTL in regions with known rearrangement between pig and human genomes. Using the Blast tool, we found orthologies between 407 of the 443 pig cDNA sequences and human genes, or to existing pig genes. Our porcine/human comparative mapping results reveal possible new homologies for SSC1, SSC3, SSC5, SSC6, SSC12 and SSC14 and add markers in synteny breakpoints for chromosome 7.

Animals↗
PubMed2003

Complementary DNA macroarray analyses of differential gene expression in porcine fetal and postnatal muscle.

To study differential gene expression in porcine skeletal muscle, a porcine complementary DNA (cDNA) macroarray was produced that contained 327 expressed sequence tags (EST) derived from whole embryo and adult skeletal muscle, and differential display PCR products from fetal and postnatal muscle. Total RNA from four muscle samples, 75- and 105-d fetal hind limb muscles, and 1- and 7-wk postnatal semitendinosus muscle was used to make radiolabeled targets for duplicate hybridization to the macroarray membranes in an initial screen for expression. All EST that gave clear signals (n = 238) were then re-arrayed, and hybridization was conducted with additional biological replication of samples in the 75-d and 1-wk ages. Signal intensity for each gene was normalized to signal intensity measured at control spots on each membrane, which consisted of total cDNA from liver, lung, spleen, and skeletal muscle. Both normalized ratio levels and a mixed linear model analyses were used to identify genes differentially expressed among the muscle samples. Results showed 28 genes had differences in expression level greater than twofold between the 75-d fetal and 1-wk muscle RNA samples. All 28 genes were also identified as genes with significantly different (P < 0.01) expression using a mixed linear model analysis. Nineteen of these 28 genes had significant matches (basic local alignment search tool [BLAST] score > 100; P < 0.01) to known genes, two matched genes encoding human hypothetical proteins, and seven had no significant matches to Genbank nonredundant and dbEST (database of expressed sequence tags) entries. These results were confirmed for representative genes with RNA blot analysis of seven developmental time points, including RNA from the same muscle samples tested previously in the macroarray. The RNA blot results confirmed the macroarray results for all selected genes, demonstrating that the macroarray technique used in this study is accurate and reproducible. An unknown muscle clone (M218) with a slightly less than twofold increase in expression from the 75-d to the 1-wk age (1 wk/75 d = 1.94; P = 0.0114) was also shown to differ between these two ages using RNA blot analysis, demonstrating the methods used to identify differentially expressed genes may be conservative. The association between expression patterns of vimentin and desmin was also investigated. Results indicate the switch in intermediate filament protein from vimentin to desmin occurs primarily at the level of transcription and/or RNA processing.

Age Factors↗
PubMed2002

Neonatal Meishan pigs show POU1F1 genotype effects on plasma GH and PRL concentration.

Chinese Meishan pigs develop rapidly with onset of puberty at less than 100 days of age, and have a smaller placental size and larger litter size as compared with British/Continental breeds. POU1F1 is a member of the POU-domain family gene and is a positive regulator for growth hormone (GH), prolactin (PRL), and thyroid-stimulating hormone beta (TSHbeta) in several mammalian species. To investigate the role of POU1F1 in controlling pig growth and reproduction traits, Meishan (MS) pigs segregating a MspI POU1F1 polymorphism were used to determine differences of GH and PRL at both mRNA and circulating hormone concentrations. Animals from nine litters were used to collect pituitary (n=60) and/or blood samples (n=80) at day 0, 15, and 30 after birth, and all animals were genotyped (CC, CD, DD) for the MspI POU1F1 polymorphism. Reverse transcriptase-polymerase chain reaction (RT-PCR) with standard curve quantification was used to quantify mRNA levels for GH, PRL, and two alternative POU1F1 transcripts, POU1F1-alpha, and POU1F1-beta. Radioimmunoassays were done to determine the circulating concentration of GH and PRL in blood plasma. Our results indicated a significant effect of POU1F1 genotype on circulating levels of both GH and PRL at birth, but not thereafter. The DD neonates had lower levels of GH, but higher levels of PRL, than other genotypes. POU1F1-alpha mRNA decreased (P<0.05) from days 0 to 30, which paralleled decreases (P<0.05) in GH mRNA as well as PRL and GH plasma levels over the same period. POU1F1-beta mRNA levels did not significantly change over this period. Correlations were significant between POU1F1-alpha mRNA and both GH mRNA and GH plasma concentration levels, as well as between the two POU1F1 mRNA isoforms. Results from this study add to our understanding of the role of POU1F1 in controlling pig development and reproduction.

