Genetic evaluation of crossbred Bos indicus cow temperament at parturition.

Cow temperament at parturition may be mostly a measure of aggressiveness. The heritability of cow temperament at parturition in Bos taurus cows has been reported to be low. The objectives of this study were to estimate the heritability of cow temperament at parturition, conduct a genome-wide association analysis of cow temperament at the time of parturition, and estimate the correspondence of cow temperament at the time of parturition with cow productive performance and early-life temperament traits in Bos indicus crossbreds. Cow temperament was assessed from 1 to 5 indicating increasing levels of aggressiveness of cows (937 cows and 4,337 parturitions) from 2005 to 2022. Estimates of heritability and repeatability were 0.12 ±â€…0.024 and 0.24 ±â€…0.018. The estimates of proportion of phenotypic variance were 0.13 ±â€…0.019 and 0.02 ±â€…0.011 for permanent and maternal permanent environmental components, respectively. Estimates of heritability for maximum lifetime temperament score and proportions of temperament scores >1 were 0.18 ±â€…0.07 and 0.13 ±â€…0.072. Within cycles (generations), 2-yr-old cows had lower temperament score means than cows in most other age categories. There were low to moderate positive estimates of unadjusted correlation coefficients (r = 0.22 to 0.29; P < 0.05) of unadjusted temperament score with temperament measured on the same females when they were 8 mo old. There were low to moderate positive estimates of correlation coefficients (r = 0.09 to 0.37; P < 0.05) of unadjusted temperament score with calving rate, weaning rate, weaning weight per cow exposed, and weaning weight per 454 kg cow weight at weaning. Cows with the lowest temperament score had lower (P < 0.05) calving and weaning rate than cows in other temperament categories. Within 3 of 5 cycles, cows with the lowest temperament score (totally docile) had lower (P < 0.05) weaning weight per cow exposed than cows in other temperament categories. There were 2 SNP on BTA 4 associated with maximum lifetime temperament score (FDR < 0.05). The non-genetic influence of a cow's mother was documented in her own temperament measured at the time of calving; this may be a consequence of learned behavior. Less aggressiveness displayed by cows at the time of calving may be accompanied by lower reproductive and maternal performance.

Cow temperament was evaluated in 1/2 Nellore 1/2 Angus cows from four distinct generations (five herds) from 2005 to 2022. Cows were scored when their calves were processed (1 d age) as 1 = totally docile, 2 = protective, but not aggressive, 3 = moderately aggressive when calf is disturbed, 4 = very aggressive when calf is disturbed, and 5 = very aggressive even when calf is not disturbed. Similar to results in Bos taurus cows, the heritability of this trait was low. The repeatability was more moderate, indicating that additional records from a cow would be beneficial for selection purposes. Young cows had lower scores, indicating more docile behavior. This may be because a strong maternal protective instinct develops and strengthens over time. Temperament measured when cows were 8 mo old was moderately associated with their temperament as mature cows at the time of parturition. Cows with low temperament scores (more docile) had, in several cases, lower reproductive performance and production. Experiential accumulation appears to be important for cow temperament near the time of calving, including the cow's experience as a calf from her dam.

Skeletal Muscle Expression of Actinin-3 (ACTN3) in Relation to Feed Efficiency Phenotype of F2 Bos indicus - Bos taurus Steers.

