Publications by authors named "John W Keele"

37 Publications

Genetic changes in beef cow traits following selection for calving ease.

Transl Anim Sci 2021 Jan 27;5(1):txab009. Epub 2021 Jan 27.

USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE.

One approach to reducing calving difficulty is to select heifers with higher breeding value for calving ease. Calving ease is often associated with lower birth weight and that may result in other possible effects on lifetime productivity. Females from experimental select and control calving ease lines within each of the seven populations were compared. Random samples of 720 heifers from lines selected for better calving ease breeding values and 190 heifers from control lines selected for average birth weights were followed through four parities. Select and control lines within the same population were selected to achieve similar yearling weight breeding values. Weights of sampled heifers in select lines were 2.6 kg ( < 0.01) lighter at birth but not different from control lines at weaning. Select lines had significantly shorter hip height, lighter mature weight, and greater calving success at second parity. Their calves were born significantly earlier with lighter weights and less assistance. Significant interactions with parity showed fewer calves assisted and greater calf survival to weaning as heifers but negligible differences with control lines in later parities. Steer progeny sampled from these dams in select lines ( = 204) were not different from steers in control lines ( = 91) for hot carcass weight but had significantly greater fat depth. Two production systems were compared considering the seven populations as replicates. The systems differed in selection history of females (select and control lines) and the use of bulls within their lines as young cows, but used the same bulls in both lines as older cows. Cows were culled after single unsuccessful breeding and kept for up to four parities. Select line cows tended ( ≤ 0.10) to wean more calves and stay in the herd longer. They were assisted significantly fewer times at calving and had greater calf weight gain to weaning when evaluated over their herd life. Mature weights were lighter in select lines, but marketable cow weight from the systems was nearly identical. Control lines did have more marketable young cow weight and select lines older cow weight. Weaned calf weight per heifer starting the system was significantly greater for the select heifer system due to greater survival of calves from heifers and greater calving success at second parity. No important unfavorable effects of genetic differences in calving ease were identified in this experiment.
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http://dx.doi.org/10.1093/tas/txab009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906445PMC
January 2021

Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts.

Front Genet 2021 5;12:635846. Epub 2021 Feb 5.

Department of Animal Science, South Dakota State University, Brookings, SD, United States.

Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. The objective of this study was to determine accuracy of pool construction of blood samples based on white blood cell counts compared to two common DNA quantification methods. Fifty individual bovine blood samples were collected, and then pooled with all individuals represented in each pool. Pools were constructed with the target of equal representation of each individual animal based on number of white blood cells, spectrophotometric readings, spectrofluorometric readings, and whole blood volume with 9 pools per method and a total of 36 pools. Pools and individual samples that comprised the pools were genotyped using a commercially available genotyping array. ASReml was used to estimate variance components for individual animal contribution to pools. The correlation between animal contributions between two pools was estimated using bivariate analysis with starting values set to the result of a univariate analysis. Adonis test on distance matrix from the animal correlation showed clustering with method, and higher correlations between methods than within ( < 1 × 10). White blood cell count was predictive of sample representation when compared to pooling based on DNA concentration. Therefore, constructing pools using white blood cell counts prior to DNA extraction may reduce cost associated with DNA extraction and genotyping and improve representation of individuals in a pool.
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http://dx.doi.org/10.3389/fgene.2021.635846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893106PMC
February 2021

Development, selection criteria, and performance of Composite IV sheep at the U.S. Meat Animal Research Center.

Transl Anim Sci 2020 Dec 22;4(Suppl 1):S150-S154. Epub 2020 Dec 22.

USDA, ARS, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE.

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http://dx.doi.org/10.1093/tas/txaa125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7754236PMC
December 2020

Genetic and nongenetic factors influencing ewe prolificacy and lamb body weight in a closed Romanov flock.

J Anim Sci 2020 Sep;98(9)

Genetics, Breeding, and Animal Health Research Unit, Roman L. Hruska U.S. Meat Animal Research Center, USDA, ARS, Clay Center, Nebraska.

The U.S. Meat Animal Research Center was the first entity in the United States to import the Romanov breed and it has been maintained as a closed flock for over 30 yr. Incorporating this super-prolific breed into crossbred and composite populations has resulted in large improvements in ewe productivity. However, few have quantified factors contributing to genetic and nongenetic variation in ewe reproduction and lamb growth within purebred Romanov populations, which were the objectives of this study. The pedigree contained a total of 8,683 lambs born to 218 and 1,600 unique sires and dams, respectively. Number of lambs born on a per ewe exposed (NLBE) and lambing (NLBL) basis were analyzed in univariate repeatability animal models. As expected, the proportion of phenotypic variance (σP2) in litter size attributable to additive genetic (0.06 to 0.08) and permanent environmental (0.05 to 0.07) effects of the ewe was low. The service sire permanent environmental effect contributed to a small but significant amount of σP2 in NLBE (0.03) but not NLBL. However, the service sire additive genetic effect did not influence σP2 in NLBE or NLBL. Lamb body weight was recorded at birth (BWB) and upon weaning from either milk replacer (~30 d; BWW-N) or their dam (~60 d; BWW-D) and were analyzed in a three-trait model with random additive direct and maternal effects. Estimated direct heritabilities were low for all body weight (BW) traits (0.07 to 0.10). Maternal heritability was moderate for BWB (0.34) but low for weaning BW (0.11 to 0.18). This was the first to report direct and maternal genetic correlations between BW of nursery- and dam-reared lambs, and both were estimated to be moderate (0.43 to 0.47). Additionally, the direct and maternal effects of BWB were more strongly correlated with BWW-N (0.74 to 0.82) than BWW-D (0.17 to 0.33). Despite inbreeding coefficients having increased at a rate of 0.33% per birth year (1986 to 2019) in this flock, they were not consistently associated with reductions in ewe or lamb performance. Parameter estimates generally agreed with those from less-prolific breeds, and results indicate that selection can be an effective means of improving subcomponents of ewe productivity.
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http://dx.doi.org/10.1093/jas/skaa283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7511059PMC
September 2020

Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing.

