Topologically associating domains in the POLLED region are the same for Angus- and Brahman-specific Hi-C reads from F1 hybrid fetal tissue

Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenotype, which are clustered in a 300-kb region on chromosome 1. As the variants are intergenic, the functional effect is unknown. The aim of this study was to determine if the POLLED variants affect chromatin structure or disrupt enhancers using publicly available data. Topologically associating domains (TADs) were analyzed using Angus- and Brahman-specific Hi-C reads from lung tissue of an Angus (Celtic allele) cross Brahman (horned) fetus. Predicted bovine enhancers and chromatin immunoprecipitation sequencing peaks for histone modifications associated with enhancers (H3K27ac and H3K4me1) were mapped to the POLLED region. TADs analyzed from Angus- and Brahman-specific Hi-C reads were the same, therefore, the Celtic variant does not appear to affect this level of chromatin structure. The Celtic variant is located in a different TAD from the Friesian, Mongolian, and Guarani variants. Predicted enhancers and histone modifications overlapped with the Guarani and Friesian variants but not the Celtic or Mongolian variants. This study provides insight into the mechanisms of the POLLED variants for disrupting horn development. These results should be validated using data produced from the horn bud region of horned and polled bovine fetuses.

Identification of genomic regions associated with total and progressive sperm motility in Italian Holstein bulls

Sperm motility is directly related to the ability of sperm to move through the female reproductive tract to reach the ovum. Sperm motility is a complex trait that is influenced by environmental and genetic factors and is associated with male fertility, oocyte penetration rate, and reproductive success of cattle. In this study we carried out a GWAS in Italian Holstein bulls to identify candidate regions and genes associated with variations in progressive and total motility (PM and TM, respectively). After quality control, the final data set consisted of 5,960 records from 949 bulls having semen collected in 10 artificial insemination stations and genotyped at 412,737 SNPs (call rate >95%; minor allele frequency >5%). (Co)variance components were estimated using single trait mixed models, and associations between SNPs and phenotypes were assessed using a genomic BLUP approach. Ten windows that explained the greatest percentage of genetic variance were located on Bos taurus autosomes 1, 2, 4, 6, 7, 23, and 26 for TM and Bos taurus autosomes 1, 2, 4, 6, 8, 16, 23, and 26 for PM. A total of 150 genes for TM and 72 genes for PM were identified within these genomic regions. Gene Ontology enrichment analyses identified significant Gene Ontology terms involved with energy homeostasis, membrane functions, sperm-egg interactions, protection against oxidative stress, olfactory receptors, and immune system. There was significant enrichment of quantitative trait loci for fertility, calving ease, immune response, feed intake, and carcass weight within the candidate windows. These results contribute to understanding the architecture of the genetic control of sperm motility and may aid in the development of strategies to identify subfertile bulls and improve reproductive success.

Disruption of pancreatic stellate cell myofibroblast phenotype promotes pancreatic tumor invasion

In pancreatic ductal adenocarcinoma (PDAC), differentiation of pancreatic stellate cells (PSCs) into myofibroblast-like cancer-associated fibroblasts (CAFs) can both promote and suppress tumor progression. Here, we show that the Rho effector protein kinase N2 (PKN2) is critical for PSC myofibroblast differentiation. Loss of PKN2 is associated with reduced PSC proliferation, contractility, and alpha-smooth muscle actin (α-SMA) stress fibers. In spheroid co-cultures with PDAC cells, loss of PKN2 prevents PSC invasion but, counter-intuitively, promotes invasive cancer cell outgrowth. PKN2 deletion induces a myofibroblast to inflammatory CAF switch in the PSC matrisome signature both in vitro and in vivo. Further, deletion of PKN2 in the pancreatic stroma induces more locally invasive, orthotopic pancreatic tumors. Finally, we demonstrate that a PKN2KO matrisome signature predicts poor outcome in pancreatic and other solid human cancers. Our data indicate that suppressing PSC myofibroblast function can limit important stromal tumor-suppressive mechanisms, while promoting a switch to a cancer-supporting CAF phenotype.

Understanding the effects of the bovine POLLED variants

Horns are paired appendages on the head of bovine species, comprising an inner bony core and outer keratin sheath. The horn bud forms during early fetal development but ossification of the developing horn does not occur until approximately 1 month after birth. Little is known about the genetic pathways that lead to horn growth. Hornless, or polled, animals are found in all domestic bovids. Histological studies of bovine fetuses have shown that the horn bud does not form in polled individuals. There are currently four known genetic variants for polledness in cattle on BTA1. All of the variants are intergenic, but probably affect regulation of nearby genes or long non-coding RNAs. Transcriptomic studies suggest that the expression of two nearby long non-coding RNAs are affected by the Celtic POLLED variant, but further studies are required to confirm these data. Candidate genes located elsewhere in the genome are involved in regulating bone formation and epithelial-to-mesenchymal transition. Expression of one of these candidate genes, RXFP2, appears to be reduced in the fetal horn bud of polled animals carrying the Celtic variant compared with horned individuals. Investigating horn ontogenesis and the genetic pathway by which the POLLED variants prevent horn development has implications for cattle breeding. If the genetic basis of horn bud formation and polledness is better understood, then new targets may be identified for precision genome editing to create polled individuals.

Profiling bovine blastocyst microRNAs using deep sequencing

MicroRNAs (miRNAs) are known to control several reproductive functions, including oocyte maturation, implantation and early embryonic development. Recent advances in deep sequencing have allowed the analysis of all miRNAs of a sample. However, when working with embryos, due to the low RNA content, miRNA profiling is challenging because of the relatively large amount of total RNA required for library preparation protocols. In the present study we compared three different procedures for RNA extraction and prepared libraries using pools of 30 bovine blastocysts. In total, 14 of the 15 most abundantly expressed miRNAs were common to all three procedures. Furthermore, using miRDeep discovery and annotation software (Max Delbrück Center), we identified 1363 miRNA sequences, of which bta-miR-10b and bta-miR-378 were the most abundant. Most of the 179 genes identified as experimentally validated (86.6%) or predicted targets (13.4%) were associated with cancer canonical pathways. We conclude that reliable analysis of bovine blastocyst miRNAs can be achieved using the procedures described herein. The repeatability of the results across different procedures and independent replicates, as well as their consistency with results obtained in other species, support the biological relevance of these miRNAs and of the gene pathways they modulate in early embryogenesis.

Landscape of copy number variations in Bos taurus: individual - and inter-breed variability

Background

The number of studies of Copy Number Variation in cattle has increased in recent years. This has been prompted by the increased availability of data on polymorphisms and their relationship with phenotypes. In addition, livestock species are good models for some human phenotypes. In the present study, we described the landscape of CNV driven genetic variation in a large population of 146 individuals representing 13 cattle breeds, using whole genome DNA sequence.