In this study, actinin-3 (ACTN3) gene expression was investigated in relation to the feed efficiency phenotype in Bos indicus - Bos taurus crossbred steers. A measure of relative feed efficiency based on residual feed intake relative to predictions from the NRC beef cattle model was analyzed by the use of a mixed linear model that included sire and family nested within sire as fixed effects and age, animal type, sex, condition, and breed as random effects for 173 F2 Nellore-Angus steers. Based on these residual intake observations, individuals were ranked from most efficient to least efficient. Skeletal muscle samples were analyzed from 54 steers in three groups of 18 (high efficiency, low efficiency, and a statistically average group). ACTN3, which encodes a muscle-specific structural protein, was previously identified as a candidate gene from a microarray analysis of RNA extracted from muscle samples obtained from a subset of steers from each of these three efficiency groups. The expression of ACTN3 was evaluated by quantitative reverse transcriptase PCR analysis. The expression of ACTN3 in skeletal muscle was 1.6-fold greater in the inefficient steer group than in the efficient group (p = 0.007). In addition to expression measurements, blocks of SNP haplotypes were assessed for breed or parent of origin effects. A maternal effect was observed for ACTN3 inheritance, indicating that a maternal B. indicus block conferred improved residual feed efficiency relative to the B. taurus copy (p = 0.03). A SNP haplotype analysis was also conducted for m-calpain (CAPN2) and fibronectin 1 (FN1), and a significant breed effect was observed for both genes, with B. indicus and B. taurus alleles each conferring favorable efficiency when inherited maternally (p = 0.03 and p = 0.04). Because the ACTN3 structural protein is specific to fast-twitch (type II) muscle fibers and not present in slow-twitch muscle fibers (type I), muscle samples used for expression analysis were also assayed for fiber type ratio (type II/type I). Inefficient animals had a fast fiber type ratio 1.8-fold greater than the efficient animals (p = 0.027). Because these fiber-types exhibit different metabolic profiles, we hypothesize that animals with a greater proportion of fast-twitch muscle fibers are also less feed efficient.

A Primer for Single-Cell Sequencing in Non-Model Organisms.

Single-cell sequencing technologies have led to a revolution in our knowledge of the diversity of cell types, connections between biological levels of organization, and relationships between genotype and phenotype. These advances have mainly come from using model organisms; however, using single-cell sequencing in non-model organisms could enable investigations of questions inaccessible with typical model organisms. This primer describes a general workflow for single-cell sequencing studies and considerations for using non-model organisms (limited to multicellular animals). Importantly, single-cell sequencing, when further applied in non-model organisms, will allow for a deeper understanding of the mechanisms between genotype and phenotype and the basis for biological variation.

Darwinian genomics and diversity in the tree of life.

Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and established laboratory models. Fewer than 18,000 of ∼2,000,000 eukaryotic species (<1%) have a representative genome sequence in GenBank, and only a fraction of these have ancillary information on genome structure, genetic variation, gene expression, epigenetic modifications, and population diversity. This imbalance reflects a perception that human studies are paramount in disease research. Yet understanding how genomes work, and how genetic variation shapes phenotypes, requires a broad view that embraces the vast diversity of life. We have the technology to collect massive and exquisitely detailed datasets about the world, but expertise is siloed into distinct fields. A new approach, integrating comparative genomics with cell and evolutionary biology, ecology, archaeology, anthropology, and conservation biology, is essential for understanding and protecting ourselves and our world. Here, we describe potential for scientific discovery when comparative genomics works in close collaboration with a broad range of fields as well as the technical, scientific, and social constraints that must be addressed.

SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes.

Copy number variants are duplications and deletions of the genome that play an important role in phenotypic changes and human disease. Many software applications have been developed to detect copy number variants using either whole-genome sequencing or whole-exome sequencing data. However, there is poor agreement in the results from these applications. Simulated datasets containing copy number variants allow comprehensive comparisons of the operating characteristics of existing and novel copy number variant detection methods. Several software applications have been developed to simulate copy number variants and other structural variants in whole-genome sequencing data. However, none of the applications reliably simulate copy number variants in whole-exome sequencing data. We have developed and tested Simulator of Exome Copy Number Variants (SECNVs), a fast, robust and customizable software application for simulating copy number variants and whole-exome sequences from a reference genome. SECNVs is easy to install, implements a wide range of commands to customize simulations, can output multiple samples at once, and incorporates a pipeline to output rearranged genomes, short reads and BAM files in a single command. Variants generated by SECNVs are detected with high sensitivity and precision by tools commonly used to detect copy number variants. SECNVs is publicly available at https://github.com/YJulyXing/SECNVs.

