Expression of candidate genes for residual feed intake in Angus cattle.

Residual feed intake (RFI) has been adopted in Australia for the purpose of genetic improvement in feed efficiency in beef cattle. RFI is the difference between the observed feed intake of an animal and the predicted feed intake based on its size and growth rate over a test period. Gene expression of eight candidate genes (AHSG, GHR, GSTM1, INHBA, PCDH19, S100A10, SERPINI2 and SOD3), previously identified as differentially expressed between divergent lines of high- and low-RFI animals, was measured in an unselected population of 60 steers from the Angus Society Elite Progeny Test Program using quantitative real-time PCR. Results showed that the levels of gene expression were significantly correlated with RFI. The genes explain around 33.2% of the phenotypic variance in RFI, and prediction equations using the expression data are reasonably accurate estimators of RFI. The association of these genes with economically important traits, such as other feed efficiency-related traits and fat, growth and carcass traits, was investigated as well. The expression of these candidate genes was significantly correlated with feed conversion ratio and daily feed intake, which are highly associated with RFI, suggesting a functional role for these genes in modulating feed utilisation. The expression of these genes did not show any association with average daily gain, eye muscle area and carcass composition.

Skin tumours in the West of Scotland renal transplant population.

BACKGROUND: Organ transplant recipients have an increased risk of skin cancers. A specialist dermatology clinic for renal transplant recipients (RTRs) was established in 2005. OBJECTIVES: To analyse the type and incidence of skin cancers in prevalent patients in the West of Scotland after renal transplant, and to analyse the impact of the time since transplant and the immunosuppression regimen. METHODS: Skin cancer data for RTRs attending the transplant dermatology clinic over a 38-month period were collected and recorded in the West of Scotland electronic renal patient record. Skin cancer data were intrinsically linked to each individual's transplant and immunosuppression data. RESULTS: Overall, 610 patients attended. The median follow-up time from the date of first transplant was 10 years. Ninety-three patients (15.2%) had experienced a total of 368 skin cancers since transplant, and the prevalence increased with time since transplant. Basal cell carcinomas (BCCs) occurred in 74 patients (12.1%) and squamous cell carcinomas (SCCs) in 42 patients (6.9%). Three patients (0.5%) had experienced a melanoma. The SCC:BCC ratio was 0.7. Survival analysis showed significant reduction in the time to develop skin cancer in patients transplanted from 1995 onwards (P < 0.0001) and in patients who had been on triple immunosuppressant therapy at 1 year after transplant, compared with dual therapy (P < 0.0001). CONCLUSIONS: This is the first study of skin cancer in prevalent Scottish RTRs. The incidence of skin cancer is high and appears to have a direct relationship to the overall burden of immunosuppression. The SCC:BCC ratio, which is lower than reports from other centres, deserves further scrutiny.

Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake.

Feed efficiency is an economically important trait in beef production. It can be measured as residual feed intake. This is the difference between actual feed intake recorded over a test period and the expected feed intake of an animal based on its size and growth rate. DNA-based marker-assisted selection would help beef breeders to accelerate genetic improvement for feed efficiency by reducing the generation interval and would obviate the high cost of measuring residual feed intake. Although numbers of quantitative trait loci and candidate genes have been identified with the advance of molecular genetics, our understanding of the physiological mechanisms and the nature of genes underlying residual feed intake is limited. The aim of the study was to use global gene expression profiling by microarray to identify genes that are differentially expressed in cattle, using lines genetically selected for low and high residual feed intake, and to uncover candidate genes for residual feed intake. A long-oligo microarray with 24 000 probes was used to profile the liver transcriptome of 44 cattle selected for high or low residual feed intake. One hundred and sixty-one unique genes were identified as being differentially expressed between animals with high and low residual feed intake. These genes were involved in seven gene networks affecting cellular growth and proliferation, cellular assembly and organization, cell signalling, drug metabolism, protein synthesis, lipid metabolism, and carbohydrate metabolism. Analysis of functional data using a transcriptional approach allows a better understanding of the underlying biological processes involved in residual feed intake and also allows the identification of candidate genes for marker-assisted selection.

Presence of beta human papillomaviruses in nonmelanoma skin cancer from organ transplant recipients and immunocompetent patients in the West of Scotland.