PLoS One 2020 13;15(7):e0235498. Epub 2020 Jul 13.

USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America.

Surveys of microbial populations in environmental niches of interest often utilize sequence variation in the gene encoding the ribosomal small subunit (the 16S rRNA gene). Generally, these surveys target the 16S genes using semi-degenerate primers to amplify portions of a subset of bacterial species, sequence the amplicons in bulk, and assign to putative taxonomic categories by comparison to databases purporting to connect specific sequences in the main variable regions of the gene to specific organisms. Due to sequence length constraints of the most popular bulk sequencing platforms, the primers selected amplify one to three of the nine variable regions, and taxonomic assignment is based on relatively short stretches of sequence (150-500 bases). We demonstrate that taxonomic assignment is improved through reduced unassigned reads by including a survey of near-full-length sequences specific to the target environment, using a niche of interest represented by the upper respiratory tract (URT) of cattle. We created a custom Bovine URT database from these longer sequences for assignment of shorter, less expensive reads in comparisons of the upper respiratory tract among individual animals. This process improves the ability to detect changes in the microbial populations of a given environment, and the accuracy of defining the content of that environment at increasingly higher taxonomic resolution.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0235498PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357769PMC
September 2020

Digestive tract microbiota of beef cattle that differed in feed efficiency.

J Anim Sci 2020 Feb;98(2)

U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE.

We hypothesized cattle that differed in BW gain had different digestive tract microbiota. Two experiments were conducted. In both experiments, steers received a diet that consisted of 8.0% chopped alfalfa hay, 20% wet distillers grain with solubles, 67.75% dry-rolled corn, and 4.25% vitamin/mineral mix (including monensin) on a dry matter basis. Steers had ad libitum access to feed and water. In experiment 1, 144 steers (age = 310 ± 1.5 d; BW = 503 ± 37.2 kg) were individually fed for 105 d. Ruminal digesta samples were collected from eight steers with the greatest (1.96 ± 0.02 kg/d) and eight steers with the least ADG (1.57 ± 0.02 kg/d) that were within ±0.32 SD of the mean (10.1 ± 0.05 kg/d) dry matter. In experiment 2, 66 steers (age = 396 ± 1 d; BW = 456 ± 5 kg) were individually fed for 84 d. Rumen, duodenum, jejunum, ileum, cecum, and colon digesta samples were collected from eight steers with the greatest (2.39 ± 0.06 kg/d) and eight steers with the least ADG (1.85 ± 0.06 kg/d) that were within ±0.55 SD of the mean dry matter intake (11.9 ± 0.1 kg/d). In both studies, DNA was isolated and the V1 to V3 regions of the 16S rRNA gene were sequenced. Operational taxonomic units were classified using 0.03 dissimilarity and identified using the Greengenes 16S rRNA gene database. In experiment 1, there were no differences in the Chao1, Shannon, Simpson, and InvSimpson diversity indexes or the permutation multivariate analysis of variance (PERMANOVA; P = 0.57). The hierarchical test returned six clades as being differentially abundant between steer classifications (P < 0.05). In experiment 2, Chao1, Shannon, Simpson, and InvSimpson diversity indexes and PERMANOVA between steer classified as less or greater ADG did not differ (P > 0.05) for the rumen, duodenum, ileum, cecum, and colon. In the jejunum, there tended to be a difference in the Chao1 (P = 0.09) and Simpson diversity (P = 0.09) indexes between steer classifications, but there was no difference in the Shannon (P = 0.14) and InvSimpson (P = 0.14) diversity indexes. Classification groups for the jejunum differed (P = 0.006) in the PERMANOVA. The hierarchical dependence false discovery rate procedure returned 11 clades as being differentially abundant between steer classifications in the jejunum (P < 0.05). The majority of the OTU were in the Families Corynebacteriaceae and Coriobacteriaceae. This study suggests that intestinal differences in the microbiota of ruminants may be associated with animal performance.
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http://dx.doi.org/10.1093/jas/skaa008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297442PMC
February 2020

Microbiome of the upper nasal cavity of beef calves prior to weaning12.

J Anim Sci 2019 May;97(6):2368-2375

USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE.

Disease incidence is intimately associated with an animal's commensal bacteria populations (microbiome), as microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. An understanding of the animal's resident respiratory pathogens, in the upper nasal cavity prior to weaning, may help us to understand the impact of these pathogens on incidence of respiratory disease. For this research, the overall goal was to characterize bacterial populations associated with calves at an early age and through time periods prior to weaning in 3 herds at the U.S. Meat Animal Research Center. Nasal swabs from the upper nasal cavity were collected at initial vaccination (approximately 40 d of age), preconditioning (approximately 130 d of age), and weaning (approximately 150 d of age) in 2015 and 2016. DNA was extracted from nasal swabs and combined into 2 pools of 10 animals for each sampling time point, in each herd, for a total of 6 pools at each sampling time point and 18 pools for all sampling time points within each year. To evaluate and compare the microbiome of each pooled sample, hypervariable regions 1 through 3 along the 16S ribosomal RNA (rRNA) gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. Alpha and beta diversity were also measured. Overall, microbial communities were different between combinations of sampling year, herd location, and sampling time prior to weaning as shown by beta diversity. Analysis of these specific respiratory pathogens prior to weaning will present a clearer picture of the distribution of microbial populations in animals prior to weaning and not exhibiting clinical signs of respiratory disease. Therefore, evaluation of the animal's resident bacterial populations in the upper nasal cavity during different phases of the beef production system may help us to understand the impact of the microbiome on incidence of respiratory disease in cattle.
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http://dx.doi.org/10.1093/jas/skz119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6541832PMC
May 2019

Animal and plant factors which affect larkspur toxicosis in cattle: Sex, age, breed, and plant chemotype.