Results

A highly significant variation among all individuals and within each breed was observed in the number of duplications (P < 10⁻¹⁵) and in the number of deletions (P < 10⁻¹⁵). We also observed significant differences between breeds for duplication (P = 0.01932) and deletion (P = 0.01006) counts. The same variation CNV length - inter-individual and inter-breed differences were significant for duplications (P < 10⁻¹⁵) and deletions (P < 10⁻¹⁵). Moreover, breed-specific variants were identified, with the largest proportion of breed-specific duplications (9.57%) found for Fleckvieh and breed-specific deletions found for Brown Swiss (5.00%). Such breed-specific CNVs were predominantly located in intragenic regions, however in Simmental, one deletion present in five individuals was found in the coding sequence of a novel gene ENSBTAG00000000688 on chromosome 18. In Brown Swiss, Norwegian Red and Simmental breed-specific deletions were located within KIT and MC1R genes, which are responsible for a coat colour. The functional annotation of coding regions underlying the breed-specific CNVs showed that in Norwegian Red, Guernsey, and Simmental significantly under- and overrepresented GO terms were related to chemical stimulus involved in sensory perception of smell and the KEGG pathways for olfactory transduction. In addition, specifically for the Norwegian Red breed, the dopaminergic synapse KEGG pathway was significantly enriched within deleted parts of the genome.

Conclusions

The CNV landscape in Bos taurus genome revealed by this study was highly complex, with inter-breed differences, but also a significant variation within breeds. The former, may explain some of the phenotypic differences among analysed breeds, and the latter contributes to within-breed variation available for selection.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4815-6) contains supplementary material, which is available to authorized users.

Evaluation of responses to vaccination of Angus cattle for four viruses that contribute to bovine respiratory disease complex

Although vaccination is an effective measure in reducing the risk of bovine respiratory disease complex (BRDC) in cattle, BRDC losses remain significant. Increasing the efficacy of vaccination depends on elucidating the protective immune response to different antigens included in vaccines, determining the best timing for vaccination, and understanding the impact of the age of the calf on vaccination. This study measured the serum antibodies present in calves following vaccination against 4 viruses commonly associated with BRDC: bovine viral diarrhea virus type 1 and 2 (BVDV1 and BVDV2), bovine respiratory syncytial virus (BRSV), and bovine herpesvirus 1 (BHV1). Serum antibody titers were measured in more than 1,600 calves at 3-wk intervals starting at the time of the first vaccination. This first vaccination occurred at weaning for approximately half of the individuals and 3 wk before weaning for the other half. Dam age (years), time of weaning (initial vaccination or booster vaccination), and age of calf within year-season (days within year-season) classification all were found to have a significant effect on measured traits such as the initial titer and overall response. An increased initial titer was negatively correlated with each response trait (initial, booster, and overall response). Calves that were weaned at initial vaccination had greater overall antibody response to BVDV1 and BVDV2 compared with calves weaned 3 wk before initial vaccination. In contrast, calves given their initial vaccination 3 wk before weaning had greater overall antibody response to BRSV and BHV1 compared with calves that were vaccinated at weaning. Furthermore, the circulating antibody titer at which each virus needed to be below for an individual calf to positively respond to vaccination was determined (log titer of 0.38 for BVDV1, 1.5 for BVDV2, 3.88 for BRSV, and 1.5 for BHV1). This information can be used to improve vaccination protocols to allow for a greater response rate of individuals to vaccination and, hopefully, improved protection.

Evidence of early defects in Cajal-Retzius cell localization during brain development in a mouse model of dystroglycanopathy

AIMS

The secondary dystroglycanopathies represent a heterogeneous group of congenital muscular dystrophies characterized by the defective glycosylation of alpha dystroglycan. These disorders are associated with mutations in at least 17 genes, including Fukutin-related protein (FKRP). At the severe end of the clinical spectrum there is substantial brain involvement, and cobblestone lissencephaly is highly suggestive of these disorders. The precise pathogenesis of this phenotype has, however, remained unclear with most attention focused on the disruption to the radial glial scaffold. Here, we set out to investigate whether lesions are apparent prior to the differentiation of the radial glia.

METHODS

A detailed investigation of the structural brain defects from embryonic day 10.5 (E10.5) up until the time of birth (P0) was undertaken in the Fkrp-deficient mice (FKRP^KD ). Reelin, and downstream PI3K/Akt signalling pathways were analysed using Western blot.

RESULTS

We show that early basement membrane defects and neuroglial ectopia precede radial glial cell differentiation. Furthermore, we identify mislocalization of Cajal-Retzius cells which nonetheless is not associated with any apparent disruption to the reelin, and downstream PI3K/Akt signalling pathways.

CONCLUSIONS

These observations identify Cajal-Retzius cell mislocalization as an early event during the development of cortical defects thereby identifying an earlier onset and more complex pathogenesis than originally reported for the secondary dystroglycanopathies. Overall this study provides new insight into central nervous system involvement in this group of diseases.

Abstract P2-13-02: Radiation and depression associated with complications of tissue expander reconstruction

Background: Rates of implant failure, wound healing delay, and infection are higher in patients having RT after tissue expander (TE) and permanent implant reconstruction. Some have suggested greater complications with increased body mass index (BMI) and with diabetes.

Patients and Methods: 127 patients had bilateral TE reconstruction and radiation from 2003 to 2013 at two centers. In 95% (121/127) of cases RT was performed while the TE was in place with the permanent implant inserted after RT. 3D-CRT technique included 50 Gy with daily or every other day bolus and forward planned segments. The supraclavicular and/or internal mammary lymph node bearing regions were treated in 82.7% (105/127) cases. The non-irradiated breast provided an internal control. Chi-squared testing of pretreatment factors included radiation, chemotherapy, and medical history of hypertension, diabetes, cardiovascular, and pulmonary disease. BMI, tobacco and alcohol use, use of antiestrogen, statin, antidepressant, antihypertensive, anxiolytics, and antidiabetic medications were also studied. Comparison of differences in means for continuous variables used analysis of variance, then multiple pairwise comparisons with Bonferroni correction of p-value.