BACKGROUND: Nonmelanoma skin cancer (NMSC) has been linked to cutaneous human papillomaviruses of the genus beta (betaPV). OBJECTIVES: We sought to assess the presence of betaPV in NMSC biopsies from a group of Scottish skin cancer patients, both immunocompetent (IC) patients and immunosuppressed (IS) organ transplant recipients. METHODS: One hundred and twenty-one paraffin-embedded skin tumours (27 actinic keratosis, 41 intraepidermal carcinoma, 53 squamous cell carcinoma) and 11 normal skin samples were analysed for the presence of betaPV by a polymerase chain reaction-reverse hybridization assay designed to detect the presence of the 25 known betaPV genotypes. RESULTS: In IC patients, betaPV was detected in 30 of 59 (51%) tumours and two of 11 (18%) normal skin samples (P = 0.046). In IS patients, betaPV was found in 27 of 62 (44%) tumours; no normal skin samples were available for comparison. The most frequently found genotypes were HPV-24, HPV-15 and HPV-38. Of those tumours infected with betaPV, 28 of 57 (49%) were infected with more than one genotype (range 2-8). Tumours from IS patients were from a younger age group (mean age 57.4 years) than IC patients (mean age 73.8 years). Multiple infections were more common in tumours from IC patients (21 of 30; 70%) compared with those from IS patients (seven of 27; 26%) (P < 0.001). In the IC group, age did not appear to influence the distribution of single and multiple infections whereas in IS patients the proportion of multiple infections to single infections increased with age. There were no multiple infections in normal skin. CONCLUSIONS: A wide spectrum of betaPV types was detected in our samples. Further characterization of betaPV in vivo is needed in order to determine the mechanisms by which the virus contributes to cutaneous carcinogenesis.

Phenotypic relationships among methane production traits assessed under ad libitum feeding of beef cattle.

Angus cattle from 2 beef cattle projects in which daily methane production (MPR) was measured were used in this study to examine the nature of the relationships among BW, DMI, and methane traits of beef cattle fed ad libitum on a roughage diet or a grain-based feedlot diet. In both projects methane was measured using the GreenFeed Emission Monitoring system, which provides multiple short-term breath measures of methane production. The data used for this study were from 119 Angus heifers over 15 d on a roughage diet and 326 Angus steers over 70 d on a feedlot diet. Mean (±SD) age, BW, and DMI were 372 ± 28 d, 355 ± 37 kg, and 8.1 ± 1.3 kg/d for the heifers and 554 ± 86 d, 577 ± 69 kg, and 13.3 ± 2.0 kg/d for the steers, respectively. The corresponding mean MPR was 212 g/d for heifers and 203 g/d for steers. Additional traits studied included methane yield (MY; MPR/DMI), methane intensity (MPR/BW), and 3 forms of residual methane production (RMP), which is a measure of actual minus predicted MPR. For RMP, RMP, and RMP predicted MPR were obtained by regression of MPR on BW, on DMI, and on both DMI and BW, respectively. The 2 data sets were analyzed separately using the same statistical procedures. For both feed types the relationships between MPR and DMI and between MPR and BW were both positive and linear. The correlation between MPR and DMI was similar to that between MPR and BW, although the correlations were stronger for the roughage diet ( = 0.75 for MPR vs. DMI; = 0.74 for MPR vs. BW) than the grain-based diet ( = 0.62 for MPR vs. DMI; = 0.66 for MPR vs. BW). The correlation between MY and DMI was negative and moderate for the roughage ( = -0.68) and grain-based ( = -0.59) diets, a finding that is different from the nonsignificant correlations reported in studies of cattle on a restricted roughage diet. The 3 RMP traits were strongly correlated ( values from 0.76 to 0.99) with each other for both the roughage and the grain-based diets, which indicates that using RMP to lower MPR could provide a result similar to using RMP in cattle. As feed intake (DMI) is more difficult to measure than BW, this result implies that under ad libitum feeding situations in which DMI cannot be measured, RMP can be used to identify higher- or lower-RMP animals with similar levels of effectiveness as RMP.

Optimizing test procedures for estimating daily methane and carbon dioxide emissions in cattle using short-term breath measures.