Transcriptomic analysis between Normal and high-intake feeding geese provides insight into adipose deposition and susceptibility to fatty liver in migratory birds.

BACKGROUND: Dysregulation of adipogenesis causes metabolic diseases, like obesity and fatty liver. Migratory birds such as geese have a high tolerance of massive energy intake and exhibit little pathological development. Domesticated goose breeds, derivatives of the wild greyleg goose (Anser anser) or swan goose (Anser cygnoides), have high tolerance of energy intake resembling their ancestor species. Thus, goose is potentially a model species to study mechanisms associated with adipogenesis. RESULTS: Phenotypically, goose liver exhibited higher fat accumulation than adipose tissues during fattening (liver increased by 3.35 fold than 1.65 fold in adipose), showing a priority of fat accumulation in liver. We found the number of differentially expressed genes in liver (13.97%) was nearly twice the number of that in adipose (6.60%). These differentially expressed genes in liver function in several important lipid metabolism pathways, immune response, regulation of cancer, while in adipose, terms closely related to protein binding, gluconeogenesis were enriched. Typically, genes like MDH2 and SCD, which have key roles in glycolysis and fatty acids metabolism, had higher fold change in liver than in adipose tissues. Three hundred two differentially expressed long noncoding RNAs involved in regulation of metabolism in liver were also identified. For example, lncRNA XLOC_292762, which was 5.7 kb downstream of FERMT2, a gene involved phosphatidylinositol-3,4,5-trisphosphate binding, was significantly down-regulated after the high-intake feeding period. Further investigation of documented obesity-related orthologous genes in goose suggested that understanding the evolutionary split from mammals in adipogenesis will make goose fatty liver a better resource for future research. CONCLUSIONS: Our research reveals that goose uses liver as the major tissue to regulate a distinct lipid synthesis and degradation flux and the dynamic expression network analyses showed numerous layers of positive responses to both massive energy intake and possible pathological development. Our results offer insights into goose adipogenesis and provide a new perspective for research in human metabolic dysregulation.

Evaluation of F1 cows sired by Brahman, Boran, and Tuli bulls for reproductive, maternal, and cow longevity traits.

This study evaluated reproductive, maternal performance, and longevity traits of 143 F1 cows sired by Brahman (Br), Boran (Bo), or Tuli (T) bulls from Angus or Hereford cows from 1994 to 2011. Cow traits were measured at 7 yr of age in 1999 and 2000 for 1992- and 1993-born cows, respectively. From 2004 to 2010, excluding 2008, incisor condition (solid, broken, smooth) scores were assigned to cows remaining in production; scores were evaluated with two models. Broken and solid mouths were each assigned a score of "1" and smooth assigned "0"; Br-sired (0.76) and Bo-sired cows (0.71) had higher scores (P < 0.05) than T-sired cows (0.54). When solid mouths were scored 1 and smooth and broken scored 0, Br-sired cows (0.34) were higher than T-sired (0.01) (P < 0.05), and Bo-sired (0.23) cows were not different from either (P > 0.05). Age level of the cow within birth year was important for all modeled calf traits (P < 0.05). Birth weights were not different among cow inheritance (P > 0.05). Cow type influenced (P < 0.05) 205-d adjusted weaning weight of calves; Br-sired dams (228.1 ± 2.37 kg) produced the greatest weaning weight, followed by Bo-sired (213.7 ± 3.10 kg), and T-sired (201.6 ± 2.69 kg) dams (P < 0.05). Adjusted means for calving rate for Bo-sired (0.92 ± 0.02) cows were higher (P < 0.05) than Br-sired (0.86 ± 0.02) and T-sired (0.86 ± 0.02) cows. Adjusted mean weaning rate was greater (P < 0.05) for Bo-sired cows (0.86 ± 0.02) than for cows sired by Br (0.77 ± 0.02) bulls, but weaning rate for T-sired cows (0.80 ± 0.02) were similar (P > 0.05). Cow weight was greater (P < 0.05) for Br-sired cows (590.5 ± 8.35 kg) than for Bo-sired (505.8 ± 10.46 kg) or T-sired cows (508.5 ± 9.37 kg). BCS at weaning for 7-yr-old cows was similar (P = 0.08) for Br-sired and Bo-sired cows and lower for T-sired cows (P = 0.0005, condition scores 6.0, 6.3, and 5.8, respectively). Boran-sired cows were older when they were removed from the herd, on average (12.7 ± 0.74 y, P = 0.03) than T-sired (10.6 ± 0.61 y); Br-sired cow persistence was intermediate and not different (11.05 ± 0.60 y, P > 0.06) from the others. Boran-sired cows had higher calving and weaning rates and better mouth scores than the other groups; consequently, they had greater longevity as well. Boran-sired and T-sired cows were moderate in size and weighed less than Br-sired cows throughout the study. Tuli-sired cows weaned the lightest calves and had the most tooth deterioration as they aged.

