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G A Rohrer

Publications and source records attributed to G A Rohrer.

At least 91 records · Page 5Linked to original sources
PubMed1997

Genomic mapping of chemokine and transforming growth factor genes in swine.

Five chemokine genes, transforming growth factors alpha, beta 2 and 3 (TGFBA, TGFB-2, and TGFB-3), interleukin 8 (IL-8), and monocyte chemoattractant protein 2 (MCP-2), were mapped to porcine linkage groups on Chromosomes 3q, 10p, 7q, 8, and 12q, respectively. Restriction fragment length polymorphisms (RFLPs) for these genes were developed by Southern blot hybridization after digestion of porcine genomic DNA with BamHI and MspI (TGFBA), BamHI and PvuII (TGFB-2), HindIII (TGFB-3), BglII (IL-8), and PstI (MCP-2) and used to genotype the USDA-MARC Swine Reference Population pigs. Sufficient informative meioses, 61 (TGFBA), 58 (TGFB-2), 28 (TGFB-3), 38 (IL-8), and 156 (MCP-2), were available to pursue two-point pairwise linkage analysis with over 1,000 existing loci in the USDA-MARC genome database to establish initial linkage (LOD > 3). Multi-point analysis with CRIMAP determined the most likely order for each new marker. The assignment of the five chemokine genes in swine concurs with previous porcine/human chromosomal homologies based on results from ZOO-FISH and chromosomal painting experiments. These findings add five new informative Type I markers within a single gene family to the swine genome and may help us understand the genetic basis for disease resistance in livestock.

Animals↗
PubMed1997

Linkage assignment of eleven genes to the porcine genome.

We report comparative linkage mapping of eleven genes in the swine genome by RFLP analysis. These genes include: Acid phosphatase type 5 (ACP5), Cholecystokinin Type B Receptor (CCKBR), Antibiotic Peptide (FALL39), Insulin-like Growth Factor 1 Receptor (IGF1R), Integrin Alpha M (ITGAM), Integrin Beta 2 (ITGbeta2), Opioid Receptor Mu-1 (OPRM1), Pro-hormone Converter (PC1/3), Retinol Binding Protein 3 (RBP3), Ribosomal DNA (RNR1), and Zona Pellucida Glycoprotein 1 (ZP1). The CCKBR and ITGbeta2 loci define the ends of the linkage groups on Chromosomes (Chro) (SSC) 9p and 13qter, respectively.

Animals↗
PubMed1997

Mapping 28 erythrocyte antigen, plasma protein and enzyme polymorphisms using an efficient genomic scan of the porcine genome.

One hundred and fifty-four microsatellite markers were selected for genomic scanning of the porcine genome and were grouped into amplification sets to reduce the cost and labour required. Thirty amplification sets had two markers (duplex), 20 sets had three markers (triplex) and five sets had four markers (quadruplex) while 14 markers were analysed separately. The selection criteria for microsatellites were: ease of scoring, level of polymorphism, genetic location and ability to be genotyped in a multiplexed polymerase chain reaction (PCR). The selected microsatellites were chosen to span the entire genome flanked by the porcine linkage map with intervals between adjacent markers of 15-20 cM where possible. The utility of this set of markers was demonstrated by linkage analyses with loci controlling blood plasma protein and red cell enzyme polymorphisms (n = 13), erythrocyte antigens (n = 15), the S blood group, coat colour and ryanodine receptor from 174 backcross Meishan-White Composite pigs. These loci displayed various forms of inheritance and most (24 loci) have been placed in linkage groups. Significant two-point linkages (lod > 3.0) were detected for each polymorphic marker. These results provide the first linkage assignments for phosphoglucomutase (PGM2) and erythrocyte antigen F (EAF) to SSC8; and serum amylase (AMY) and erythrocyte antigen I (EAI) to SSC18. All of the remaining polymorphic loci (n = 24) mapped to previously identified regions confirming earlier results. Most of the markers used in this study should be useful in resource populations of various breed crosses as the number of alleles detected in a multibreed reference population was one of the selection criteria.

Animals↗
PubMed1997

Mapping genes located on human chromosomes 2 and 12 to porcine chromosomes 15 and 5.

Informative microsatellites associated with two genes on HSA12 (lysozyme, LYZ; tumour necrosis factor receptor, TNFR) and one gene on HSA2 (glutamic acid decarboxylase 1, GAD1) were mapped in the US Meat Animal Research Center (MARC) swine reference population and the physical assignment of a-lactalbumin (LALBA) was determined. A comparative map for HSA2 and HSA12 with SSC15 and SSC5, respectively, was developed by combining the results from this study with published type I loci mapped in both species. One rearrangement between HSA2 and SSC15 was detected while the number of rearrangements between HSA12 and SSC5 were numerous. These results indicated that conservation of synteny does not imply a conservation of gene order and that additional type I markers need to be mapped in the pig to fully understand the chromosomal rearrangements that occurred during the evolution of mammals.

Animals↗
PubMed1997

Evidence for quantitative trait loci affecting ovulation rate in pigs.

Fifty-five microsatellite markers were scored in an F2 population of pigs (n = 114 females) developed at the University of Nebraska. The population was produced by crossing a line previously selected for 10 generations using an index of ovulation rate and embryonal survival and a line selected at random. The lines were from a common base population and differed by 6.7 ovulations and 3.1 fetuses at 50 d of gestation. Ovulation rate and number of fully formed and mummified pigs were recorded for each female. Data were analyzed with regression models that included random animal effects. Likelihood-ratio tests were used to test for quantitative trait loci (QTL) effects by deviating the log-likelihood for the full model that included additive and dominance QTL effects from the log-likelihood for the reduced model that did not contain QTL effects. A QTL for ovulation rate was found on chromosome 8 (P < .001) with an additive effect of 3.07 ovulations. Other evidence of potential QTL affecting ovulation rate was found on chromosomes 4 (P < .10), 13, and 15 (P < .05). Effects on chromosomes 4, 13 and 15 were not significant for fan experiment-wise threshold value of P < .001. No significant QTL for litter size or number of mummified pigs were found. Additional data are needed to confirm the location and the effect of QTL found for ovulation rate before markers associated with them can be used in marker-assisted selection.