Respiration chambers are considered the reference method for quantifying the daily CH production rate (MPR) and CO production rate (CPR) of cattle; however, they are expensive, labor intensive, cannot be used in the production environment, and can be used to assess only a limited number of animals. Alternative methods are now available, including those that provide multiple short-term measures of CH and CO, such as the GreenFeed Emission Monitoring (GEM) system. This study was conducted to provide information for optimizing test procedures for estimating MPR and CPR of cattle from multiple short-term CH and CO records. Data on 495 Angus steers on a 70-d ad libitum feedlot diet with 46,657 CH and CO records and on 121 Angus heifers on a 15-d ad libitum roughage diet with 7,927 CH and CO records were used. Mean (SD) age and BW were 554 d (SD 92) and 506 kg (SD 73), respectively, for the steers and 372 d (SD 28) and 348 kg (SD 37), respectively, for the heifers. The 2 data sets were analyzed separately but using the same procedures to examine the reduction in variance as more records are added and to evaluate the level of precision with 2 vs. 3 min as the minimum GEM visit duration for a valid record. The moving averages procedure as well as the repeated measures procedure were used to calculate variances for both CH and CO, starting with 5 records and progressively increasing to a maximum of 80 records. For both CH and CO and in both data sets, there was a sharp reduction in the variances obtained by both procedures as more records were added. However, there was no substantial reduction in the variance after 30 records had been added. Inclusion of records with a minimum of 2-min GEM visit duration resulted in reduction in precision relative to a minimum of 3 min, as indicated by significantly ( < 0.05) more heterogeneous variances for all cases except CH4 in steers. In addition, more records were required to achieve the same level of precision relative to data with minimum GEM visit durations of 3 min. For example, in the steers, 72% reduction in initial variance was achieved with 30 records for both CH and CO when minimum GEM visit duration was 3 min, relative to 45 records when data with a minimum visit duration of 2 min were included. It is concluded from this study that when using records of multiple short-term breath measures of CH or CO for the computation of an animal's MPR or CPR, a minimum of 30 records, each record obtained from a minimum GEM visit duration of 3 min, are required.

Associations among methane emission traits measured in the feedlot and in respiration chambers in Angus cattle bred to vary in feed efficiency.

The objective of the study was to evaluate associations among animal performance and methane emission traits under feedlot conditions and in respiration chambers in Angus cattle bred to vary in residual feed intake (RFI), which is a measure of feed efficiency. Fifty-nine cattle were tested for feedlot RFI, of which 41 had methane production recorded on an ad libitum grain-based ration in the feedlot, 59 on a restricted grain-based ration in respiration chambers, and 57 on a restricted roughage ration in respiration chambers. The cattle became older and heavier as they went through the different phases of the experiment, but their feed intake (expressed as DMI) and daily emission of enteric methane (methane production rate; MPR) did not increase proportionally, as feed offered was restricted in the respiration chamber tests. Methane emissions by individual animals relative to their DMI were calculated as methane yield (MY; MPR/DMI) and as 2 measures of residual methane production (RMP and RMP), which were calculated as the difference between measured MPR and that predicted from feed intake by 2 different equations. Within each test regime, MPR was positively correlated ( = 0.28 to 0.61) with DMI. Phenotypic correlations for MY, RMP, and RMP between the feedlot test and the restricted grain test ( = 0.40 to 0.43) and between the restricted grain test and the restricted roughage test were moderate ( = 0.36 to 0.41) and moderate to strong between the feedlot test and the restricted roughage test ( = 0.54 to 0.58). These results indicate that the rankings of animals for methane production relative to feed consumed are relatively stable over the 3 test phases. Feedlot feed conversion ratio and RFI were not correlated with MPR in the feedlot test and grain-based chamber test but were negatively correlated with MPR in the chamber roughage test ( = -0.31 and -0.37). Both were negatively correlated with MY and RMP in the feedlot test ( = -0.42 to -0.54) and subsequent chamber roughage test ( = -0.27 to -0.49). Midparent estimated breeding values for RFI tended to be negatively correlated with MY and RMP in the feedlot test ( = -0.27 and -0.27) and were negatively correlated with MY, RMP, and RMP in the chamber roughage test ( = -0.33 to -0.36). These results showed that in young growing cattle, lower RFI was associated with higher MY, RMP, and RMP but had no significant association with MPR.

Genetic and phenotypic variance and covariance components for methane emission and postweaning traits in Angus cattle.