Genome-wide association study for stayability measures in Nellore-Angus crossbred cows.

Beef cow stayability is a complex, economically important trait often used as an indicator of a cow's potential lifetime productivity. Stayability is defined as capability of a cow to maintain a perfect record up to 6 yr of age. This age is commonly cited as a financial break-even point, where initial costs of cow development and maintenance are recovered by her cumulative net income from yearly calf receipts. Later-maturing Bos indicus-Bos taurus crossbred cows may experience reproductive difficulty early in life but have a high potential for a long reproductive life span. It was the objective of this study to identify genetic variants associated with measures of beef cow stayability. A population of B. indicus-B. taurus crossbred cows (n = 305) from central Texas was used. Phenotypes for various measures of stayability to 6 yr of age were produced by artificially imposing five different culling criteria on data from the population. Cows were scored either as a 1 (indicating a perfect record through 6 yr) or a 0 (indicating failure at or before 6 yr), under each criterion. Genome-wide association studies (GWAS) were conducted for each criterion using univariate procedures and prefitting the fixed effect of cow contemporary group. SNP associations for two criteria surpassed the false discovery threshold of 0.15, when a cow was scored as 0 upon her first failure to wean a calf, regardless of reason, through 6 yr (criterion 2), and when a cow was scored as 0 upon her first failure to give birth to a calf, through 6 yr (criterion 3). Associated SNP were found on bovine chromosomes (BTA) 1, 2, 5, 9, 18, and 21 for criterion 2 and on BTA 1, 5, 11, 15, and 24 for criterion 3. A critical region on BTA 5: 43-50 Mb was identified for each criterion. Due to the similarities to prior work, the tendency for B. indicus cattle to experience reproductive difficulties early in life, and due to the large proportion of cows that left the herd at an early age under these criteria, these results suggest that the associations are likely driven by an early life trait such as age at puberty or rate of heifer development.

Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber.

The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole-rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ecological constraints model of eusocial evolution, early genetic studies reported high levels of relatedness in naked mole-rats, providing a compelling argument that low dispersal rates and consanguineous mating (inbreeding as a mating system) are the driving forces for the evolution of this eusocial species. One caveat to accepting this long-held view is that the original genetic studies were based on limited sampling from the species' geographic distribution. A growing body of evidence supports a contrary view, with the original samples not representative of the species-rather reflecting a single founder event, establishing a small population south of the Athi River. Our study is the first to address these competing hypotheses by examining patterns of molecular variation in colonies sampled from north and south of the Athi and Tana rivers, which based on our results, serve to isolate genetically distinct populations of naked mole-rats. Although colonies south of the Athi River share a single mtDNA haplotype and are fixed at most microsatellite loci, populations north of the Athi River are considerably more variable. Our findings support the position that the low variation observed in naked mole-rat populations south of the Athi River reflects a founder event, rather than a consequence of this species' unusual mating system.