Toxicon 2019 Jul 25;165:31-39. Epub 2019 Apr 25.

USDA-ARS, Poisonous Plant Research Laboratory, Logan, UT 84341, United States.

Larkspur (Delphinium spp.) poisoning is a long-term problem for cattle grazing on rangelands of western North America. Recent research has shown that both plant and animal-based factors are critical in understanding and mitigating larkspur poisoning in cattle. Non-toxicological factors including sex, age, cattle breed, and plant chemotype affect cattle responses to larkspur. For example, Angus heifers are more susceptible to larkspur intoxication than are steers or bulls. Young cattle appear to be more susceptible to larkspur poisoning than mature animals. Beef breeds of cattle are more susceptible to larkspur intoxication than dairy breeds. In addition to animal factors, plant alkaloid composition (chemotype) affects the potential toxicity for cattle because of differences in the ratios and concentrations of highly toxic N-(methylsuccinimido) anthranoyllycoctonine (MSAL)-type alkaloids compared to less lethal non-MSAL-type alkaloids. Animal- and plant-based factors can provide substantial information to inform livestock producers on management to reduce risk and cattle losses to various larkspur species in western North America.
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http://dx.doi.org/10.1016/j.toxicon.2019.04.013DOI Listing
July 2019

Sex-dependent differences for larkspur (Delphinium barbeyi) toxicosis in yearling Angus cattle1.

J Anim Sci 2019 Mar;97(3):1424-1432

USDA-ARS, Poisonous Plant Research Laboratory, Logan, UT.

Larkspur (Delphinium spp.) poisoning is a long-term problem for cattle grazing on rangelands of western North America. Results from preliminary experiments have suggested that differences in larkspur toxicity may exist between heifers and bulls. The objective of this study was to compare the physiological responses of yearling Angus heifers, steers, and bulls with a standardized dose of Delphinium barbeyi and to test the hypothesis that the response is sex dependent. Clinical signs of intoxication, including muscle coordination and function, were measured 24 h after oral dosing with larkspur by walking the cattle at a pace of 5 to 6 km h-1 for up to 40 min on an oval dirt track. Due to the experimental methods used, the variation in susceptibility to larkspur was not quantifiable for walking times of 0 or 40 min or more. Larkspur susceptible animals that were not able to walk (0 min; 36% of the animals) or larkspur resistant animals that walked the entire test period of 40 min (9% of the animals) resulted in censored or truncated data. The statistical methods (censReg and lmec) were used to adjust for data truncation or censoring. The heifers were only able to walk -8.9 ± 3.9 min (65.5% censored on the left) compared with 13.2 ± 3.7 min for bulls and 15.9 ± 2.7 min for steers. When heifers were compared with bulls and steers together, heifers walked 23.4 ± 4.5 min less (P < 0.0001). Serum alkaloid concentrations were measured immediately before walking, and deltaline concentrations averaged 266 ± 28, 131 ± 20, and 219 ± 28 ng mL-1 for all heifers, steers, and bulls, respectively, and serum methyllycaconitine concentrations averaged 660 ± 46, 397 ± 32, and 612 ± 34 ng mL-1 for all heifers, steers, and bulls, respectively. The relative risk of a zero walk time for yearling heifers is 330% that of yearling bulls (P = 0.0008). These results suggest that yearling Angus heifers are more susceptible to larkspur intoxication and, when possible, heifers should be kept from grazing larkspur-infested rangelands as a simple management tool to reduce the risk of fatal poisoning.
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http://dx.doi.org/10.1093/jas/skz002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396263PMC
March 2019

Complete blood count data and leukocyte expression of cytokine genes and cytokine receptor genes associated with bovine respiratory disease in calves.

BMC Res Notes 2018 Nov 3;11(1):786. Epub 2018 Nov 3.

USDA, ARS, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, NE, 68933, USA.

Objective: The purpose of this study was to evaluate potential relationships between cytokine gene expression, complete blood counts (CBC) and animals that were sick or would become sick. The CBC and the transcript abundance of cytokines and their receptors expressed in leukocytes were measured from calves at two early timepoints, and again after diagnosis with bovine respiratory disease (BRD).

Results: Blood was collected from calves at pre-conditioning (n = 796) and weaning (n = 791) for CBC. Blood counts were also measured for the calves with BRD (n = 13), and asymptomatic calves (n = 75) after weaning. The CBC were compared for these animals at 3 time points. At diagnosis, neutrophils were higher and basophils lower in sick animals (P < 0.05). To further characterize BRD responses, transcript abundance of 84 cytokine genes were evaluated in 5 calves with BRD and 9 asymptomatic animals at all time points. There was more data for CBC than transcript abundance; hence, animal and temporary environmental correlations between CBC and transcript abundance were exploited to improve the power of the transcript abundance data. Expression of CCL16, CXCR1, CCR1 was increased in BRD positive animals compared to controls (P-corrected < 0.1). Cytokine expression data may help to provide insight into an animal's health.
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http://dx.doi.org/10.1186/s13104-018-3900-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6215650PMC
November 2018

RNA-Seq Meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers.

BMC Genomics 2018 Jun 4;19(1):430. Epub 2018 Jun 4.

USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.

