Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations.

Many of the world's agriculturally important plant and animal populations consist of hybrids of subspecies. Cattle in tropical and sub-tropical regions for example, originate from two subspecies, Bos taurus indicus (Bos indicus) and Bos taurus taurus (Bos taurus). Methods to derive the underlying genetic architecture for these two subspecies are essential to develop accurate genomic predictions in these hybrid populations. We propose a novel method to achieve this. First, we use haplotypes to assign SNP alleles to ancestral subspecies of origin in a multi-breed and multi-subspecies population. Then we use a BayesR framework to allow SNP alleles originating from the different subspecies differing effects. Applying this method in a composite population of B. indicus and B. taurus hybrids, our results show that there are underlying genomic differences between the two subspecies, and these effects are not identified in multi-breed genomic evaluations that do not account for subspecies of origin effects. The method slightly improved the accuracy of genomic prediction. More significantly, by allocating SNP alleles to ancestral subspecies of origin, we were able to identify four SNP with high posterior probabilities of inclusion that have not been previously associated with cattle fertility and were close to genes associated with fertility in other species. These results show that haplotypes can be used to trace subspecies of origin through the genome of this hybrid population and, in conjunction with our novel Bayesian analysis, subspecies SNP allele allocation can be used to increase the accuracy of QTL association mapping in genetically diverse populations.

Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available.

BACKGROUND: It has been challenging to implement genomic selection in multi-breed tropical beef cattle populations. If commercial (often crossbred) animals could be used in the reference population for these genomic evaluations, this could allow for very large reference populations. In tropical beef systems, such animals often have no pedigree information. Here we investigate potential models for such data, using marker heterozygosity (to model heterosis) and breed composition derived from genetic markers, as covariates in the model. Models treated breed effects as either fixed or random, and included genomic best linear unbiased prediction (GBLUP) and BayesR. A tropically-adapted beef cattle dataset of 29,391 purebred, crossbred and composite commercial animals was used to evaluate the models. RESULTS: Treating breed effects as random, in an approach analogous to genetic groups allowed partitioning of the genetic variance into within-breed and across breed-components (even with a large number of breeds), and estimation of within-breed and across-breed genomic estimated breeding values (GEBV). We demonstrate that moderately-accurate (0.30-0.43) GEBV can be calculated using these models. Treating breed effects as random gave more accurate GEBV than treating breed as fixed. A simple GBLUP model where no breed effects were fitted gave the same accuracy (and correlations of GEBV very close to 1) as a model where GEBV for within-breed and the GEBV for (random) across-breed effects were included. When GEBV were predicted for herds with no data in the reference population, BayesR resulted in the highest accuracy, with 3% accuracy improvement averaged across traits, especially when the validation population was less related to the reference population. Estimates of heterosis from our models were in line with previous estimates from beef cattle. A method for estimating the number of effective breed comparisons for each breed combination accumulated across contemporary groups is presented. CONCLUSIONS: When no pedigree is available, breed composition and heterosis for inclusion in multi-breed genomic evaluation can be estimated from genotypes. When GEBV were predicted for herds with no data in the reference population, BayesR resulted in the highest accuracy.

Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes.

Cattle enterprises are one of the major livestock production systems globally and are forecasted to have stable growth in the next decade. To facilitate sustainable live weight production, optimal reproductive performance is essential. Microbial colonisation in the reproductive tract has been demonstrated as one of the factors contributing to bovine reproductive performance. Studies also implied that reproductive metagenomes are different at each stage of the estrous cycle. This study applied Oxford Nanopore Technologies' adaptive long-read sequencing to profile the bovine reproductive microbiome collected from tropical cattle in northern Queensland, Australia. The microbiome samples were collected from cattle of different sexes, reproductive status and locations to provide a comprehensive view of the bovine reproductive microbiome in northern Australian cattle. Ascomycota, Firmicutes and Proteobacteria were abundant phyla identified in the bovine reproductive metagenomes of Australian cattle regardless of sexes, reproductive status and location. The species level taxonomical investigation suggested that gastrointestinal metagenome and the surrounding environment were potentially the origins of the bovine reproductive metagenome. Functional profiles further affirmed this implication, revealing that the reproductive metagenomes of the prepubertal and postpartum animals were dominated by microorganisms that catabolise dietary polysaccharides as an energy substrate while that of the pregnant animals had the function of harvesting energy from aromatic compounds. Bovine reproductive metagenome investigations can be employed to trace the origins of abnormal metagenomes, which is beneficial for disease prevention and control. Additionally, our results demonstrated different reproductive metagenome diversities between cattle from two different locations. The variation in diversity within one location can serve as the indicator of abnormal reproductive metagenome, but between locations inferences cannot be made. We suggest establishing localised metagenomic indices that can be used to infer abnormal reproductive metagenomes which contribute to abortion or sub-fertility.