Comparison of breeding value prediction for two traits in a Nellore-Angus crossbred population using different Bayesian modeling methodologies.

The objectives of this study were to 1) compare four models for breeding value prediction using genomic or pedigree information and 2) evaluate the impact of fixed effects that account for family structure. Comparisons were made in a Nellore-Angus population comprising F2, F3 and half-siblings to embryo transfer F2 calves with records for overall temperament at weaning (TEMP; n = 769) and Warner-Bratzler shear force (WBSF; n = 387). After quality control, there were 34,913 whole genome SNP markers remaining. Bayesian methods employed were BayesB (π̃ = 0.995 or 0.997 for WBSF or TEMP, respectively) and BayesC (π = 0 and π̃), where π̃ is the ideal proportion of markers not included. Direct genomic values (DGV) from single trait Bayesian analyses were compared to conventional pedigree-based animal model breeding values. Numerically, BayesC procedures (using π̃) had the highest accuracy of all models for WBSF and TEMP (ρ̂gg = 0.843 and 0.923, respectively), but BayesB had the least bias (regression of performance on prediction closest to 1, ß̂y,x = 2.886 and 1.755, respectively). Accounting for family structure decreased accuracy and increased bias in prediction of DGV indicating a detrimental impact when used in these prediction methods that simultaneously fit many markers.

Alternative parameterizations of relatedness in whole genome association analysis of pre-weaning traits of Nelore-Angus calves.

Gestation length, birth weight, and weaning weight of F2 Nelore-Angus calves (n = 737) with designed extensive full-sibling and half-sibling relatedness were evaluated for association with 34,957 SNP markers. In analyses of birth weight, random relatedness was modeled three ways: 1) none, 2) random animal, pedigree-based relationship matrix, or 3) random animal, genomic relationship matrix. Detected birth weight-SNP associations were 1,200, 735, and 31 for those parameterizations respectively; each additional model refinement removed associations that apparently were a result of the built-in stratification by relatedness. Subsequent analyses of gestation length and weaning weight modeled genomic relatedness; there were 40 and 26 trait-marker associations detected for those traits, respectively. Birth weight associations were on BTA14 except for a single marker on BTA5. Gestation length associations included 37 SNP on BTA21, 2 on BTA27 and one on BTA3. Weaning weight associations were on BTA14 except for a single marker on BTA10. Twenty-one SNP markers on BTA14 were detected in both birth and weaning weight analyses.

Identification of a major locus interacting with MC1R and modifying black coat color in an F2 Nellore-Angus population.

BACKGROUND: In cattle, base color is assumed to depend on the enzymatic activity specified by the MC1R locus, i.e. the extension locus, with alleles coding for black (E(D)), red (e), and wild-type (E+). In most mammals, these alleles are presumed to follow the dominance model of E(D) > E+ > e, although exceptions are found. In Bos indicus x Bos taurus F2 cattle, some E(D)E+ heterozygotes are discordant with the dominance series for MC1R and display various degrees of red pigmentation on an otherwise predicted black background. The objective of this study was to identify loci that modify black coat color in these individuals. RESULTS: Reddening was classified with a subjective scoring system. Interval analyses identified chromosome-wide suggestive (P < 0.05) and significant (P < 0.01) QTL on bovine chromosomes (BTA) 4 and 5, although these were not confirmed using single-marker association or Bayesian methods. Evidence of a major locus (F = 114.61) that affects reddening was detected between 60 and 73 Mb on BTA 6 (Btau4.0 build), and at 72 Mb by single-marker association and Bayesian methods. The posterior mean of the genetic variance for this region accounted for 43.75% of the genetic variation in reddening. This region coincided with a cluster of tyrosine kinase receptor genes (PDGFRA, KIT and KDR). Fitting SNP haplotypes for a 1 Mb interval that contained all three genes and centered on KIT accounted for the majority of the variation attributed to this major locus, which suggests that one of these genes or associated regulatory elements, is responsible for the majority of variation in degree of reddening. CONCLUSIONS: Recombinants in a 5 Mb region surrounding the cluster of tyrosine kinase receptor genes implicated PDGFRA as the strongest positional candidate gene. A higher density marker panel and functional analyses will be required to validate the role of PDGFRA or other regulatory variants and their interaction with MC1R for the modification of black coat color in Bos indicus influenced cattle.