Ruminants contribute 80% of the global livestock greenhouse gas (GHG) emissions mainly through the production of methane, a byproduct of enteric microbial fermentation primarily in the rumen. Hence, reducing enteric methane production is essential in any GHG emissions reduction strategy in livestock. Data on 1,046 young bulls and heifers from 2 performance-recording research herds of Angus cattle were analyzed to provide genetic and phenotypic variance and covariance estimates for methane emissions and production traits and to examine the interrelationships among these traits. The cattle were fed a roughage diet at 1.2 times their estimated maintenance energy requirements and measured for methane production rate (MPR) in open circuit respiration chambers for 48 h. Traits studied included DMI during the methane measurement period, MPR, and methane yield (MY; MPR/DMI), with means of 6.1 kg/d (SD 1.3), 132 g/d (SD 25), and 22.0 g/kg (SD 2.3) DMI, respectively. Four forms of residual methane production (RMP), which is a measure of actual minus predicted MPR, were evaluated. For the first 3 forms, predicted MPR was calculated using published equations. For the fourth (RMP), predicted MPR was obtained by regression of MPR on DMI. Growth and body composition traits evaluated were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), final weight (FWT), and ultrasound measures of eye muscle area, rump fat depth, rib fat depth, and intramuscular fat. Heritability estimates were moderate for MPR (0.27 [SE 0.07]), MY (0.22 [SE 0.06]), and the RMP traits (0.19 [SE 0.06] for each), indicating that genetic improvement to reduce methane emissions is possible. The RMP traits and MY were strongly genetically correlated with each other (0.99 ± 0.01). The genetic correlation of MPR with MY as well as with the RMP traits was moderate (0.32 to 0.63). The genetic correlation between MPR and the growth traits (except BWT) was strong (0.79 to 0.86). These results indicate that selection for lower MPR may have undesired effect on animal productivity. On the other hand, MY and the RMPR were either not genetically correlated or weakly correlated with BWT, YWT, and FWT (-0.06 to 0.23) and body composition traits (-0.18 to 0.18). Therefore, selection for lower MY or RMPR would lead to lower MPR without impacting animal productivity. Where the use of a ratio trait (e.g., MY) is not desirable, selection on any of the forms of RMP would be an alternative.

Genomic heritabilities and genomic estimated breeding values for methane traits in Angus cattle.

Enteric methane emissions from beef cattle are a significant component of total greenhouse gas emissions from agriculture. The variation between beef cattle in methane emissions is partly genetic, whether measured as methane production, methane yield (methane production/DMI), or residual methane production (observed methane production - expected methane production), with heritabilities ranging from 0.19 to 0.29. This suggests methane emissions could be reduced by selection. Given the high cost of measuring methane production from individual beef cattle, genomic selection is the most feasible approach to achieve this reduction in emissions. We derived genomic EBV (GEBV) for methane traits from a reference set of 747 Angus animals phenotyped for methane traits and genotyped for 630,000 SNP. The accuracy of GEBV was tested in a validation set of 273 Angus animals phenotyped for the same traits. Accuracies of GEBV ranged from 0.29 ± 0.06 for methane yield and 0.35 ± 0.06 for residual methane production. Selection on GEBV using the genomic prediction equations derived here could reduce emissions for Angus cattle by roughly 5% over 10 yr.

Cardiac effects of sodium stibogluconate: myocardial, electrophysiological and biochemical studies.

The pentavalent antimonial sodium stibogluconate is the mainstay of anti-leishmanial therapy. Sodium stibogluconate is less cardiotoxic than antimony and the trivalent derivatives, but has been associated with dose-related electrocardiographic changes. The effect of the currently-used regimen of sodium stibogluconate (20 mg/kg/day for 20 days) on cardiac function is uncertain. We studied 12 soldiers, mean age 24 years, with proven cutaneous leishmaniasis treated with this regimen. There were no significant changes in echocardiographic indices of left ventricular systolic or diastolic function during treatment. Indices of myocardial electrical stability (heart-rate variability and episodes of overt supraventricular and ventricular arrhythmias) were unchanged, but there was a reversible decrease in T-wave amplitude during treatment. Systolic and diastolic blood pressure fell and the heart rate increased during treatment. This regimen of sodium stibogluconate does not measurably impair left ventricular systolic or diastolic function. Minor T-wave changes occur during treatment, but there is no increase in arrhythmia frequency or change in heart-rate variability. In most young fit patients, this regimen has no cardiac side-effects. However, idiosyncratic reactions cannot be excluded, and patients with malnutrition, impaired renal function or pre-existing heart disease may be more sensitive to any cardiotoxic properties of sodium stibogluconate.