Results: Mean age was 53 ± 10.1 years with just 14.6% African- American. Twelve (9.4%) were BRCA positive (9 BRCA1, 4 BRCA2, 1 Both). Nearly all complications were in the radiated breast. Complications were: Grade 0 (no complication; 43.9%), Grade 1 (tightness and/or drifting of implant or Baker grade II capsular contracture; 30.9 %), Grade 2 (infection, hypertrophic scarring, or incisional necrosis; 9.8%), Grade 3 (Baker grade III capsular contracture, wound dehiscence, or impending exposure of implant; 5.7%), Grade 4 (implant failure, exchange of implant, or Baker grade IV capsular contracture; 9.8%). 15.3 percent (19 cases) experienced grade 3 or 4 complication and 9.8% (12 cases) had grade 4 complication. Considering non-irradiated breasts, there were two (1.6%) Grade 3-4 complications. For BMI, there was no significant difference by category as defined by the CDC (p=0.91). Patients history of HRT tended to be more likely to have Grade 3 or 4 complications (31.8% vs 12.4% respectively; p=0.08). Patients with depression were more likely to experience a Grade 3 or 4 complication (29.4% vs 13.2%; p=0.01). Multiple logistic regression was used to predict the probability of a Grade 3 or 4 complication with HR use and depression as independent variables. Patients with depression were 4.2 times more likely to have a Grade 3 or 4 complication (OR=4.2, p=0.03) and patients with a history of HRT use were 3.4 times more likely to experience a Grade 3 or 4 complication (OR = 3.4, p=0.04). Only clinical diagnosis of depression was considered as 12/31 (38.7%) with antidepressants used only venlafaxine. Neither BRCA status (p=0.72) nor chemotherapy factors (p=0.42) were associated with complication rates.

Conclusions: Higher rates of TE reconstruction complications may be expected in patients receiving radiotherapy. Patients reporting medical history of depression or HRT use showed statistically significant increase in complication rates. This effect might be attributed to a drug effect or to patient factors such as body image.

Citation Format: Wagner RM, Spzunar SM, Stefani WA, Falk JS, Williams JL, Edhayan E, Dul CL, Rodriguez D, Busuito MJ, Browne CH, Aref A, Rabbani AN, Chuba PJ. Radiation and depression associated with complications of tissue expander reconstruction. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-13-02.

Degree of Cajal-Retzius Cell Mislocalization Correlates with the Severity of Structural Brain Defects in Mouse Models of Dystroglycanopathy

The secondary dystroglycanopathies are characterized by the hypoglycosylation of alpha dystroglycan, and are associated with mutations in at least 18 genes that act on the glycosylation of this cell surface receptor rather than the Dag1 gene itself. At the severe end of the disease spectrum, there are substantial structural brain defects, the most striking of which is often cobblestone lissencephaly. The aim of this study was to determine the gene-specific aspects of the dystroglycanopathy brain phenotype through a detailed investigation of the structural brain defects present at birth in three mouse models of dystroglycanopathy-the FKRP(KD) , which has an 80% reduction in Fkrp transcript levels; the Pomgnt1null , which carries a deletion of exons 7-16 of the Pomgnt1 gene; and the Large(myd) mouse, which carries a deletion of exons 5-7 of the Large gene. We show a rostrocaudal and mediolateral gradient in the severity of brain lesions in FKRP(KD) , and to a lesser extent Pomgnt1null mice. Furthermore, the mislocalization of Cajal-Retzius cells is correlated with the gradient of these lesions and the severity of the brain phenotype in these models. Overall these observations implicate gene-specific differences in the pathogenesis of brain lesions in this group of disorders.

Comparison of arthroscopic and MRI findings of osteochondral damage in knees

Magnetic resonance imaging (MRI) scans are widely used in the assessment of knees, often prior to arthroscopic procedures. The reporting of osteochondral damage on MRI scans can be variable. The correlation between MRI reports of osteochondral damage and that found at arthroscopy is often inconsistent. A retrospective case-note review of a single-surgeon series of 175 arthroscopic procedures was performed. Eighty-three patients were included in the study. The remainder were excluded if an MRI scan had not been performed or had been performed more than 3-months before surgery. The condition of the articular cartilage demonstrated by MRI was compared to that found at arthroscopy. Data was analysed for presence and extent of osteochondral damage. Comparison between MRI and arthroscopy findings showed high specificity (90%) and negative predictive values (89%) for osteochondral damage but low sensitivity (46%). Cohen's kappa values < 0.2 revealed very poor correlation for the extent of damage. This study demonstrates MRI as a good identifier of osteochondral damage but an unreliable descriptor for such change.

Hyponatraemia in cancer patients on an inpatient rehabilitation unit

This study identifies the incidence of hyponatraemia in cancer patients on an inpatient rehabilitation unit and examines the association between admission hyponatraemia and rehabilitation length of stay (LOS), functional outcome, and survival. After institutional review committee's approval, we retrospectively reviewed medical records of 295 consecutive patients who were admitted to this inpatient cancer rehabilitation unit between 27 January 2009 through 31 July 2010 in a tertiary cancer centre. The incidence of hyponatraemia in cancer patients admitted to our inpatient rehabilitation unit was 41.4%. Median rehabilitation LOS for patients with mild (Na 130-134 mEq/L) and moderate-severe (Na < 130 mEq/L) hyponatraemia was 11 and 15 days, respectively, which was significantly longer than patients with eunatraemia (10 days; P = 0.03). Functional Independence Measure gain for ambulation and transfers during inpatient rehabilitation stay was not significantly different between three different patient groups. We concluded that large portion of patients who require acute inpatient rehabilitation presented with hyponatraemia, which is associated with prolonged rehabilitation LOS. Whether aggressive management of hyponatraemia will shorten rehabilitation stay needs further study.

Genes involved in muscle lipid composition in 15 European Bos taurus breeds

Consumers demand healthy and palatable meat, both factors being affected by fat composition. However, red meat has relatively high concentration of saturated fatty acids and low concentration of the beneficial polyunsaturated fatty acids. To select animals prone to produce particular fat types, it is necessary to identify the genes influencing muscle lipid composition. This paper describes an association study in which a large panel of candidate genes involved in adipogenesis, lipid metabolism and energy homoeostasis was tested for effects on fat composition in 15 European cattle breeds. Sixteen genes were found to have significant effects on different lipid traits, and among these, CFL1 and MYOZ1 were found to have large effects on the ratio of 18:2/18:3, CRI1 on the amount of neutral adrenic acid (22:4 n-6), MMP1 on docosahexaenoic acid (22:6 n-3) and conjugated linoleic acid, PLTP on the ratio of n-6:n-3 and IGF2R on flavour. Several genes - ALDH2, CHRNE, CRHR2, DGAT1, IGFBP3, NEB, SOCS2, SUSP1, TCF12 and FOXO1 - also were found to be associated with both lipid and organoleptic traits although with smaller effect. The results presented here help in understanding the genetic and biochemical background underlying variations in fatty acid composition and flavour in beef.