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

High-resolution haplotype block structure in the cattle genome.

BACKGROUND: The Bovine HapMap Consortium has generated assay panels to genotype ~30,000 single nucleotide polymorphisms (SNPs) from 501 animals sampled from 19 worldwide taurine and indicine breeds, plus two outgroup species (Anoa and Water Buffalo). Within the larger set of SNPs we targeted 101 high density regions spanning up to 7.6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use. RESULTS: From the 101 targeted high-density regions on bovine chromosomes 6, 14, and 25, between 57 and 95% of the SNPs were informative in the individual breeds. The regions of high LD extend up to ~100 kb and the size of haplotype blocks ranges between 30 bases and 75 kb (10.3 kb average). On the scale from 1-100 kb the extent of LD and haplotype block structure in cattle has high similarity to humans. The estimation of effective population sizes over the previous 10,000 generations conforms to two main events in cattle history: the initiation of cattle domestication (~12,000 years ago), and the intensification of population isolation and current population bottleneck that breeds have experienced worldwide within the last ~700 years. Haplotype block density correlation, block boundary discordances, and haplotype sharing analyses were consistent in revealing unexpected similarities between some beef and dairy breeds, making them non-differentiable. Clustering techniques permitted grouping of breeds into different clades given their similarities and dissimilarities in genetic structure. CONCLUSION: This work presents the first high-resolution analysis of haplotype block structure in worldwide cattle samples. Several novel results were obtained. First, cattle and human share a high similarity in LD and haplotype block structure on the scale of 1-100 kb. Second, unexpected similarities in haplotype block structure between dairy and beef breeds make them non-differentiable. Finally, our findings suggest that ~30,000 uniformly distributed SNPs would be necessary to construct a complete genome LD map in Bos taurus breeds, and ~580,000 SNPs would be necessary to characterize the haplotype block structure across the complete cattle genome.

An assessment of population structure in eight breeds of cattle using a whole genome SNP panel.

BACKGROUND: Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from Bos indicus and Bos taurus. RESULTS: Two thousand six hundred and forty one single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds. CONCLUSION: The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.

Molecular characterization of the Rocky Mountain elk (Cervus elaphus nelsoni) PRNP putative promoter.

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) affecting deer (Odocoileus spp.), moose (Alces alces), and Rocky Mountain elk (Cervus elaphus nelsoni). Leucine homozygosity at elk PRNP codon 132 has been associated with reduced CWD susceptibility. However, naturally acquired CWD has been detected in elk possessing the 132 Leu/Leu genotype. Recent human and bovine studies indicate that PRNP regulatory polymorphisms may also influence TSE occurrence. Therefore, we generated sequences for the elk PRNP putative promoter (2.2 kb), exon 1 (predicted; 54 bp), intron 1 (predicted; 193 bp), and exon 3 (771 bp). Promoter prediction analysis using CpGProD yielded a single elk PRNP promoter that was homologous to regions of known promoter activity in cow and sheep. Molecular interrogation of the elk PRNP putative promoter revealed 32 diallelic single-nucleotide polymorphisms (SNPs). No variation was detected within the predicted exon 1 or intron 1 sequences. Evaluation of elk PRNP exon 3 revealed 3 SNPs (63Y, 312R, 394W-->Met/Leu). Bayesian haplotype reconstruction resulted in 3 elk PRNP haplotypes, with complete linkage disequilibrium observed between all PRNP putative promoter SNPs and codon 132. The results of this study provide the initial genomic foundation for future comparative and haplotype-based elk PRNP studies.