Basic laser principles.

Skin diseases have been treated with lasers since the early 1960s. The three principal chromophores in the skin--hemoglobin, melanin, and water--have different absorption spectra that selectively absorb certain wavelengths of electromagnetic radiation. A given wavelength and pulse duration will selectively treat a target containing a chromophore. The wide variety of lasers and their applications are discussed.

Neonatal cerebral arterial flow velocity waveforms in term infants with and without metabolic acidosis at delivery.

To define the effects of acid base status at delivery on neonatal cerebral artery flow velocity waveform patterns obtained using Doppler ultrasound during the first week of life, a longitudinal comparative study of neonates born at term with and without evidence of metabolic acidosis in the umbilical artery was undertaken. Eighty-two appropriate for gestational age infants delivered after uncomplicated pregnancies with non-acidotic umbilical artery blood gases and in whom no neonatal complications were noted were studied to establish reference values of neonatal cerebral arterial vascular resistance index (RI) in normal term infants during the first week of life. A further 189 infants were grouped according to the presence and severity of metabolic acidosis at delivery, and also the presence of high risk features in the antenatal period. In the normal non-acidotic infants, over the first 24 h of life, there was a significant fall in the cerebral arterial resistance index (RI) in all the vessels examined, after which a steady state value was attained with no significant changes in vascular resistance index being noted during the remainder of the study period. The fall in RI between 12 and 24 h of age was consistent in all study groups. Infants with metabolic acidosis at delivery had blood flow patterns compatible with decreased resistance to flow in both anterior and middle cerebral arteries which persisted throughout the first week of life. This reduction in cerebral vascular resistance was most marked in those infants with severe metabolic acidosis. The majority of severely acidotic infants had a benign clinical outcome in the first week of life and all infants had normal cerebral ultrasound scans during the neonatal period. These findings suggest that metabolic acidosis at birth is associated with changes in neonatal cerebral arterial vascular resistance during the first week of life, and in the presence of benign clinical course the significance of this observation with regard to neurodevelopmental outcome requires evaluation.

Optimum postweaning test for measurement of growth rate, feed intake, and feed efficiency in British breed cattle.

The optimum duration of test for measurement of growth rate, feed intake, feed conversion, and residual feed intake was examined using postweaning feed intake and weight data from 760 Angus, Hereford, Polled Hereford, and Shorthorn heifer and Angus bull progeny from 78 sires. Variance components, heritability, phenotypic and genetic correlations, and the efficiency of selection using shortened tests compared with a 199-d test were used as criteria to assess the optimum test length. The results indicated that a 35-d test was sufficient for measurement of feed intake, whereas a 70-d test was required to measure growth rate, feed conversion, and residual feed intake without compromising the accuracy of measurement. When a 70-d test is used to measure growth rate, feed conversion, and residual feed intake there is minimal loss in accuracy when weights are collected every 2 wk instead of weekly, but a further increase in the interval between weights to 5 wk caused a decline in the accuracy of the test. Therefore a 70-d test with cattle weighed every 2 wk seems to be optimal for measuring these traits in British breed cattle.

Genetic and phenotypic variance and covariance components for feed intake, feed efficiency, and other postweaning traits in Angus cattle.