Genotype by environment interaction for growth due to altitude in United States Angus cattle

The objectives of this study were to determine if sires perform consistently across altitude and to quantify the genetic relationship between growth and survival at differing altitudes. Data from the American Angus Association included weaning weight (WW) adjusted to 205 (n = 77,771) and yearling weight adjusted to 365 (n = 39,450) d of age from 77,771 purebred Angus cattle born in Colorado between 1972 and 2007. Postweaning gain (PWG) was calculated by subtracting adjusted WW from adjusted yearling weight. Altitude was assigned to each record based upon the zip code of each herd in the database. Records for WW and PWG were each split into 2 traits measured at low and high altitude, with the records from medium altitude removed from the data due to inconsistencies between growth performance and apparent culling rate. A binary trait, survival (SV), was defined to account for censored records at yearling for each altitude. It was assumed that, at high altitude, individuals missing a yearling weight either died or required relocation to a lower altitude predominantly due to brisket disease, a condition common at high altitude. Model 1 considered each WW and PWG measured at 2 altitudes as separate traits. Model 2 treated PWG and SV measured as separate traits due to altitude. Models included the effects of weaning contemporary group, age of dam, animal additive genetic effects, and residual. Maternal genetic and maternal permanent environmental effects were included for WW. Heritability estimates for WW in Model 1 were 0.28 and 0.26 and for PWG were 0.26 and 0.19 with greater values in low altitude. Genetic correlations between growth traits measured at different altitude were moderate in magnitude: 0.74 for WW and 0.76 for PWG and indicate possibility of reranking of sires across altitude. Maternal genetic correlation between WW at varying altitude of 0.75 also indicates these may be different traits. In Model 2, heritabilities were 0.14 and 0.27 for PWG and 0.36 and 0.47 for SV. Genetic correlation between PWG measured at low and high altitude was 0.68. Favorable genetic correlations were estimated between SV and PWG within and between altitudes, suggesting that calves with genetics for increased growth from weaning to yearling also have increased genetic potential for SV. Genetic evaluations of PWG in different altitudes should consider preselection of the data, by using a censoring trait, like survivability to yearling.

Behavioral changes in neonatal swine after an 8-hour rest during prolonged transportation

Long distance transportation of weaned piglets (Sus scrofa) is increasingly common in the united states and may result in delayed eating, drinking, or normal social behaviors. A potential solution is a mid-journey rest (lairage). The objective of this study was to determine if a lairage altered behavior after a 16-h transport. Pigs that weighed approximately 18 kg each (n = 894) were housed in 16 pens with 8 pens per treatment. Lairaged pigs were transported for 8 h and given an 8-h rest with food and water, whereas control pigs were transported continuously for 16 h. The heaviest, the lightest, and 2 average-BW pigs relative to the average weight of the pen were observed by video recording for 24 h immediately before and after transport, and during d 6 and 13 after transport. Postures (lying, sitting, and standing) were recorded using 10-min-interval scan sampling, and behavioral categories included inactivity, activities (eating, drinking, alert, manipulating pen, rooting, and walking) and social interactions (aggression, belly nosing, playing, tail biting, and positive social behaviors). In both treatments, sitting occurred most before transport (P < 0.01) than at other times, but did not differ between treatments. Standing increased (time effect; P < 0.01) for both treatments immediately after transport through d 6, but returned to pre-transport values by d 13. In contrast, lying decreased (time effect; P < 0.01) after transport, but returned to above pre-transport values by d 13. Time effects were evident for activity (P < 0.01), pen manipulation (P = 0.05), rooting (P < 0.01), initiation of belly-nosing (P = 0.01), and receiving belly-nosing (P = 0.03); however, initiation of aggression did not differ for day (P = 0.19) or treatment (P = 0.56). Lairaged pigs initiated more (P = 0.05) play than continuously transported pigs, but no differences (P = 0.84) were seen in receipt of play behavior. Pigs that were to be transported for 16 h continuously walked less pre-transport, walked more post-transport (treatment × time interaction; P = 0.02), and drank less pre-transport, but drank more on all days post-transport compared with the lairage group (treatment × time interaction; P = 0.001). This study indicated that extended transport without lairage alters some swine behaviors relevant to production (water consumption) and demonstrated that a long-duration transport, regardless of the mid-journey lairage treatment, affects a number of behaviors up to 13 d after transportation.

Genotype by region and season interactions on weaning weight in United States Angus cattle

The objective of this study was to determine if weaning weight performance is genetically consistent across different environments in the United States. The American Angus Association provided weight and pedigree data. Weaning weights observed in the Southeast (SoE) and Northwest (NW) were the focus of this study, as these regions are perceived as opposite extremes in climate. The 2 most represented calving seasons in each region were fall and winter in the SoE and winter and spring in the NW. The original data were edited to remove weaning weight records outside of 3 SD from the respective region-season mean, contemporary groups smaller than 20, and single-sire contemporary groups. The final dataset included 884,465 weaning weight records with 64,907 from fall-born calves in the SoE, 74,820 from winter-born calves in the SoE, 346,724 from winter-born calves in the NW and 398,014 from spring-born calves in the NW. Weaning weights of calves born in different region-season classes adjusted to 205 d of age were considered different but genetically correlated traits in a multivariate analysis. The sole fixed effect was weaning contemporary group and random effects included direct, maternal, maternal permanent environment, and a residual. Direct heritability estimates differed little across environments: 0.31 and 0.35 for weight in fall- and winter-born calves in the SoE, and 0.29 and 0.32 for winter- and spring-born calves in NW. Maternal heritability estimates ranged from 0.12 in the NW to 0.16 the SoE. Genetic correlations spanned from 0.69 to 0.93 among direct effects and from 0.65 to 0.95 among maternal effects. All heritability estimates had small (0.01 to 0.04) SE. The most distinct environments appeared to be winter in SoE and spring in NW (correlations of 0.69 and 0.65 for the direct and maternal effects). Different choices of sires for different environments might be justified to achieve the growth performance expected.

Investigation of the genetic architecture of a bone carcass weight QTL on BTA6

A previous analysis of an F(2) /Backcross Charolais × Holstein cross population identified the presence of a highly significant QTL on chromosome 6 (BTA6) affecting the proportion of bone in the carcass. Two closely linked QTL affected birth weight (BW) and body length at birth (BBL). In this report, the marker density around the QTL on BTA6 was increased, adding four additional microsatellite markers across the chromosome and 46 SNPs within the target QTL confidence interval. Of the SNPs, 26 were in positional candidate genes and the remaining 20 provided an even distribution of markers in the target QTL region. As a bone-related trait, the sum of the bone weight for all the left fore- and hindquarter joints of the carcass was analysed. We also studied the BW and BBL. Analyses of the data substantially reduced the QTL confidence interval. No strong evidence was found that the QTL for the three traits studied are different, and we conclude that the results are consistent with a single pleiotropic QTL influencing the three traits, with the largest effects on the proportion of bone in the carcass. The analyses also suggest that none of the SNPs tested is the sole causative variant of the QTL effects. Specifically, the SNP in the NCAPG gene previously reported as a causal mutation for foetal growth and carcass traits in other cattle populations was excluded as the causal mutation for the QTL reported here. Polymorphisms located in other previously identified candidate genes including SPP1, ABCG2, IBSP, MEPE and PPARGC1A were also excluded. The results suggest that SNP51_BTA-119876 is the polymorphism in strongest linkage disequilibrium with the causal mutation(s). Further research is required to identify the causal variant(s) associated with this bone-related QTL.