Whole genome linkage disequilibrium maps in cattle.

BACKGROUND: Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides background information concerning the extent of long range linkage disequilibrium in cattle. RESULTS: Linkage disequilibrium was assessed using r2 among all pairs of syntenic markers within eight breeds of cattle from the Bos taurus and Bos indicus subspecies. Bos taurus breeds included Angus, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black and Limousin while Bos indicus breeds included Brahman and Nelore. Approximately 2670 markers spanning the entire bovine autosomal genome were used to estimate pairwise r2 values. We found that the extent of linkage disequilibrium is no more than 0.5 Mb in these eight breeds of cattle. CONCLUSION: Linkage disequilibrium in cattle has previously been reported to extend several tens of centimorgans. Our results, based on a much larger sample of marker loci and across eight breeds of cattle indicate that in cattle linkage disequilibrium persists over much more limited distances. Our findings suggest that 30,000-50,000 loci will be needed to conduct whole genome association studies in cattle.

A physical map of the bovine genome.

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.

Steroid hormones acutely regulate expression of a Nudix protein-encoding gene in the endometrial epithelium of sheep.

Steroid hormones regulate endometrial gene expression to meet the needs of developing embryos. Our hypothesis is that steroid hormones transiently induce expression of genes in the endometrial epithelium to make the uterine environment different between the earliest days of pregnancy. We identified one such gene product using differential display-polymerase chain reactions. The gene product that was strongly induced in ewes between day 3 and 6 of the estrous cycle was cloned and sequenced to identify it as encoding a member of the Nudix family of hydrolase enzymes. Northern blot analyses indicated that NUDT16 mRNA concentrations were elevated 10-fold in the endometrium of sheep from day 5 to 9 of the estrous cycle and returned to basal levels by day 11. In assays of RNA samples from 15 different tissues from an adult ewe, the concentrations of NUDT16 mRNA were greatest in endometrium. In situ hybridization localized NUDT16 mRNA exclusively to the endometrial epithelial cells of the glands and uterine lumen. In ovariectomized ewes, NUDT16 mRNA was induced by a regimen of alternating estrogen and progesterone therapy designed to mimic the hormonal experiences of a ewe at day 6 of the estrous cycle. The final estrogen treatment in the regimen was critical to the expression of NUDT16 as well as progesterone receptor and estrogen receptor-beta genes. Characterization of the NUDT16 gene identified putative steroid hormone response elements, which can now be investigated to understand its unique pattern of regulation in the earliest days of pregnancy.

Multiclonal pattern of Jaagsiekte sheep retrovirus integration sites in ovine pulmonary adenocarcinoma.

Insertional mutagenesis and envelope (Env)-mediated oncogenesis are hypothesized mechanisms by which Jaagsiekte sheep retrovirus (JSRV) causes ovine pulmonary adenocarcinoma (OPA). Twenty-eight JSRV integration sites in lung tumors (LTs) from four sheep with OPA were cloned and sequenced by a multiple step gene walking technique. Using nested PCR, clonal expansion of these integration sites could be detected, if at all, only in the localized regions of LT from which the integration sites were derived. One sheep had a viral integration site in a sequence with 85 and 81% identity, respectively, over 100 bp to exon 2 of the human and mouse receptor protein tyrosine phosphatase gamma genes. Clonal integration of Jaagsiekte sheep retrovirus in this gene was demonstrated by nested PCR and Southern blot hybridization in the DNA sample from which the integration site was cloned, but not in other LT or kidney DNA samples from the same sheep. OPA may develop from multiple independent oncogenic events and a role for insertional mutagenesis cannot be ruled out.