Background: Feed intake and body weight gain are economically important inputs and outputs of beef production systems. The purpose of this study was to discover differentially expressed genes that will be robust for feed intake and gain across a large segment of the cattle industry. Transcriptomic studies often suffer from issues with reproducibility and cross-validation. One way to improve reproducibility is by integrating multiple datasets via meta-analysis. RNA sequencing (RNA-Seq) was performed on longissimus dorsi muscle from 80 steers (5 cohorts, each with 16 animals) selected from the outside fringe of a bivariate gain and feed intake distribution to understand the genes and pathways involved in feed efficiency. In each cohort, 16 steers were selected from one of four gain and feed intake phenotypes (n = 4 per phenotype) in a 2 × 2 factorial arrangement with gain and feed intake as main effect variables. Each cohort was analyzed as a single experiment using a generalized linear model and results from the 5 cohort analyses were combined in a meta-analysis to identify differentially expressed genes (DEG) across the cohorts.

Results: A total of 51 genes were differentially expressed for the main effect of gain, 109 genes for the intake main effect, and 11 genes for the gain x intake interaction (P < 0.05). A jackknife sensitivity analysis showed that, in general, the meta-analysis produced robust DEGs for the two main effects and their interaction. Pathways identified from over-represented genes included mitochondrial energy production and oxidative stress pathways for the main effect of gain due to DEG including GPD1, NDUFA6, UQCRQ, ACTC1, and MGST3. For intake, metabolic pathways including amino acid biosynthesis and degradation were identified, and for the interaction analysis the pathways identified included GADD45, pyridoxal 5'phosphate salvage, and caveolar mediated endocytosis signaling.

Conclusions: Variation among DEG identified by cohort suggests that environment and breed may play large roles in the expression of genes associated with feed efficiency in the muscle of beef cattle. Meta-analyses of transcriptome data from groups of animals over multiple cohorts may be necessary to elucidate the genetics contributing these types of biological phenotypes.
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http://dx.doi.org/10.1186/s12864-018-4769-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987596PMC
June 2018

Genetic variation in humoral response to an Escherichia coli O157:H7 vaccine in beef cattle.

PLoS One 2018 14;13(5):e0197347. Epub 2018 May 14.

Department of Animal Science, South Dakota State University, Brookings, South Dakota, United States of America.

Individuals often respond differently to the same vaccine; some of this variation may be caused by genetic differences among animals. Our objective was to estimate heritability and identify genomic regions associated with humoral response to an Escherichia coli O157:H7 vaccine in beef cattle. Crossbred beef cattle (n = 651) were vaccinated with a commercially available E. coli O157:H7 vaccine. Serum was collected at time of initial vaccination (d 0), booster (d 21), and d 56 after initial vaccination. Total antibodies specific to siderophore receptor and porin proteins in the vaccine were quantified by enzyme-linked immunosorbent assay. Genomic DNA was isolated from whole blood and genotyped with the bovine GeneSeek Genomic Profiler-High Density 78K or 26K Single Nucleotide Polymorphism BeadChip and imputed to 777,000 SNP genotypes. Heritability was estimated by restricted maximum likelihood (REML) using both 1) pedigree and 2) genomic relationships among individuals. Fixed effects were contemporary group, calf age, sex, principal components from SNP genotype data, and pedigree-derived heterozygosity effects. Additive and dominance effects of SNPs were estimated individually while accounting for contemporary group, sex, and the top 20 principal components calculated from the genomic relationship matrix. Heritability of initial response to vaccination (d 21 -d 0) was 0.10 ± 0.175 using pedigree relationships and 0.14 ± 0.149 using genomic relationships, but neither estimate was statistically different from zero. Heritability of booster (d 56 -d 21) and overall (d 56 -d 0) responses were low and not statistically significant from zero. There were no clusters of linked SNP associated with vaccine response, but eight regionally isolated SNPs were significantly associated with initial or overall response to vaccination. Regional genetic variation for initial response to an E. coli O157:H7 vaccine was observed, although overall heritability of this response was not statistically significant from zero.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197347PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5951538PMC
December 2018

Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC).

J Anim Sci 2018 Apr 12. Epub 2018 Apr 12.

USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE.

Bovine respiratory disease complex (BRDC) is a multifactor disease, and disease incidence may be associated with an animal's commensal bacterial populations (microbiome) in the upper nasal cavity. Identifying these commensal bacterial populations in the upper nasal cavity may help us to understand the impact of the microbiome on incidence of BRDC in cattle. Various sampling techniques have previously been utilized to evaluate the microbiome of different locations of the upper nasal cavity in cattle. Therefore, our objective was to determine whether bacterial populations of the nasal cavity vary based on these sampling locations. Two common sampling techniques were evaluated, including 6-inch nasal swabs and deep nasopharyngeal swabs. Nasal swabs from calves were collected when the animal was diagnosed with BRDC after weaning in the feedlot in addition to collection of samples from asymptomatic cohorts. Samples were pooled in groups based on year the animal was in the feedlot (2015 or 2016), when the animal was diagnosed with BRDC (1 to 5 weeks after weaning), type of sample (6-inch nasal swab or deep nasopharyngeal swab), and health status (diagnosis with BRDC or control). Variable regions 1 through 3 along the 16S rRNA gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. Overall, sampling site did not consistently influence diversity of the bacterial populations of the upper nasal cavity. However, the effect of disease incidence on the microbiome was depended on sampling time after weaning (P = 0.0462) for 2015, while the main effects of sampling time after weaning (P = 0.00992) and disease phenotype (P = 0.012) were significant for 2016. These data for 2016 demonstrate that in addition to bacterial profiles changing throughout weaning, calves diagnosed with BRDC have different bacterial profiles compared to their control cohorts. In addition, evaluation of the microbiome identified predominant bacteria genera in the upper nasal cavity included those previously reported to be associated with cattle diagnosed with BRDC including Mycoplasma sp., Psychrobacter sp., and Mannheimia sp. In summary, these results demonstrate that shorter, less invasive 6-inch nasal swabs produce similar results to deep nasopharyngeal swabs.
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http://dx.doi.org/10.1093/jas/sky032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6140963PMC
April 2018

Transcriptome differences in the rumen of beef steers with variation in feed intake and gain.