Microarray analysis in caudal medulla of cattle orally challenged with bovine spongiform encephalopathy

Bovine spongiform encephalopathy (BSE) is a fatal disorder in cattle characterized by progressive neurodegeneration of the central nervous system. We investigated the molecular mechanisms involved in neurodegeneration during prion infection through the identification of genes that are differentially expressed (DE) between experimentally infected and non-challenged cattle. Gene expression of caudal medulla from control and orally infected animals was compared by microarray analysis using 24,000 bovine oligonucleotides representing 16,846 different genes to identify DE genes associated with BSE disease. In total, 182 DE genes were identified between normal and BSE-infected tissues (>2.0-fold change, P < 0.01); 81 DE genes had gene ontology functions, which included synapse function, calcium ion regulation, immune and inflammatory response, apoptosis, and cytoskeleton organization; 13 of these genes were found to be involved in 26 different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The expression of five DE genes associated with synapse function (tachykinin, synuclein, neuropeptide Y, cocaine, amphetamine-responsive transcript, and synaptosomal-associated protein 25 kDa) and three DE genes associated with calcium ion regulation (parvalbumin, visinin-like, and cadherin) was further validated in the medulla tissue of cattle at different infection times (6, 12, 42, and 45 months post-infection) by qRT-PCR. These data will contribute to a better understanding of the molecular mechanisms of neuropathology in bovine species.

Investigating meniscal symptoms in patients with knee osteoarthritis--is MRI an unnecessary investigation?

The aim of this study was to evaluate the relationship between radiographic knee osteoarthritis and the presence of a relevant meniscal tear detected on MRI in symptomatic patients over the age of 60. Seventy seven patients over the age of 60 who had been investigated with a knee MRI over a 1-year period were identified. Sixty patients had a full set of data available for analysis. Their plain radiographs were blindly graded for osteoarthritis using the Kellgren-Lawrence (K-L) scale. The indications for the MRI were subdivided into: meniscal symptoms, general knee pain and "other". These indications were correlated with the K-L grade and result of the MRI. Overall, 40% of patients with a K-L grade of 0 had a meniscal tear compared to 89% of patients with a K-L score of 3, and 88% with a K-L score of 4. The indications for an MRI were grouped into meniscal symptoms (49), general pain (6) and other (5). In the group investigated for meniscal symptoms, the incidence of meniscal tears was 92% and 100% with a K-L grade of 3 and 4 respectively. This equated to a positive predictive value of 93% for K-L grade 3 and above, and 100% for K-L grade 4 alone. Given the predictability of the MRI findings in patients with significant osteoarthritis as well as meniscal symptoms, we conclude that this is an unnecessary investigation when used for this indication.

Epidemiology and practice patterns of achalasia in a large multi-centre database

BACKGROUND

Due to its rarity, achalasia remains a difficult disease to study.

AIMS

To describe the epidemiology of achalasia and practice patterns in its endoscopic management, utilising patient records from a large national database of endoscopic procedures.

METHODS

The Clinical Outcomes Research Initiative maintains a database of endoscopic procedures in diverse clinical practices. The data from 89 endoscopy practices distributed throughout the US during 2000-2008 were used to analyse the characteristics and therapy of patients with achalasia.

RESULTS

Among 521,497 upper endoscopies during the study period, we identified 896 patients with achalasia. Compared with the entirety of all other endoscopic diagnoses, achalasia was more common in men than in women (OR=1.39, CI 1.22-1.59), but similar among nonwhites and whites (OR=0.87, CI 0.74-1.03). Relatively, more achalasia patients were treated at university than at community practices (OR=1.52, CI 1.30-1.78). Botox injection was most frequently used as first choice of endoscopic therapy in 41%, followed by balloon dilation in 21%, Savary dilation in 20%, Maloney dilation in 10%, Rigiflex in 4% and other modalities in 4% of patients. One quarter of achalasia patients treated endoscopically underwent a repeat therapy about every 14 months.

CONCLUSIONS

Botox has become the primary choice of initial endoscopic therapy in achalasia. Despite their partial deviation from guidelines and recommendations, these endoscopic patterns reflect the current clinical practice in the United States.

Relationships between Podolic cattle breeds assessed by single nucleotide polymorphisms (SNPs) genotyping

Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure.

PCR-RFLP genotyping protocol for chicken Mx gene G/A polymorphism associated with the S631N mutation

The Mx (myxovirus resistance) gene codes for a protein with antiviral activity. Non-synonymous G/A polymorphism at position 2032 of chicken Mx cDNA results in a change at amino acid 631 of the Mx protein. This mutation has been shown to affect the antiviral activity of the Mx molecule, although recent studies have not confirmed this effect in response to some influenza strains. Nevertheless, the G/A polymorphism could be important for the chicken's response to other viruses. A robust PCR-RFLP protocol for genotyping chicken Mx gene polymorphism associated with the S631N mutation was developed. The F primer anneals to the last intron of the Mx gene, and the R primer anneals to the last exon of the gene, with an expected PCR product of 299 bp. PCR products were digested with Hpy8I. This enzyme cuts the sequence 5'-GTN|NAC-3', 2 bp downstream of the Mx polymorphism for the G allele, whereas the fragment containing the A allele is not cleaved. One hundred and twenty-seven chickens (commercial broilers, White Leghorn and New Hampshire) were genotyped using this protocol, and genotyping data were validated by sequencing. Full identity of results between the two genotyping methods was observed for all 127 samples, proving the reliability and robustness of this PCR-RFLP protocol.