Aging↗
PubMed2002

Precise mapping of breakpoints in conserved synteny between human chromosome 1 and pig chromosomes 4, 6 and 9.

Previous comparative mapping suggested that at least five pig chromosomes (Sscr4, 6, 9, 10 and 14) share homology with human chromosome 1 (Hsap1). A significant quantitative trait loci (QTL) for fat deposition has been identified on Sscr4 that appears to be near the junction region between Sscr4 and Sscr9 relative to Hsap1. It is of interest to define the boundaries of conserved synteny between pig chromosomes and Hsap1 to use human map information to identify putative comparative positional candidates for this QTL. Eleven genes, including Janus kinase 1 (JAK1), Prostaglandin E receptor3 (PTGER3), urate oxidase (UOX), coagulation factor 3 (F3), vascular cell adhesion molecule 1 (VCAM1), ribosomal protein L5 (RPL5), POU domain, class 2, transcription factor 1 (POU2F1), coagulation factor 5 (F5), Prostaglandin endoperoxide synthase-2 (PTGS2), myosin binding protein H (MYBPH) and Antithrombin III (SERPINC1), were selected to refine the boundaries of the blocks of conserved synteny between Hsap1 and pig chromosomes. Pig sequence tagged sites (STSs) were developed and used to physically map these 11 genes using a somatic cell hybrid panel. Eight loci have been mapped by using fluorescent in situ hybridization (FISH) to improve map resolution. Heterologous FISH was used to refine the location of VCAM1 on human chromosomes. In addition, human yeast artificial chromosomes (YACs) were mapped by heterologous FISH on pig metaphases to refine the boundaries of the regions of homology between Sscr4 and Sscr9 on Hsap1. Results from this study suggest the precise break in conserved synteny on Hsap1 corresponding to the Sscr4/6 and Sscr4/9 transitions are most likely on the Hsap1p22 and Hsap1q24-25 regions, respectively. Further, our data predict that Hsap1q21-24 is a candidate region for the backfat QTL localized to Sscr4.

Animals↗
PubMed2001

Radiation hybrid comparative mapping between human chromosome 17 and porcine chromosome 12 demonstrates conservation of gene order.

A comparative study of human chromosome 17 (HSA17) and pig chromosome 12 (SSC12) was conducted using both somatic cell hybrid panel (SCHP) and radiation hybrid (RH) panel analysis. Sequences from an expressed sequence tag (EST) project in pig reproduction were examined and six genes and ESTs originally believed to map to HSA17 were selected for this study. The genes/ESTs were TATA box binding protein-associated factor (TAF2N/RBP56), alpha-2-plasmin inhibitor (SERPINF2/PLI), H3 histone family 3B (H3F3B), aminopeptidase puromycin sensitive (NPEPPS), an expressed sequence tag (ESTMI015) and P311 protein (P311). The SCHP analysis mapped five genes/ESTs (TAF2N, H3F3B, SERPINF2, NPEPPS and ESTMI015) to SSC12q11-q15 and SSC12p11-p15 with 100% concordance, and assigned P311 to SSC2 (1/2q24)-q29 with 100% concordance. Radiation hybrid analysis of all six genes confirmed the SCHP mapping results, with average retention frequency of 25%. Recent human sequence data demonstrated that P311 is actually located on HSA5q. As HSA5q and SSC2q show conserved syntenic regions predicted from bi-directional painting, our P311 mapping data is consistent with these results. An expanded comparative SSC12 RH map integrating the five new type I markers and 23 previously mapped loci was established using a LOD score threshold of 4.8. The gene order of the five genes/ESTs on the SSC12 framework RH map (H3F3B-ESTMI015-NPEPPS-TAF2N-SERPINF2) is identical to the HSA17 GB4 map but with inversion of the map as conventionally drawn.

Animals↗