Records on 1,180 young Angus bulls and heifers involved in performance tests were used to estimate genetic and phenotypic parameters for feed intake, feed efficiency, and other postweaning traits. The mean age was 268 d at the start of the performance test, which comprised 21-d adjustment and 70-d test periods. Traits studied included 200-d weight, 400-d weight, scrotal circumference, ultrasonic measurements of rib and rump fat depths and longissimus muscle area, ADG, metabolic weight, daily feed intake, feed conversion ratio, and residual feed intake. For all traits except the last five, additional data from the Angus Society ofAustralia pedigree and performance database were included, which increased the number of animals to 27,229. Genetic (co)variances were estimated by REML using animal models. Direct heritability estimates for 200-d weight, 400-d weight, rib fat depth, ADG, feed conversion,and residual feed intake were 0.17 +/- 0.03, 0.27 +/- 0.03, 0.35 +/- 0.04, 0.28 +/- 0.04, 0.29 +/- 0.04, and 0.39 +/- 0.03, respectively. Feed conversion ratio was genetically (r(g) = 0.66 ) and phenotypically (r(p) = 0.53) correlated with residual feed intake. Feed conversion ratio was correlated (r(g) = -0.62, r(p) = -0.74) with ADG, whereas residual feed intake was not (rg = -0.04, r(p) = -0.06). Genetically, both residual feed intake and feed conversion ratio were negatively correlated with direct effects of 200-d weight (r(g) = -0.45 and -0.21) and 400-d weight (r(g) = -0.26 and -0.09). The correlations between the remaining traits and the feed efficiency traits were near zero, except between feed intake and feed conversion ratio (r(g) = 0.31, r(p) = 0.23), feed intake and residual feed intake (r(g) = 0.69, r(p) = 0.72), and rib fat depth and residual feed intake (r(g) = 0.17, r(p) = 0.14). These results indicate that genetic improvement in feed efficiency can be achieved through selection and, in general, correlated responses in growth and the other postweaning traits will be minimal.

Excision biopsy of malignant melanoma by general practitioners in south east Scotland 1982-91.

OBJECTIVE: To examine the management of patients who had a malignant melanoma excised initially by general practitioners in south east Scotland over the past 10 years and to assess the impact of the April 1990 contract on this. DESIGN: A retrospective case-control study. SETTING: South east Scotland. SUBJECTS: All patients in south east Scotland who had malignant melanomas excised by general practitioners in 1982-91. OUTCOME MEASURES: Demographic details of patients; Breslow thickness, clearance of excision. RESULTS: 42 patients had malignant melanomas excised by general practitioners in 1982-91: 15 in 1982-9 and 27 in 1990-1. These patients were significantly younger than those who had their tumours excised initially in hospital. Although the longest diameter of melanomas excised by general practitioners was significantly less than of those excised in hospital, the Breslow thicknesses were similar. Completeness of initial excision was doubtful or incomplete in nine (23%) general practitioner excisions compared with 4% of hospital excisions, but the time interval between excision biopsy and wide excision was similar. Pathology requests accompanying excision biopsies mentioned melanoma as a possible diagnosis in 15% (6/40) of general practitioner cases compared with 79% of hospital cases. Thirty nine general practitioners responded to a questionnaire and only 12 had considered melanoma in the differential diagnosis. CONCLUSIONS: General practitioners need to think more often of malignant melanoma when they excise pigmented lesions and when they consider this tumour a possibility should perform an excision biopsy with a lateral clearance of at least 2 mm.

Measures of methane production and their phenotypic relationships with dry matter intake, growth, and body composition traits in beef cattle.

Ruminants contribute up to 80% of greenhouse gas (GHG) emissions from livestock, and enteric methane production by ruminants is the main source of these GHG emissions. Hence, reducing enteric methane production is essential in any GHG emissions reduction strategy in livestock. Data from 2 performance-recording research herds of Angus cattle were used to evaluate a number of methane measures that target methane production (MPR) independent of feed intake and to examine their phenotypic relationships with growth and body composition. The data comprised 777 young bulls and heifers that were fed a roughage diet (ME of 9 MJ/kg DM) at 1.2 times their maintenance energy requirements and measured for MP in open circuit respiration chambers for 48 h. Methane traits evaluated included DMI during the methane measurement period, MPR, and methane yield (MY; MPR/DMI), with means (± SD) of 6.2 ± 1.4 kg/d, 187 ± 38 L/d, and 30.4 ± 3.5 L/kg, respectively. Four forms of residual MPR (RMP), which is a measure of actual minus predicted MPR, were evaluated. For the first 3 forms, predicted MPR was calculated using published equations. For the fourth (RMPR), predicted MPR was obtained by regression of MPR on DMI. Growth traits evaluated were BW at birth, weaning (200 d of age), yearling age (400 d of age), and 600 d of age, with means (± SD) of 34 ± 4.6, 238 ± 37, 357 ± 45, and 471 ± 53 kg, respectively. Body composition traits included ultrasound measures (600 d of age) of rib fat, rump fat, and eye muscle area, with means (± SD) of 3.8 ± 2.6 mm, 5.4 ± 3.8 mm, and 61 ± 7.7 cm(2), respectively. Methane production was positively correlated (r ± SE) with DMI (0.65 ± 0.02), MY (0.72 ± 0.02), the RMP traits (r from 0.65 to 0.79), the growth traits (r from 0.19 to 0.57), and the body composition traits (r from 0.13 to 0.29). Methane yield was, however, not correlated (r ± SE) with DMI (-0.02 ± 0.04) as well as the growth (r from -0.03 to 0.11) and body composition (r from 0.01 to 0.06) traits. All the RMP traits were strongly correlated to MY (r from 0.82 to 0.95). These results indicate that reducing MPR per se can have a negative impact on growth and body composition of cattle. Reducing MY, however, will likely have the effect of reducing MPR without impacting productivity. Where a ratio trait is undesirable, as in animal breeding, any of the RMP traits can be used instead of MY. However, where independence from DMI is desired, RMPR should be a trait worth considering.

Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle.

The aim of this study was to assess the accuracy of genomic predictions for 19 traits including feed efficiency, growth, and carcass and meat quality traits in beef cattle. The 10,181 cattle in our study had real or imputed genotypes for 729,068 SNP although not all cattle were measured for all traits. Animals included Bos taurus, Brahman, composite, and crossbred animals. Genomic EBV (GEBV) were calculated using 2 methods of genomic prediction [BayesR and genomic BLUP (GBLUP)] either using a common training dataset for all breeds or using a training dataset comprising only animals of the same breed. Accuracies of GEBV were assessed using 5-fold cross-validation. The accuracy of genomic prediction varied by trait and by method. Traits with a large number of recorded and genotyped animals and with high heritability gave the greatest accuracy of GEBV. Using GBLUP, the average accuracy was 0.27 across traits and breeds, but the accuracies between breeds and between traits varied widely. When the training population was restricted to animals from the same breed as the validation population, GBLUP accuracies declined by an average of 0.04. The greatest decline in accuracy was found for the 4 composite breeds. The BayesR accuracies were greater by an average of 0.03 than GBLUP accuracies, particularly for traits with known genes of moderate to large effect mutations segregating. The accuracies of 0.43 to 0.48 for IGF-I traits were among the greatest in the study. Although accuracies are low compared with those observed in dairy cattle, genomic selection would still be beneficial for traits that are hard to improve by conventional selection, such as tenderness and residual feed intake. BayesR identified many of the same quantitative trait loci as a genomewide association study but appeared to map them more precisely. All traits appear to be highly polygenic with thousands of SNP independently associated with each trait.

Genome-wide association studies for feedlot and growth traits in cattle.

A genome wide-association study for production traits in cattle was carried out using genotype data from the 10K Affymetrix (Santa Clara, CA) and the 50K Illumina (San Diego, CA) SNP chips. The results for residual feed intake (RFI), BW, and hip height in 3 beef breed types (Bos indicus, Bos taurus, and B. indicus × B. taurus), and for stature in dairy cattle, are presented. The aims were to discover SNP associated with all traits studied, but especially RFI, and further to test the consistency of SNP effects across different cattle populations and breed types. The data were analyzed within data sets and within breed types by using a mixed model and fitting 1 SNP at a time. In each case, the number of significant SNP was more than expected by chance alone. A total of 75 SNP from the reference population with 50K chip data were significant (P < 0.001) for RFI, with a false discovery rate of 68%. These 75 SNP were mapped on 24 different BTA. Of the 75 SNP, the 9 most significant SNP were detected on BTA 3, 5, 7, and 8, with P ≤ 6.0 × 10(-5). In a population of Angus cattle divergently selected for high and low RFI and 10K chip data, 111 SNP were significantly (P < 0.001) associated with RFI, with a false discovery rate of 7%. Approximately 103 of these SNP were therefore likely to represent true positives. Because of the small number of SNP common to both the 10K and 50K SNP chips, only 27 SNP were significantly (P < 0.05) associated with RFI in the 2 populations. However, other chromosome regions were found that contained SNP significantly associated with RFI in both data sets, although no SNP within the region showed a consistent effect on RFI. The SNP effects were consistent between data sets only when estimated within the same breed type.