Estimation of breed and heterosis effects for growth and carcass traits in cattle using published crossbreeding studies

Current genetic evaluations are performed separately for each breed. Multiple breed genetic evaluations, however, assume a common base among breeds, enabling producers to compare cattle of different breed makeup. Breed and heterosis effects are needed in a multibreed evaluation because databases maintained by breed associations include few crossbred animals, which may not be enough to accurately estimate these effects. The objective of this study was to infer breed effects, maternal effects, direct heterosis effects, and maternal heterosis effects for growth and carcass traits using least squares means estimates from crossbreeding studies published in the literature from 1976 to 1996. The data set was formed by recording each least squares mean along with the breed composition, maternal breed composition, and direct and maternal heterozygosity. Each trait was analyzed using a single trait fixed effect model, which included study as a fixed effect and breed composition and heterozygosity as covariates. Breed solutions for each trait were expressed relative to the Angus breed. Direct breed effects for weaning weight ranged from -7.0 +/- 0.67 kg (British Dairy) to 29.3 +/- 0.74 kg (Simmental), and maternal effects ranged from -11.7 +/- 0.24 kg (Hereford) to 31.1 +/- 2.22 kg (Gelbvieh). Direct breed effects for birth weight ranged from -0.5 +/- 0.14 kg (British Dairy) to 10.1 +/- 0.46 kg (Continental Beef), and maternal effects ranged from -7.2 +/- 0.13 kg (Brahman) to 6.0 +/- 1.07 kg (Continental Beef). Direct breed effects ranged from -17.9 +/- 1.64 kg (Brahman) to 21.6 +/- 1.95 kg (Charolais), from -6.5 +/- 1.29 kg (Brahman) to 55.8 +/- 1.47 kg (Continental Beef), from -8.1 +/- 0.48 cm(2) (Shorthorn) to 21.0 +/- 0.48 cm(2) (Continental Beef), and from -1.1 +/- 0.02 cm (Continental Beef) to 0 +/- 0.00 cm (Angus) for postweaning BW gain, carcass weight, LM area, and fat thickness, respectively. The use of literature estimates to predict direct and maternal breed and heterosis effects may supplement their direct prediction in a multibreed evaluation.

Production of alloantisera against class II bovine lymphocyte antigens (BoLA) by cross-immunization between class I matched cattle

This paper describes the production of alloantisera directed against bovine major histocompatibility complex (MHC) (BoLA) class II antigens in animals whose MHC phenotypes had been defined by one dimensional isoelectric focusing. Animals of closely matched BoLA class I types were selected by serology and subsequently typed for class I and class II by 1D-IEF of immunoprecipitated antigens. Those with similar class I type by both methods, but differing at the class II locus, were chosen for reciprocal immunization. Cross-immunization was by two skin implantations 6 weeks apart. The resulting antisera showed low titre after the first immunization and elevated titre 3 weeks after the second immunization. The sera reacted strongly with cells expressing specific BoLA class II antigens. The pattern of reactivity correlated well with IEF class II typing on a panel of animals representing all of the class II IEF types present in the Friesian population.

The analyses of antigen and DNA polymorphism within the bovine major histocompatibility complex: 1. The class I antigens

Serology, isoelectric focusing (IEF) of expressed antigens, and restriction fragment length polymorphisms (RFLP) were compared for the identification of BoLA class I haplotypes. Expressed antigens identified as bands by IEF correlated well with serological definition confirming and extending our earlier findings (Joosten et al. 1988). Comparison of serology and isoelectric focusing bands with restriction fragments was more complicated; fragments were found which correlated both with broadly reacting and antigen specific sera. We also found correlation of fragments with two or more sera which showed no cross-reactivity. Fragments unique to particular haplotypes were also observed. Serology remains the simplest method of typing BoLA class I antigens. Isoelectric focusing generally agrees with serological definition of antigens and detects antigens not yet defined by serology. It may also be useful in defining the products of other expressed BoLA class I loci. In order to identify RFLPs which could be used for typing, comparison with serology or IEF is essential. Haplotype specific RFLPs could be useful in identifying genes linked to the MHC.

Characterization of class I bovine lymphocyte antigens (BoLA) by one-dimensional isoelectrofocusing

BoLA class I antigens were characterized in a group of British and Dutch Friesian cattle by one-dimensional isoelectric focusing (1D-IEF) and the results compared with serology using alloantisera and microcytotoxicity. For IEF analysis, non-stimulated peripheral blood mononuclear cells (PBM) were metabolically labelled with 35S methionine, detergent lysates were prepared and MHC molecules precipitated with the monoclonal antibodies (mAbs) W6/32 or B1.1G6. Staphylococcus protein A precipitated antigens were separated on a vertical slab gel under denaturing conditions. The banding patterns seen for the W6/32 precipitated molecules obtained by 1D-IEF were compared with the serological specificities. Characteristic banding patterns were observed for most serological specificities as well as workshop undefined haplotypes. These patterns were seen both in families and the outbred population. In families IEF haplotypes segregated with serotypes. Additional MHC class I products were suggested by variable banding patterns for different w10 haplotypes and when using the different mAbs. A pulse chase experiment with a w12 animal also suggested more than one expressed product. The w2 and w5 specificities were not precipitated by either W6/32 or B1.1G6 and w6.2 and w6.4 were precipitated by W6/32 but not by B1.1G6. These results show that 1D-IEF is useful for BoLA typing. For the characterization of class I antigens, however, much depends on the mAbs used.

The effects of a mutation in the myostatin gene on meat and carcass quality

This study examined the effects of a mutation that inactivates the myostatin gene on calving, growth, carcass and meat quality traits in South Devon cattle. This breed carries at intermediate frequency an 11-bp deletion (MH) in the myostatin gene, known to be associated with the double-muscling phenotype, thus allowing a comparison of three genotype classes. The MH allele was associated with increased calving difficulty, carcass weight, muscle conformation and ratio of polyunsaturated to saturated fatty acids, as well as with reduced growth rate, carcass and meat fatness, and desirable flavour. However, the nature of the genetic effects differed between traits: in some cases the heterozygote MH carriers were more similar to the non-carriers than to homozygote carriers and in some cases, intermediate between the two homozygotes. The direction of these genetic effects has implications for the management of this genetic variation in the South Devon and other breeds.

Reducing bias in maintenance energy expected progeny difference by accounting for selection on weaning and yearling weights