Gene 2016 Jul 29;586(1):12-26. Epub 2016 Mar 29.

Department of Animal Science, University of Wyoming, Laramie, WY 82070, USA. Electronic address:

Background: Feed intake and gain are economically important traits in beef production. The rumen wall interacts with feed, microbial populations, and fermentation products important to cattle nutrition. As such, it is likely to be a critical component in the beef steer's ability to utilize feedstuffs efficiently. To identify genes associated with steer feed intake and body weight gain traits, and to gain an understanding of molecules and pathways involved in feed intake and utilization, RNA sequencing (RNA-Seq) was performed on rumen papillae from 16 steers with variation in gain and feed intake. Four steers were chosen from each of the four Cartesian quadrants for gain×feed intake and used to generate individual RNA-Seq libraries.

Results: Normalized read counts from all of the mapped reads from each of the four groups of animals were individually compared to the other three groups. In addition, differentially expressed genes (DEGs) between animals with high and low gain, as well as high and low intake were also evaluated. A total of 931 genes were differentially expressed in the analyses of the individual groups. Eighty-nine genes were differentially expressed between high and low gain animals; and sixty-nine were differentially expressed in high versus low intake animals. Several of the genes identified in this study have been previously associated with feed efficiency. Among those are KLK10, IRX3, COL1A1, CRELD2, HDAC10, IFITM3, and VIM.

Conclusions: Many of the genes identified in this study are involved with immune function, inflammation, apoptosis, cell growth/proliferation, nutrient transport, and metabolic pathways and may be important predictors of feed intake and gain in beef cattle.
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http://dx.doi.org/10.1016/j.gene.2016.03.034DOI Listing
July 2016

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds.

Front Genet 2013 18;4:176. Epub 2013 Sep 18.

Bovine Functional Genomics Laboratory, BARC, Agriculture Research Service, United States Department of Agriculture Beltsville, MD, USA.

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.
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http://dx.doi.org/10.3389/fgene.2013.00176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776237PMC
September 2013

Gene number determination and genetic polymorphism of the gamma delta T cell co-receptor WC1 genes.

BMC Genet 2012 Oct 16;13:86. Epub 2012 Oct 16.

Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA.

Background: WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR) superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1(+) γδ T cells. We have previously identified partial or complete genomic sequences for thirteen different WC1 genes through annotation of the bovine genome Btau_3.1 build. We also identified two WC1 cDNA sequences from other cattle that did not correspond to sequences in the Btau_3.1 build. Their absence in the Btau_3.1 build may have reflected gaps in the genome assembly or polymorphisms among animals. Since the response of γδ T cells to bacterial challenge is determined by WC1 gene expression, it was critical to understand whether individual cattle or breeds differ in the number of WC1 genes or display polymorphisms.

Results: Real-time quantitative PCR using DNA from the animal whose genome was sequenced ("Dominette") and sixteen other animals representing ten breeds of cattle, showed that the number of genes coding for WC1 co-receptors is thirteen. The complete coding sequences of those thirteen WC1 genes is presented, including the correction of an error in the WC1-2 gene due to mis-assembly in the Btau_3.1 build. All other cDNA sequences were found to agree with the previous annotation of complete or partial WC1 genes. PCR amplification and sequencing of the most variable N-terminal SRCR domain (domain 1 which has the SRCR "a" pattern) of each of the thirteen WC1 genes showed that the sequences are highly conserved among individuals and breeds. Of 160 sequences of domain 1 from three breeds of cattle, no additional sequences beyond the thirteen described WC1 genes were found. Analysis of the complete WC1 cDNA sequences indicated that the thirteen WC1 genes code for three distinct WC1 molecular forms.

Conclusion: The bovine WC1 multi-gene family is composed of thirteen genes coding for three structural forms whose sequences are highly conserved among individual cattle and breeds. The sequence diversity necessary for WC1 genes to function as a multi-genic pattern recognition receptor array is encoded in the genome, rather than generated by recombinatorial diversity or hypermutation.
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http://dx.doi.org/10.1186/1471-2156-13-86DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511184PMC
October 2012

Genomic regions associated with kyphosis in swine.

BMC Genet 2010 Dec 21;11:112. Epub 2010 Dec 21.

USDA, ARS, U,S, Meat Animal Research Center, Clay Center, NE 68933-0166, USA.

Background: A back curvature defect similar to kyphosis in humans has been observed in swine herds. The defect ranges from mild to severe curvature of the thoracic vertebrate in split carcasses and has an estimated heritability of 0.3. The objective of this study was to identify genomic regions that affect this trait.

Results: Single nucleotide polymorphism (SNP) associations performed with 198 SNPs and microsatellite markers in a Duroc-Landrace-Yorkshire resource population (U.S. Meat Animal Research Center, USMARC resource population) of swine provided regions of association with this trait on 15 chromosomes. Positional candidate genes, especially those involved in human skeletal development pathways, were selected for SNP identification. SNPs in 16 candidate genes were genotyped in an F2 population (n = 371) and the USMARC resource herd (n = 1,257) with kyphosis scores. SNPs in KCNN2 on SSC2, RYR1 and PLOD1 on SSC6 and MYST4 on SSC14 were significantly associated with kyphosis in the resource population of swine (P ≤ 0.05). SNPs in CER1 and CDH7 on SSC1, PSMA5 on SSC4, HOXC6 and HOXC8 on SSC5, ADAMTS18 on SSC6 and SOX9 on SSC12 were significantly associated with the kyphosis trait in the F2 population of swine (P ≤ 0.05).

