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J W Keele

Publications and source records attributed to J W Keele.

At least 55 records · Page 3Linked to original sources
PubMed1998

Identification of quantitative trait loci affecting carcass composition in swine: II. Muscling and wholesale product yield traits.

A genomic scan was conducted on 540 reciprocal backcross Meishan x White composite pigs for hot carcass weight (HCWT); loin eye area (LOIN); carcass length (CRCL); belly weight (BELLY); and weight of trimmed ham, loin, picnic, and Boston butt adjusted to a constant live (TWPLWT) or carcass (TWPCWT) weight. Genetic markers spanned the entire porcine linkage map and were spaced at approximately 20-cM intervals. Grandparental breed of origin for all chromosomal segments was determined using multipoint linkage procedures, and a least squares regression analysis was conducted. Nominal P-values were converted to a genome-wide level of significance to adjust for the number of tests actually conducted. Seven associations were significant at the genome-wide level relating to chromosomes 1 (SSC 1), 7 (SSC 7), and X (SSC X). The SSC 1 region affected LOIN, TWPLWT, and TWPCWT; SSC 7 affected HWCT and CRCL; and SSC X affected TWPLWT and TWPCWT. Twelve associations relating to seven chromosomal regions (including SSC 1 and X) presented suggestive evidence for quantitative trait loci (QTL), and many of these regions are likely to contain QTL. Chromosomes 8 and 14 had two and three traits with suggestive evidence for QTL, respectively. Many pleiotropic effects were detected for regions on SSC 1, 7, 14, and X in this study and a companion study looking for fat deposition QTL in the same population. In addition, SSC 4 was nearly significant for CRCL in the same region identified as affecting backfat in a wild boar x Large White population. These results expand our knowledge of the inheritance of quantitative traits and are directly relevant to composite populations containing Meishan germplasm.

Alleles↗
PubMed1997

A second-generation linkage map of the bovine genome.

We report a bovine linkage map constructed with 1236 polymorphic DNA markers and 14 erythrocyte antigens and serum proteins. The 2990-cM map consists of a sex-specific, X chromosome linkage group and 29 sex-averaged, autosomal linkage groups with an average interval size of 2.5 cM. The map contains 627 new markers and 623 previously linked markers, providing a basis for integrating the four published bovine maps. Orientation and chromosomal assignment of all the linkage groups, except BTA20 and BTA22, was provided by 88 markers that were assigned previously to chromosomes. This map provides sufficient marker density for genomic scans of populations segregating quantitative trait loci (QTL) and subsequent implementation of marker-assisted selection (MAS) mating schemes.

Animals↗
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↗
PubMed1995

A small-insert bovine genomic library highly enriched for microsatellite repeat sequences.

A bovine genomic phagemid library was constructed with randomly sheared DNA. Enrichment of this single-stranded DNA library with CA or GT primers resulted in 45% positive clones. The 14% of positive clones with (CA.GT) > 12, and not containing flanking repetitive elements, were sequenced, and the efficiency of marker production was compared with random M13 bacteriophage libraries. Primer sequences and genotyping information are presented for 390 informative bovine microsatellite markers. The genomic frequency for 11 tri- and tetranucleotide repeats was estimated by hybridization to a lambda genomic library. Only GCT, GGT, and GGAT were estimated to have a frequency of > 100 per genome. Enrichment of the phagemid library for these repeats failed to provide a viable source of microsatellite markers in the bovine. Comparison of map interval lengths between 100 markers from the enriched library prepared from randomly sheared DNA and M13 bacteriophage libraries prepared from Mbo1 restriction digests suggested no bias in skeletal genomic coverage based on source of small insert DNA. In conclusion, enrichment of the bovine phagemid library provides a sufficient source of microsatellites so that small repeat lengths and flanking repetitive sequences common in the bovine can be eliminated, resulting in a high percentage of informative markers.

Animals↗
PubMed1995

Simulated influence of postweaning production system on performance of different biological types of cattle: I. Estimation of model parameters.