Maintenance energy requirements of cattle can be predicted from published equations utilizing metabolic BW and milk production potential. Metabolic BW is a function of BW at a constant fat percentage or BCS. Pedigree and performance records can be used in random regression models to predict genetic merit for metabolic BW and milk production potentials. The purpose of this study was to present a methodology for predicting mature cow maintenance energy EPD using mature cow BW and BCS and accounting for prior selection of replacement females at weaning and yearling ages. Variance components were obtained for direct and maternal effects on weaning weight, direct effects on postweaning BW gain, and direct coefficients for random regression on mature weights (MW) adjusted for BCS. These BW were transformed into metabolic BW by taking BW to the power of 0.75, variance components were estimated for metabolic BW, and were then used to predict breeding values from which cow maintenance energy EPD could be derived. Data used in this analysis were obtained from the Red Angus Association of America and limited to herds with MW and corresponding BCS observations. The data set included 52,338 BW records on 21,103 individuals. Weaning and yearling contemporaries to those with MW observations, but with no MW records themselves, were included to account for selection occurring before maturity. Heritability estimates for weaning weight direct, weaning weight maternal, and postweaning BW gain were 0.18 +/- 0.02, 0.16 +/- 0.02, and 0.18 +/- 0.02, respectively. Mature BW observed at 2, 3, 4, 5, and 6 yr of age had heritability estimates of 0.45 +/- 0.03, 0.44 +/- 0.03, 0.49 +/- 0.03, 0.66 +/- 0.04, and 0.62 +/- 0.05, respectively. Correlations between weaning weight direct and MW ranged from 0.65 +/- 0.07 to 0.82 +/- 0.04, and correlations between MW at different ages ranged from 0.95 +/- 0.03 to 0.99 +/- 0.01. The genetic correlations between postweaning BW gain and MW ranged from 0.48 +/- 0.06 to 0.59 +/- 0.06. The 15-yr genetic increase in metabolic BW was 3.6 kg(0.75), greater than the value of 0.23 kg(0.75) obtained from the same data ignoring weaning and yearling contemporaries with unobserved MW, the approach currently used in the derivation of cow maintenance EPD published by the Red Angus Association of America.

Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle

A genome scan to detect QTL influencing growth and carcass-related traits was conducted in a Charolais x Holstein crossbred cattle population. Phenotypic measurements related to growth and carcass traits were made on the 235 second-generation crossbred males of this herd (F2 and reciprocal backcrosses), which were born in 4 consecutive annual cohorts. Traits measured in vivo were related to birth dimensions, growth rates, and ultrasound measurements of fat and muscle depth. The animals were slaughtered near a target BW of 550 kg, and a wide range of postmortem traits were measured: visual assessment of carcass conformation and carcass fatness, estimated subcutaneous fat percentage, weights of kidney knob and channel fat, and weights of carcass components after commercial and full-tissue dissections. The whole population, including grandparents, parents, and the crossbred bulls, was genotyped initially for 139 genome-wide microsatellite markers. Twenty-six additional markers were subsequently analyzed to increase marker density on some of the chromosomes where QTL had been initially identified. The linear regression analyses based on the 165 markers revealed a total of 51 significant QTL at the suggestive level, 21 of which were highly significant (F-value >or=9; based on the genome-wide thresholds obtained in the initial scan). A large proportion of the highly significant associations were found on chromosomes 5 and 6. The most highly significant QTL was localized between markers DIK1054 and DIK082 on chromosome 6 and explained about 20% of the phenotypic variance for the total bone proportion estimated after the commercial dissection. In the adjacent marker interval on this chromosome, 2 other highly significant QTL were found that explain about 30% of the phenotypic variance for birth dimension traits (BW and body length at birth). On chromosome 5, the most significant association influenced the lean:bone ratio at the forerib joint and was flanked by markers DIK4782 and BR2936. Other highly significant associations were detected on chromosomes 10 (estimated subcutaneous fat percentage), 11 (total saleable meat proportion), 16 (prehousing growth rate), and 22 (bone proportion at the leg joint). These results provide a useful starting point for the identification of the genes associated with traits of direct interest to the beef industry, using fine mapping or positional candidate gene approaches.

Assessment of AFLP marker behaviour in enriching STS radiation hybrid maps

Radiation hybrid (RH) mapping provides a powerful tool to build high-resolution maps of genomes. Here, we demonstrate the use of the AFLP technique for high-throughput typing of RH cell lines. Cattle were used as the model species because an RH panel was available to investigate the behaviour of AFLP markers within the microsatellite- and STS-based maps of this species. A total of 747 AFLP markers were typed on the TM112 RH radiation panel and 651 of these were assigned by two-point analysis to the 29 bovine autosomes and sex chromosomes. AFLP markers were added to the 1222 microsatellite and STS markers that were included in earlier RH maps. Multipoint maps were constructed for seven example chromosomes, which retained 248 microsatellite and STS markers, and added 123 AFLP markers at LOD 4. The addition of the AFLP markers increased the number of markers by 42.1% and the map length by 10.4%. The AFLP markers showed lower retention frequency (RF) values than the STS markers. The comparison of RF values in AFLP markers and their corresponding AFLP-derived STSs demonstrated that the lower RF values were due to the lower detection sensitivity of the AFLP technique. Despite these differences, AFLP and AFLP-derived STS markers mapped to identical or similar positions. These results demonstrate that it is possible to merge AFLP and microsatellite markers in the same map. The application of AFLP technology could permit the rapid construction of RH maps in species for which extensive genome information and large numbers of SNP and microsatellite markers are not available.

Characterization of a 320-kb region containing the HEXA gene on bovine chromosome 10 and analysis of its association with BSE susceptibility

Bovine spongiform encephalopathy (BSE) belongs to a group of neurodegenerative diseases known as transmissible prion diseases. Recently, variants in the promoter region of the prion protein (PRNP) gene have been shown to have a considerable effect on the susceptibility to BSE. However, a previous genome scan revealed other putative BSE-susceptibility loci. Here, we analysed such a region on BTA10, which contains the functional candidate gene HEXA. Three hundred and twenty kilobases that, besides HEXA, also contain ARIH1, BRUNOL6 and PARP6 were characterized and screened for polymorphisms. Genotyping of 38 SNPs in Holstein-Friesian animals from the UK (350 diseased and 270 controls) revealed two intronic SNPs that were associated with BSE incidence, with experiment-wise P-values of 3.5 x 10(-3) and 7.7 x 10(-3) respectively. Both SNPs were in strong linkage disequilibrium and the rare alleles had a protective effect. These alleles were contained in a haplotype dubbed 'UK-protective' that was significantly overrepresented in the controls with a permuted P-value of 2 x 10(-3). An association study in German Holstein animals (73 diseased and 627 controls) revealed an opposite effect of the 'UK-protective' haplotype in this population, i.e. it was overrepresented in the diseased animals, although not significant after correction for multiple testing. These findings indicate a causal variant for BSE susceptibility on BTA10 in linkage disequilibrium with the markers studied. Candidate gene analyses of the surrounding region and additional association studies will help to clarify the origin of the protective effects and to identify causal variants for BSE susceptibility on BTA10.

Fine-mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds

A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over the whole chromosome in the 16 original families and 18 additional half-sib families. This enabled linkage disequilibrium information to be used in the analysis. Data were analysed by an approach that combines information from linkage and linkage disequilibrium, which allowed the QTL affecting clinical mastitis to be mapped to a small interval (<1 cM) between the markers BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker-assisted selection. Pleiotropic effects of the mastitis QTL were studied for three milk production traits and eight udder conformation traits. This QTL was also associated with yield traits in DR but not in FA or SRB. No QTL were found for udder conformation traits on chromosome 9.