Conclusions: These data suggest that this kyphosis trait may be affected by several loci and that these may differ by population. Carcass value could be improved by effectively removing this undesirable trait from pig populations.
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http://dx.doi.org/10.1186/1471-2156-11-112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018398PMC
December 2010

An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation.

Genome Biol 2010 20;11(10):R102. Epub 2010 Oct 20.

USDA-ARS US Meat Animal Research Center, State Spur 18 D, Clay Center, NE 68901, USA.

Background: A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines.

Results: The Bovine Gene Atlas was generated from 7.2 million unique digital gene expression tag sequences (300.2 million total raw tag sequences), from which 1.59 million unique tag sequences were identified that mapped to the draft bovine genome accounting for 85% of the total raw tag abundance. Filtering these tags yielded 87,764 unique tag sequences that unambiguously mapped to 16,517 annotated protein-coding loci in the draft genome accounting for 45% of the total raw tag abundance. Clustering of tissues based on tag abundance profiles generally confirmed ontology classification based on anatomy. There were 5,429 constitutively expressed loci and 3,445 constitutively expressed unique tag sequences mapping outside annotated gene boundaries that represent a resource for enhancing current gene models. Physical measures such as inferred transcript length or antisense tag abundance identified tissues with atypical transcriptional tag profiles. We report for the first time the tissue-specific variation in the proportion of mitochondrial transcriptional tag abundance.

Conclusions: The Bovine Gene Atlas is the deepest and broadest transcriptome survey of any livestock genome to date. Commonalities and variation in sense and antisense transcript tag profiles identified in different tissues facilitate the examination of the relationship between gene expression, tissue, and gene function.
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http://dx.doi.org/10.1186/gb-2010-11-10-r102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218658PMC
June 2011

Analysis of copy number variations among diverse cattle breeds.

Genome Res 2010 May 8;20(5):693-703. Epub 2010 Mar 8.

USDA-ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA.

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or approximately 1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.
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http://dx.doi.org/10.1101/gr.105403.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860171PMC
May 2010

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Science 2009 Apr;324(5926):522-8

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

A sequencing strategy for identifying variation throughout the prion gene of BSE-affected cattle.

BMC Res Notes 2008 Jun 23;1:32. Epub 2008 Jun 23.

United States Department of Agriculture (USDA), Agricultural Research Service (ARS), US Meat Animal Research Center (USMARC), Clay Center, NE 68933, USA.

Background: Classical and atypical bovine spongiform encephalopathies (BSEs) are cattle prion diseases. Distinct bovine prion gene (PRNP) alleles have been associated with classical and atypical BSE susceptibility. However, the full extent of PRNP allele association with BSE susceptibility is not known. A systematic sequence-based genotyping method that detects variation throughout PRNP would be useful for: 1) detecting rare PRNP alleles that may be present in BSE-affected animals and 2) testing PRNP alleles for an association with either classical or atypical BSE susceptibility.

Findings: We improved a Sanger-based sequencing strategy for detecting bovine PRNP variation through all exons, introns, and part of the promoter (25.2 kb). Our current method can detect 389 known and other potentially unknown PRNP polymorphisms that may be present in BSE-affected cattle. We determined PRNP genotypes for the first U.S. BSE case and her sire. Previously unknown PRNP polymorphisms were not detected in either animal and all PRNP genotypes support the sire-daughter relationship.

Conclusion: The methodologies described here characterize variation throughout PRNP. Consequently, rare PRNP alleles that may be present in BSE-affected cattle can be detected.
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http://dx.doi.org/10.1186/1756-0500-1-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525647PMC
June 2008

Prevalence of the prion protein gene E211K variant in U.S. cattle.

BMC Vet Res 2008 Jul 14;4:25. Epub 2008 Jul 14.

USDA, ARS, U, S, Meat Animal Research Center (USMARC), State Spur 18D, P.O. Box 166, Clay Center, NE 68933, USA.

Background: In 2006, an atypical U.S. case of bovine spongiform encephalopathy (BSE) was discovered in Alabama and later reported to be polymorphic for glutamate (E) and lysine (K) codons at position 211 in the bovine prion protein gene (Prnp) coding sequence. A bovine E211K mutation is important because it is analogous to the most common pathogenic mutation in humans (E200K) which causes hereditary Creutzfeldt - Jakob disease, an autosomal dominant form of prion disease. The present report describes a high-throughput matrix-associated laser desorption/ionization-time-of-flight mass spectrometry assay for scoring the Prnp E211K variant and its use to determine an upper limit for the K211 allele frequency in U.S. cattle.

Results: The K211 allele was not detected in 6062 cattle, including those from five commercial beef processing plants (3892 carcasses) and 2170 registered cattle from 42 breeds. Multiple nearby polymorphisms in Prnp coding sequence of 1456 diverse purebred cattle (42 breeds) did not interfere with scoring E211 or K211 alleles. Based on these results, the upper bounds for prevalence of the E211K variant was estimated to be extremely low, less than 1 in 2000 cattle (Bayesian analysis based on 95% quantile of the posterior distribution with a uniform prior).

Conclusion: No groups or breeds of U.S. cattle are presently known to harbor the Prnp K211 allele. Because a carrier was not detected, the number of additional atypical BSE cases with K211 will also be vanishingly low.
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http://dx.doi.org/10.1186/1746-6148-4-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478677PMC
July 2008

A physical map of the bovine genome.

Genome Biol 2007 ;8(8):R165

USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA.

Background: Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project.

Results: A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly.

Conclusion: Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.
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http://dx.doi.org/10.1186/gb-2007-8-8-r165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374996PMC
February 2008

Novel porcine repetitive elements.

BMC Genomics 2006 Dec 1;7:304. Epub 2006 Dec 1.