High frequency of delayed milk delivery to neonates in tropical beef herds.

Beef-calf mortality rates across tropical and subtropical Australia are high, with sub-optimal nutrition in pregnant cows being the primary risk. The nutritional deficiencies associated with calf mortality are the same as those associated with reduced milk yields. Although the highest mortality risk occurs during neonatal life, the role of inadequate milk delivery to beef neonates is not well established. This study investigated the frequency of low milk delivery in tropically adapted neonatal calves and the time for their dams to initiate full lactation in five management groups of Brahman and Droughtmaster calving cows in the dry tropics of northern Queensland, Australia. Change in calf weight in the days following birth was the primary measure of milk uptake. Plasma globulin concentration was used to indicate colostrum uptake. Across management groups, data were available on 250 calves for regression analysis of average daily gain vs. globulin and on 78 for plotting calf growth profiles. Calves had one of two growth profiles, either with immediate high growth from birth (day one) or with high growth delayed until day three. The frequency of delayed growth calves (with inadequate milk intake to gain at least 0.5 kg by day three after birth) was on average 30% across management groups, with management groups ranging 25%-50%. The frequency of calves growing ≤0.2 kg/day to day three was 15%-37%, depending on management group. The frequency of calves growing ≤0.2 kg/day to day five was 7%-20%, depending on management group. Calf globulin explained only 25% of the variation in calf average daily gain. Our study shows that a third of tropically adapted calves may experience a three-day delay to initiation of full lactation by their dams. Although study conditions were relatively benign, any additional risks with milk delivery, such as those that occur widely in tropical and subtropical northern Australia, would place such calves at risk of dehydration and mortality. Calf plasma globulin should not be used as a standalone measure of adequacy of neonatal milk delivery, especially when comparing across herds. This study demonstrates a fundamental problem of high frequency in northern Australia. The underlying risks for delayed milk delivery should be considered in the quest for practical solutions to reduce tropically adapted beef-calf mortalities.

Environmental variation effects fertility in tropical beef cattle.

The northern Australia beef cattle industry operates in harsh environmental conditions which consistently suppress female fertility. To better understand the environmental effect on cattle raised extensively in northern Australia, new environmental descriptors were defined for 54 commercial herds located across the region. Three fertility traits, based on the presence of a corpus luteum at 600 d of age, indicating puberty, (CL Presence, n = 25,176), heifer pregnancy (n = 20,989) and first lactation pregnancy (n = 10,072) were recorded. Temperature, humidity, and rainfall were obtained from publicly available data based on herd location. Being pubertal at 600 d (i.e. CL Presence) increased the likelihood of success at heifer pregnancy and first lactation pregnancy (P < 0.05), underscoring the importance of early puberty in reproductive success. A temperature humidity index (THI) of 65-70 had a significant (P < 0.05) negative effect on first lactation pregnancy rate, heifer pregnancy and puberty at 600 d of age. Area under the curve of daily THI was significant (P < 0.05) and reduced the likelihood of pregnancy at first lactation and puberty at 600 days. Deviation from long-term average rainfall was not significant (P < 0.05) for any trait. Average daily weight gain had a significant and positive relationship (P < 0.05) for heifer and first lactation pregnancy. The results indicate that chronic or cumulative heat load is more determinantal to reproductive performance than acute heat stress. The reason for the lack of a clear relationship between acute heat stress and reproductive performance is unclear but may be partially explained by peak THI and peak nutrition coinciding at the same time. Sufficient evidence was found to justify the use of average daily weight gain and chronic heat load as descriptors to define an environmental gradient.