Breed parameters for a computer model that simulated differences in the composition of empty-body gain of beef cattle, resulting from differences in postweaning level of nutrition that are not associated with empty BW, were estimated for 17 biological types of cattle (steers from F1 crosses of 16 sire breeds [Hereford, Angus, Jersey, South Devon, Limousin, Simmental, Charolais, Red Poll, Brown Swiss, Gelbvieh, Maine Anjou, Chianina, Brahman, Sahiwal, Pinzgauer, and Tarentaise] mated to Hereford and Angus dams). One value for the maximum fractional growth rate of fat-free matter (KMAX) was estimated and used across all breed types. Mature fat-free matter (FFMmat) was estimated from data on mature cows for each of the 17 breed types. Breed type values for a fattening parameter (THETA) were estimated from growth and composition data at slaughter on steers of the 17 breed types, using the previously estimated constant KMAX and breed values for FFMmat. For each breed type, THETA values were unique for given values of KMAX, FFMmat, and composition at slaughter. The results showed that THETA was most sensitive to KMAX and had similar sensitivity to FFMmat and composition at slaughter. Values for THETA were most sensitive for breed types with large THETA values (Chianina, Charolais, and Limousin crossbred steers) and least sensitive for breed types with small THETA values (purebred Angus, crossbred Jersey, and Red Poll steers).(ABSTRACT TRUNCATED AT 250 WORDS)

Aging↗
PubMed1995

Simulated influence of postweaning production system on performance of different biological types of cattle: II. Carcass composition, retail product, and quality.

A computer simulation model was used to characterize the response in carcass composition, retail product, and quality of steers from F1 crosses of 16 sire breeds (Hereford, Angus, Jersey, South Devon, Limousin, Simmental, Charolais, Red Poll, Brown Swiss, Gelbvieh, Maine Anjou, Chianina, Brahman, Sahiwal, Pinzgauer, and Tarentaise) mated to Hereford and Angus dams, grown under nine backgrounding systems, and finished at either a low (1.0 kg) or high (1.36 kg) ADG. The backgrounding systems were a high ADG (.9 kg) for 111, 167, or 222 d, a medium ADG (.5 kg) for 200, 300, or 400 d, a low ADG (.25 kg) for 300 or 400 d and 0 d backgrounding. For specific genotype x production system combinations, results showed that carcasses of compensating steers may be either leaner, not different in fatness, or fatter than carcasses of steers put on a finishing diet directly after weaning. Systems in which steers gained a greater proportion of the final slaughter weight over long durations of growth restriction resulted in leaner carcasses. There were 12 common production systems in which 13 of the genotypes produced a carcass with a maximum of 28% fat or with a marbling score of 11 or greater. These results suggest sire breeds used to produce these steers can be used over a wide range of nutritional and management environments, and that a mixed group of steers can be fed and managed similarly from weaning to slaughter to produce a carcass with a specified composition, retail product, or quality.

Aging↗
PubMed1995

Simulated influence of postweaning production system on performance of different biological types of cattle: III. Biological efficiency.

Methods were developed and incorporated into a previously published computer model to predict ME intake and calculate biological efficiencies in terms of grams of empty BW (EBW) and fat-free matter (FFM) gained/megacalorie of ME consumed from weaning to slaughter. Efficiencies were calculated for steers from F1 crosses of 16 sire breeds (Hereford, Angus, Jersey, South Devon, Limousin, Simmental, Charolais, Red Poll, Brown Swiss, Gelbvieh, Maine Anjou, Chianina, Brahman, Sahiwal, Pinzgauer, and Tarentaise) mated to Hereford and Angus dams, grown under nine backgrounding systems, finished at either a low (1.0 kg) or high (1.36 kg) ADG, and slaughtered at 300 kg carcass weight, small or greater degree of marbling, and 28% carcass fat. Backgrounding systems were high ADG (.9 kg) for 111, 167, or 222 d, medium ADG (.5 kg) for 200, 300, or 400 d, and low ADG (.25 kg) for 300 or 400 d, and 0 d backgrounding. The high ADG finishing system was more biologically efficient than the low ADG finishing system, and generally backgrounding systems were less biologically efficient than direct finishing after weaning (0 d backgrounding). Large-framed breeds were more efficient at the constant carcass weight and carcass fatness end point, and breeds that achieved the marbling end point at low levels of carcass fatness were more efficient at this end point. Some small-framed breeds gained EBW more efficiently but gained FFM less efficiently than some of the large-framed breeds. Variation in efficiency between genotypes was greatest with 0 d backgrounding and decreased in the other backgrounding systems.