USDA, ARS U, S, Meat Animal Research Center, Clay Center, NE, USA.

Background: Repetitive elements comprise approximately 45% of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression and by affecting genomic size, diversity and evolution. The ubiquity and increasingly understood importance of repetitive elements contribute to the need to identify and annotate them. We set out to identify previously uncharacterized repetitive DNA in the porcine genome. Once found, we characterized the prevalence of these repeats in other mammals.

Results: We discovered 27 repetitive elements in 220 BACs covering 1% of the porcine genome (Comparative Vertebrate Sequencing Initiative; CVSI). These repeats varied in length from 55 to 1059 nucleotides. To estimate copy numbers, we went to an independent source of data, the BAC-end sequences (Wellcome Trust Sanger Institute), covering approximately 15% of the porcine genome. Copy numbers in BAC-ends were less than one hundred for 6 repeat elements, between 100 and 1000 for 16 and between 1,000 and 10,000 for 5. Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor. None of the repeat elements were found in primate, rodent or dog genomes. We were unable to identify any of the replication machinery common to active transposable elements in these newly identified repeats.

Conclusion: The presence of both orthologous and non-orthologous sites indicates that some sites existed prior to speciation and some were generated later. The identification of low to moderate copy number repetitive DNA that is specific to artiodactyls will be critical in the assembly of livestock genomes and studies of comparative genomics.
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http://dx.doi.org/10.1186/1471-2164-7-304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1713245PMC
December 2006

Prion gene haplotypes of U.S. cattle.

BMC Genet 2006 Nov 8;7:51. Epub 2006 Nov 8.

United States Department of Agriculture, Agricultural Research Service, U,S, Meat Animal Research Center, Clay Center, NE 68933, USA.

Background: Bovine spongiform encephalopathy (BSE) is a fatal neurological disorder characterized by abnormal deposits of a protease-resistant isoform of the prion protein. Characterizing linkage disequilibrium (LD) and haplotype networks within the bovine prion gene (PRNP) is important for 1) testing rare or common PRNP variation for an association with BSE and 2) interpreting any association of PRNP alleles with BSE susceptibility. The objective of this study was to identify polymorphisms and haplotypes within PRNP from the promoter region through the 3'UTR in a diverse sample of U.S. cattle genomes.

Results: A 25.2-kb genomic region containing PRNP was sequenced from 192 diverse U.S. beef and dairy cattle. Sequence analyses identified 388 total polymorphisms, of which 287 have not previously been reported. The polymorphism alleles define PRNP by regions of high and low LD. High LD is present between alleles in the promoter region through exon 2 (6.7 kb). PRNP alleles within the majority of intron 2, the entire coding sequence and the untranslated region of exon 3 are in low LD (18.0 kb). Two haplotype networks, one representing the region of high LD and the other the region of low LD yielded nineteen different combinations that represent haplotypes spanning PRNP. The haplotype combinations are tagged by 19 polymorphisms (htSNPS) which characterize variation within and across PRNP.

Conclusion: The number of polymorphisms in the prion gene region of U.S. cattle is nearly four times greater than previously described. These polymorphisms define PRNP haplotypes that may influence BSE susceptibility in cattle.
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http://dx.doi.org/10.1186/1471-2156-7-51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1654178PMC
November 2006

Software agents in molecular computational biology.

Brief Bioinform 2005 Dec;6(4):370-9

United States Meat Animal Research Center, State Spur 18D, Clay Center, Nebraska 68933, USA.

Progress made in applying agent systems to molecular computational biology is reviewed and strategies by which to exploit agent technology to greater advantage are investigated. Communities of software agents could play an important role in helping genome scientists design reagents for future research. The advent of genome sequencing in cattle and swine increases the complexity of data analysis required to conduct research in livestock genomics. Databases are always expanding and semantic differences among data are common. Agent platforms have been developed to deal with generic issues such as agent communication, life cycle management and advertisement of services (white and yellow pages). This frees computational biologists from the drudgery of having to re-invent the wheel on these common chores, giving them more time to focus on biology and bioinformatics. Agent platforms that comply with the Foundation for Intelligent Physical Agents (FIPA) standards are able to interoperate. In other words, agents developed on different platforms can communicate and cooperate with one another if domain-specific higher-level communication protocol details are agreed upon between different agent developers. Many software agent platforms are peer-to-peer, which means that even if some of the agents and data repositories are temporarily unavailable, a subset of the goals of the system can still be met. Past use of software agents in bioinformatics indicates that an agent approach should prove fruitful. Examination of current problems in bioinformatics indicates that existing agent platforms should be adaptable to novel situations.
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http://dx.doi.org/10.1093/bib/6.4.370DOI Listing
December 2005

Characterization of 954 bovine full-CDS cDNA sequences.

BMC Genomics 2005 Nov 23;6:166. Epub 2005 Nov 23.

USDA-ARS-U,S, Meat Animal Research Center, Clay Center, NE 68901, USA.

Background: Genome assemblies rely on the existence of transcript sequence to stitch together contigs, verify assembly of whole genome shotgun reads, and annotate genes. Functional genomics studies also rely on transcript sequence to create expression microarrays or interpret digital tag data produced by methods such as Serial Analysis of Gene Expression (SAGE). Transcript sequence can be predicted based on reconstruction from overlapping expressed sequence tags (EST) that are obtained by single-pass sequencing of random cDNA clones, but these reconstructions are prone to errors caused by alternative splice forms, transcripts from gene families with related sequences, and expressed pseudogenes. These errors confound genome assembly and annotation. The most useful transcript sequences are derived by complete insert sequencing of clones containing the entire length, or at least the full protein coding sequence (CDS) portion, of the source mRNA. While the bovine genome sequencing initiative is nearing completion, there is currently a paucity of bovine full-CDS mRNA and protein sequence data to support bovine genome assembly and functional genomics studies. Consequently, the production of high-quality bovine full-CDS cDNA sequences will enhance the bovine genome assembly and functional studies of bovine genes and gene products. The goal of this investigation was to identify and characterize the full-CDS sequences of bovine transcripts from clones identified in non-full-length enriched cDNA libraries. In contrast to several recent full-length cDNA investigations, these full-CDS cDNAs were selected, sequenced, and annotated without the benefit of the target organism's genomic sequence, by using comparison of bovine EST sequence to existing human mRNA to identify likely full-CDS clones for full-length insert cDNA (FLIC) sequencing.