Alleles↗
PubMed1996

A comprehensive map of the porcine genome.

We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups (18 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization (FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on 11q1.7-qter and 14 cen-q1.2. Recombination rates (cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci (QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.

Animals↗
PubMed1996

Cloning and characterization of 414 polymorphic porcine microsatellites.

We report the sequences, sizes, and number of alleles of 414 new porcine microsatellites that were cloned in our laboratory and 21 microsatellites derived from GenBank DNA sequences. We also confirm the usefulness of porcine microsatellite primer pairs derived from short interdispersed elements.

Alleles↗
PubMed1995

Porcine SINE-associated microsatellite markers: evidence for new artiodactyl SINEs.

Approximately 24% (170/710) of porcine (dG-dT)n.(dC-dA)n microsatellites isolated in our laboratory are associated with a previously described porcine Short Interdispersed Element (SINE) termed PRE-1 SINE. Another 5.6% (40/710) of the microsatellites were adjacent to two previously unidentified SINE sequences, which we have designated ARE-1P (Artiodactyl Repetitive Element-1 Porcine) and ARE-2P. The ARE repeats were also found in bovine microsatellite and genomic sequences in the GenBank database. Genotypic information was obtained from 68.9% of primers where at least one primer sequence was obtained from the PRE-1 SINE and 66.6% of primer pairs designed from the ARE SINEs. The use of primers derived from SINEs significantly increases the number of primer pairs available for genetic linkage studies in swine.

Animals↗
PubMed1995

Directed integration of the physical and genetic linkage maps of swine chromosome 7 reveals that the SLA spans the centromere.

The first integrated physical and genetic linkage map encompassing the entire swine chromosome 7 (SSC7) reveals that the porcine MHC (SLA) spans the centromere. A SLA class II antigen gene lies on the q arm, whereas class I and III genes lie on the p arm, suggesting that the presence of a centromere within the SLA does not preclude a functional complex. The SLA appears smaller than other mammalian MHC, as the genetic distance across two class I, three class II, and three class III SLA gene markers is only 1.1 cM. There are significant variations in recombination rates as a function of position along the chromosome, and the SLA lies in the region with the lowest rate. Furthermore, the directed integration approach used in this study was more efficient than previous efforts that emphasized the screening of large insert libraries for random microsatellites.

Animals↗
PubMed1995

First international workshop on porcine chromosome 6. Report and abstracts.

Recent advances in the use of microsatellite markers and the development of comparative gene mapping techniques have made the construction of high resolution genetic maps of livestock species possible. Framework and comprehensive genetic linkage maps of porcine chromosome 6 have resulted from the first international effort to integrate genetic maps from multiple laboratories. Eleven highly polymorphic genetic markers were exchanged and mapped by four independent laboratories on a total of 583 animals derived from four reference populations. The chromosome 6 framework map consists of 10 markers ordered with high local support. The average marker interval of the framework map is 15.1 cM (sex averaged). The framework map is 135, 175 and 109 cM in length (for sex averaged, female and male maps, respectively). The comprehensive map includes a total of 48 type I and type II markers with a sex averaged interval of 3.5 cM and is 166, 196 and 126 cM (for sex averaged, female and male maps, respectively). Additional markers within framework map marker intervals can thus be selected from the comprehensive map for further analysis of quantitive trait loci (QTL) located on chromosome 6. The resulting maps of swine chromosome 6 provide a valuable tool for analysing and locating QTL.

Animals↗
PubMed1994

A simplified procedure for entry of raw genotypic data.

Genotypic data entry is a time-consuming and tedious task in genetic linkage studies. Success of the study is dependent upon the accuracy of the data. To simplify the process and eliminate data entry errors, we developed procedures that enable scientists to rapidly enter large quantities of data and compare the data entered with those entered by another individual. These procedures significantly reduce the time required to enter data while improving its integrity. The procedure relies on quick association of a single-digit pattern number with the visual image of an animal's genotype. This association is facilitated by a standard set of rules applicable to all possible outcomes (pseudocode provided). Fewer data entry errors are made because the procedure reduces required keystrokes by 75% and short-term memory load. These procedures have been used as independent programs operating in PC environments (programmed in FORTRAN) as well as linked with a relational database on an IBM 9377 [programmed in CSP(AE/AD) and SQL/DS].

Animals↗
PubMed1994

A conceptual database model for genomic research.

We describe a conceptual model for genome databases that facilitates the process of building, maintaining, and disseminating physically anchored genetic linkage maps. The model has been implemented as a relational database at the Roman L. Hruska U.S. Meat Animal Research Center (MARC). Development of consensus maps using disparate data from different reference pedigrees or laboratories is supported. The model is of use to quantitative and population geneticists interested in loci that affect phenotypes and marker-assisted selection, and it is sufficiently flexible for centralized, species genome databases facilitating comparative mapping. The MARC genome database is used to assemble, maintain, and disseminate physically anchored genetic linkage maps for cattle, swine, and sheep currently based on more than 100,000 genotypes from 1,000 markers. Integrated with linkage analysis software, this database permits frequent updates of physically anchored genetic linkage maps.

Algorithms↗