Detection of quantitative trait loci for meat quality traits in cattle

A whole-genome scan was carried out to detect quantitative trait loci (QTL) affecting sensory, organoleptic, physical and chemical properties of meat. The study used phenotypic data from 235 second-generation cross-bred bull calves of a Charolais x Holstein experimental population. Loin muscle samples were evaluated for yield force, intramuscular fat and nitrogen contents, myofibrillar fragmentation index, haem pigment concentration, moisture content and pH at 24 h postmortem. A sensory assessment was performed on grilled loin and roasted silverside joints by trained panellists. A linear regression analysis based on 165 markers revealed 35 QTL at the 5% chromosome-wide significance level (20 for sensory traits and 15 for physical and chemical traits), five of which were highly significant (F-value: > or =9). The most significant QTL was located on chromosome 6 (with the best likely position at 39 cM) and affected haem pigment concentration. The Holstein allele for this QTL was associated with an increase of 0.53 SD in the haem scores. A QTL for pH(24h) was identified on chromosome 14 (at 40 cM) and a QTL for moisture content was identified on chromosome 22 (at 21 cM). Two highly significant QTL were identified for sensory panel-assessed traits: beef odour intensity (grilled sample) on chromosome 10 (at 119 cM), and juiciness (roast sample) on chromosome 16 (at 70 cM). The proportion of phenotypic variance explained by the significant QTL ranged from 3.6% (for nitrogen content on chromosome 10) to 9.5% (for juiciness, roast sample on chromosome 16).

An advanced sheep (Ovis aries, 2n = 54) cytogenetic map and assignment of 88 new autosomal loci by fluorescence in situ hybridization and R-banding

Presented herein is an updated sheep cytogenetic map that contains 452 loci (291 type I and 161 type II) assigned to specific chromosome bands or regions on standard R-banded ideograms. This map, which significantly extends our knowledge of the physical organization of the ovine genome, includes new assignments for 88 autosomal loci, including 74 type I loci (known genes) and 14 type II loci (SSRs/microsatellite marker/STSs), by FISH-mapping and R-banding. Comparison of the ovine map to the cattle and goat cytogenetic maps showed that common loci were located within homologous chromosomes and chromosome bands, confirming the high level of conservation of autosomes among ruminant species. Eleven loci that were FISH-mapped in sheep (B3GAT2, ASCC3, RARSL, BRD2, POLR1C, PPP2R5D, TNRC5, BAT2, BAT4, CDC5L and OLA-DRA) are unassigned in cattle and goat. Eleven other loci (D3S32, D1S86, BMS2621, SFXN5, D5S3, D5S68, CSKB1, D7S49, D9S15, D9S55 and D29S35) were assigned to specific ovine chromosome (OAR) bands but have only been assigned to chromosomes in cattle and goat.

Differentiation of European cattle by AFLP fingerprinting

The Neolithic introduction of domestic cattle into Europe was followed by differential adaptation, selection, migration and genetic isolation, leading ultimately to the emergence of specialized breeds. We have studied the differentiation of European cattle by amplified fragment length polymorphism (AFLP) fingerprinting. Combining AFLP data sets from two laboratories yielded 81 biallelic polymorphic markers scored in 19-22 individual animals from 51 breeds. Model-based clustering differentiated Podolian cattle as well as French and Alpine breeds from other European cattle. AFLP genetic distances correlated well with microsatellite-based genetic distances calculated for the same breeds. However, the AFLP data emphasized the divergence of taurine and indicine cattle relative to the variation among European breeds and indicated an Eastern influence on Italian and Hungarian Podolian breeds. This probably reflects import from the East after the original introduction of domestic cattle into Europe. Our data suggest that Italian cattle breeds are relatively diverse at the DNA sequence level.

Polymorphisms of the prion protein gene coding region in born-after-the-reinforced-ban (BARB) bovine spongiform encephalopathy cattle in Great Britain

Polymorphisms of the prion protein gene are associated with differing susceptibilities to transmissible spongiform encephalopathy diseases, as shown for variant Creutzfeldt–Jakob disease in humans and scrapie in sheep, but not yet in cattle. Imposition of control measures in the UK, including a reinforced ruminant feed ban in 1996, has led to a reduction in the incidence of bovine spongiform encephalopathy (BSE). BSE-affected cattle born after 1996 in Great Britain have been termed born-after-the-reinforced-ban (BARB) cases. In this study, the PrP gene coding region from 100 BARB BSE cases and 66 matched healthy-control cattle was sequenced to investigate whether this would reveal a genetic basis to their origin. Polymorphisms identified were not found to be associated with increased susceptibility to BSE in the BARB cases. Analysis of BARB cases grouped either by clinical status or by whether they formed an isolated or clustered case was also undertaken, but differences were not found to be significant.

Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping

High-density whole-genome maps are essential for ordering genes or markers and aid in the assembly of genome sequence. To increase the density of markers on the bovine radiation hybrid map, and hence contribute to the assembly of the bovine genome sequence, an Illumina® BeadStation was used to simultaneously type large numbers of markers on the Roslin-Cambridge 3000 rad bovine–hamster whole-genome radiation hybrid panel (WGRH₃₀₀₀). In five multiplex reactions, 6738 sequence tagged site (STS) markers were successfully typed on the WGRH₃₀₀₀ panel DNA. These STSs harboured SNPs that were developed as a result of the bovine genome sequencing initiative. Typically, the most time consuming and expensive part of creating high-density radiation hybrid (RH) maps is genotyping the markers on the RH panel with conventional approaches. Using the method described in this article, we have developed a high-density whole-genome RH map with 4690 loci and a linkage map with 2701 loci, with direct comparison to the bovine whole-genome sequence assembly (Btau_2.0) in a fraction of the time it would have taken with conventional typing and genotyping methods.

Radiation hybrid mapping of all 10 characterized bovine Toll-like receptors

Toll-like receptors (TLRs) are cell-surface signalling molecules that recognize a range of highly conserved pathogen molecules and instigate the appropriate immune response. Here, we report the mapping of all 10 characterized bovine TLR genes using a radiation hybrid panel. The genomic organization of the bovine TLRs is similar to that of humans and mice. TLR1, TLR6 and TLR10 map closely together on Bos taurus chromosome 6 (BTA6), while TLR7 and TLR8 map to the X chromosome. TLR2, TLR3, TLR4, TLR5 and TLR9 map to BTA17, BTA27, BTA8, BTA16 and BTA22 respectively. Our increased knowledge of the genomic organization of the bovine TLR genes may promote our understanding of their evolution and help in the identification of bovine genes underlying disease-resistance traits.