Aging↗
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↗
PubMed1994

A microsatellite linkage map of the porcine genome.

We report the most extensive genetic linkage map for a livestock species produced to date. We have linked 376 microsatellite (MS) loci with seven restriction fragment length polymorphic loci in a backcross reference population. The 383 markers were placed into 24 linkage groups which span 1997 cM. Seven additional MS did not fall into a linkage group. Linkage groups are assigned to 13 autosomes and the X chromosome (haploid n = 19). This map provides the basis for genetic analysis of quantitative inheritance of phenotypic and physiologic traits in swine.

Animals↗
PubMed1994

A genetic linkage map for cattle.

We report the most extensive physically anchored linkage map for cattle produced to date. Three-hundred thirteen genetic markers ordered in 30 linkage groups, anchored to 24 autosomal chromosomes (n = 29), the X and Y chromosomes, four unanchored syntenic groups and two unassigned linkage groups spanning 2464 cM of the bovine genome are summarized. The map also assigns 19 type I loci to specific chromosomes and/or syntenic groups and four cosmid clones containing informative microsatellites to chromosomes 13, 25 and 29 anchoring syntenic groups U11, U7 and U8, respectively. This map provides the skeletal framework prerequisite to development of a comprehensive genetic map for cattle and analysis of economic trait loci (ETL).

Animals↗
PubMed1994

Linkage of bovine erythrocyte antigen loci B, C, L, S, Z, R' and T' and the serum protein loci post-transferrin 2 (PTF 2), vitamin D binding protein (GC) and albumin (ALB) to DNA microsatellite markers.

Seven bovine erythrocyte antigen loci and three serum protein loci were tentatively assigned to chromosomes or synteny groups by linkage analysis to previously assigned microsatellite DNA markers. The erythrocyte antigen locus EAB was mapped to synteny group U27; EAC to chromosome 18, synteny group U9; EAL to chromosome 3, synteny group U6; EAS to chromosome 21, synteny group U4; EAZ to chromosome 10, synteny group U5; EAR' to chromosome 16, synteny group U1; and EAT' to chromosome 19, synteny group U21. The vitamin D binding protein (GC) and albumin (ALB) loci were assigned to chromosome 6, synteny group U15 and post-transferrin 2 (PTF 2) to chromosome 19, synteny group U21.

Animals↗
PubMed1992

A computer model to predict empty body weight in cattle from diet and animal characteristics.

A computer model was developed to predict empty BW in cattle as a function of diet (forage NDF, physical form of forage [hay vs silage and pasture], proportion of dietary concentrates) and animal (full BW) characteristics. The model was empty BW = full BW * (1 - GFILL), where GFILL is gut fill expressed as a fraction of full BW. An equation obtained from published data (GFILL = .05354 + .329 * NDF) was used to provide a base prediction of GFILL from the fraction of NDF in the forage. Predicted GFILL was then corrected for full BW, physical form of forage, and fraction of concentrates using multiplicative factors obtained from published data. The model was evaluated with data from 11 published experiments. Several breeds of cattle, a wide range of forage types, and diets with 0 to 93% concentrates were represented in these data. Observed values for empty BW were compared to model-predicted values and to values predicted by systems published by the Agricultural Research Council (ARC) and National Research Council (NRC). Sums of squared deviations of predicted values from observed (n = 64) were 3,074, 37,327, and 25,920 for the model, ARC, and NRC systems, respectively. After fitting predicted empty BW values to observed values, proportion of concentrates and forage NDF accounted for a significant (P less than .01) amount of the residual variation with the ARC and NRC systems, but not for the model. This finding suggests that the model will predict empty BW more accurately than the ARC and NRC systems with diets similar to those used in the evaluation.