Results: The predicted bovine protein lengths, 5' UTR lengths, and Kozak consensus sequences from 954 bovine FLIC sequences (bFLICs; average length 1713 nt, representing 762 distinct loci) are all consistent with previously sequenced mammalian full-length transcripts.

Conclusion: In most cases, the bFLICs span the entire CDS of the genes, providing the basis for creating predicted bovine protein sequences to support proteomics and comparative evolutionary research as well as functional genomics and genome annotation. The results demonstrate the utility of the comparative approach in obtaining predicted protein sequences in other species.
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http://dx.doi.org/10.1186/1471-2164-6-166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1314900PMC
November 2005

Linkage mapping bovine EST-based SNP.

BMC Genomics 2005 May 19;6:74. Epub 2005 May 19.

US Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, Nebraska 68933-0166, USA.

Background: Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL.

Results: Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM. Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP.

Conclusion: Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and refine assembly of bovine genome sequence. Even after the bovine genome is completely sequenced, the map will continue to be a useful tool to link observable phenotypes and animal genotypes to underlying genes and molecular mechanisms influencing economically important beef and dairy traits.
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http://dx.doi.org/10.1186/1471-2164-6-74DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166549PMC
May 2005

Integrating linkage and radiation hybrid mapping data for bovine chromosome 15.

BMC Genomics 2004 Oct 8;5:77. Epub 2004 Oct 8.

USDA, ARS, U,S, Meat Animal Research Center, Spur 18D, Clay Center, Nebraska 68933-0166, USA.

Background: Bovine chromosome (BTA) 15 contains a quantitative trait loci (QTL) for meat tenderness, as well as several breaks in synteny with human chromosome (HSA) 11. Both linkage and radiation hybrid (RH) maps of BTA 15 are available, but the linkage map lacks gene-specific markers needed to identify genes underlying the QTL, and the gene-rich RH map lacks associations with marker genotypes needed to define the QTL. Integrating the maps will provide information to further explore the QTL as well as refine the comparative map between BTA 15 and HSA 11. A recently developed approach to integrating linkage and RH maps uses both linkage and RH data to resolve a consensus marker order, rather than aligning independently constructed maps. Automated map construction procedures employing this maximum-likelihood approach were developed to integrate BTA RH and linkage data, and establish comparative positions of BTA 15 markers with HSA 11 homologs.

Results: The integrated BTA 15 map represents 145 markers; 42 shared by both data sets, 36 unique to the linkage data and 67 unique to RH data. Sequence alignment yielded comparative positions for 77 bovine markers with homologs on HSA 11. The map covers approximately 32% of HSA 11 sequence in five segments of conserved synteny, another 15% of HSA 11 is shared with BTA 29. Bovine and human order are consistent in portions of the syntenic segments, but some rearrangement is apparent. Comparative positions of gene markers near the meat tenderness QTL indicate the region includes separate segments of HSA 11. The two microsatellite markers flanking the QTL peak are between defined syntenic segments.

Conclusions: Combining data to construct an integrated map not only consolidates information from different sources onto a single map, but information contributed from each data set increases the accuracy of the map. Comparison of bovine maps with well annotated human sequence can provide useful information about genes near mapped bovine markers, but bovine gene order may be different than human. Procedures to connect genetic and physical mapping data, build integrated maps for livestock species, and connect those maps to more fully annotated sequence can be automated, facilitating the maintenance of up-to-date maps, and providing a valuable tool to further explore genetic variation in livestock.
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http://dx.doi.org/10.1186/1471-2164-5-77DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC526187PMC
October 2004

Beta-2-microglobulin haplotypes in U.S. beef cattle and association with failure of passive transfer in newborn calves.

Mamm Genome 2004 Mar;15(3):227-36

United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center (MARC), Spur 18D, P.O. Box 166, Clay Center, Nebraska 68933, USA.

Failure of passive transfer (FPT) is a condition in which neonates do not acquire protective serum levels of maternal antibodies. A principal component of antibody transport is the neonatal receptor for the Fc portion of immunoglobulin, a heterodimer of a MHC-1 alpha-chain homolog ( FCGRT) and beta-2-microglobulin ( B2M). Previously, two FCGRT haplotypes were associated with differences in immunoglobulin G (IgG) passive transfer in cattle (Laegreid et al. (2002) Mamm Genome 13, 704-710). The present study had two objectives: first, to characterize the B2M haplotype structure in a diverse group of U.S. beef cattle, and second, to evaluate those haplotypes for association with either high or low serum IgG levels in newborn calves. Twelve single nucleotide polymorphisms (SNPs), assorted into eight haplotypes, were identified by sequencing regions of B2M exons II and IV in a multi-breed panel of 96 beef cattle. Calves homozygous for one of the eight haplotypes ( B2M 2,2) were at increased risk of FPT (odds ratio = 10.60, CI(95%) 2.07-54.24, p = 0.005). These results indicate that this haplotype is in linkage disequilibrium with genetic risk factors affecting passive transfer of IgG in beef calves, an important determinant of neonatal calf morbidity and mortality.
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http://dx.doi.org/10.1007/s00335-003-2320-xDOI Listing
March 2004