Animal Feed↗
PubMed1992

A computer model to predict the effects of level of nutrition on composition of empty body gain in beef cattle: I. Theory and development.

A computer model was developed to simulate differences in the composition of empty body gain of beef cattle resulting from differences in postweaning level of nutrition that are not associated with empty BW. Differences in rate of empty body gain of cattle of similar genotype reflect differences in the level of nutrition; hence, empty body gain was used to represent level of nutrition. The model was based on four assumptions: 1) as animals mature, the proportion of fat is greater in gain than in body weight, 2) effects on body composition caused by plane of nutrition that are not associated with empty BW are predictable from rate of empty BW gain, 3) effects resulting from changes in nutrition are not exerted immediately nor are they permanent, and 4) cattle approach an empty body composition equilibrium when empty body gain is zero. Six parameters were used to characterize mature fat-free matter, rate of change to body composition equilibrium, minimum and maximum fractional growth rate relative to fractional growth rate for empty BW, time lag of response to change in nutrition, and influence of stage of maturity and nutrition on rate of change for fat-free matter. Two parameters were specific for genotype and gender. Using results from the model, we were able to explain conflicting results obtained from compensatory gain experiments.

Adipose Tissue↗
PubMed1992

A computer model to predict the effects of level of nutrition on composition of empty body gain in beef cattle: II. Evaluation of the model.

A computer model developed to predict composition of empty body gain of beef cattle fed at different levels of nutrition was evaluated with data from one unpublished and seven published experiments. These experiments used several breeds of beef cattle growing at rates that varied from negative to fast and various combinations of these growth rates. There was close agreement between observed and simulated absolute treatment means for fatness, except when animals were fed diets low in protein. In this case, experimental animals fed inadequate protein grew at slower rates and became fatter than contemporaries fed adequate protein, whereas the model predicted the opposite. Ability of the model to predict effects of nutrition not associated with changes in BW was evaluated using the proportion of residual variation in experimental fat percentage accounted for by the model, after fitting linear and quadratic terms for empty BW. The model accounted for 13.8 to 56.2% of the residual variation in observed fatness in four experiments in which significant differences in fatness were observed among nutritional treatments after accounting for differences in empty BW. Regression of observed fatness on model-simulated fatness resulted in regression coefficients that were positive and close to 1 in these four experiments. This suggests that the model can accurately predict some of the effects of nutrition on fatness that are not associated with changes in empty BW.

Adipose Tissue↗
PubMed1991

Comparison of methods of estimating variance components in pigs.

Components of variance due to average effects of genes (sigma 2g), environmental effects common to littermates (sigma 2c), and environmental effects peculiar to individual pigs (sigma 2e) were estimated (--) by the Pseudo Expectation Approach (PE). Data were litter size (LS), backfat (BF; centimeter) and ADG (kilograms/day) collected from the Nebraska Gene Pool swine population between 1967 and 1986. Mean square errors (MSE) for h--2 and c--2 (sigma--2g and sigma--2c divided by phenotypic variance) by PE and nested ANOVA and h2 estimated by offspring on parent regression (REGOP) were evaluated using simulation of 200 repetitions of the Nebraska Gene Pool population. Parameter values for sigma 2g, sigma 2c, and sigma 2e used in simulations were PE estimates from the Gene Pool population. Estimates of h2 from PE were .18 +/- .06 for LS, .56 +/- .06 for BF, and .16 +/- .05 for ADG. Estimates of c2 from PE were .01 +/- .03 for LS, .09 +/- .02 for BF, and .19 +/- .03 for ADG. Compared with REGOP, PE yielded h--2 with smaller MSE for BF and ADG and larger MSE for LS. The MSE of PE was smaller than the MSE of the nested ANOVA estimate for all estimates and traits. These results were interpreted to suggest that considerable gains in precision in estimation of genetic parameters could be achieved by accounting for all relationships in lieu of accounting for only half- and full-sib relationships or parent-offspring relationships.

Adipose Tissue↗