Detection and distribution of Stephanofilaria sp. in buffalo flies and buffalo fly lesions in north Australian beef cattle.

Buffalo flies (Haematobia irritans exigua) are ectoparasites of major animal health and production concern in north Australian beef herds. Skin lesions associated with buffalo fly infestation, cause hide damage and welfare issues and are manifested as dermatitis or ulcerated areas found most commonly near the medial canthus of the eye, along the lateral and ventral neck and on the abdomen. Buffalo flies can transmit a nematode, Stephanofilaria sp., which has been considered the main aetiological agent for buffalo fly lesions, but the role of nematodes in the development of the lesions has not been defined. To investigate the geographical distribution of Stephanofilaria, swabs were taken from the surface of lesions and buffalo flies were netted from the backs of beef cattle from 20 properties located in northern, central and southern Queensland. Swabs and buffalo flies were then tested for the presence of Stephanofilaria by qPCR. In northern and central Queensland, all properties except one, tested positive for the presence of Stephanofilaria in either buffalo flies or swabs, or in both. The infection rate varied amongst sites ranging from 0% to 100% in lesions and 0-34% in female buffalo flies. No nematodes were found in male buffalo flies. In contrast, none of the 66 lesion swabs or 1220 buffalo flies collected from southern Queensland tested positive for Stephanofilaria infection despite the frequent occurrence of lesions in the herds from which samples were collected. These findings suggest that infection with Stephanofilaria, although frequently detected, is not essential for the development of buffalo fly lesions and other factors may contribute to the initiation of lesions. This study also confirmed the potential for using surface swabs as a quicker and less invasive means of sampling lesions than dermal biopsies when testing for the presence of Stephanofilaria by qPCR, but further studies will be required to estimate the sensitivity of this technique. Understanding the pathogenesis of buffalo fly lesions will aid the development of optimal treatment and control strategies.

Pregnancy rate per cycle is heritable and reduces with cycle in naturally mated tropically adapted beef cows.

Pregnancy in cattle is the outcome of the complex process of initiation of cycling, fertilization, maternal recognition of pregnancy and foeto-placental development. Though much is known about initiation of cycling and associated risk factors, there are virtually no data on pregnancy rate per cycle for naturally mated cattle, especially for extensively managed, tropically adapted genotypes, which this study aimed to determine. Tropical composite (Bos indicus and African Sanga crosses with Bos taurus) and Brahman cattle (n = 2,181) of known pedigree in four-year groups at four sites were mated annually for 84 days. Body condition, ovarian function, pregnancies, calving and lactation were monitored through six full reproductive cycles using 4-8 weekly ultrasound of the reproductive tract outside the calving period and daily monitoring during calving. From this, dates of commencement of cycling and conception in each year were estimated for each animal, enabling calculation of established pregnancy for consecutive 21-day periods while cycling and of pregnancies within four months of calving while lactating (P4M). Pregnancy per 21-day period (cycle) during mating for cycling animals averaged 63%, 71%, 41% and 28% in four consecutive cycles. Pregnant per cycle was 2%-11% higher in tropical composites than in Brahmans. The only other consistently significant risk to becoming pregnant was if cycling commenced later than three weeks before mating commenced. P4M averaged 62% and was lower for cows in sub-optimal body condition and in first-parity and later-calving cows. Pregnant per cycle was moderately heritable (~20%), while heritability was moderate to high (33%) for P4M. Selection for pregnant per cycle could be achieved indirectly by selection for P4M, a trait that is readily measured.

Use of whole-genome sequence data and novel genomic selection strategies to improve selection for age at puberty in tropically-adapted beef heifers.

BACKGROUND: In tropically-adapted beef heifers, application of genomic prediction for age at puberty has been limited due to low prediction accuracies. Our aim was to investigate novel methods of pre-selecting whole-genome sequence (WGS) variants and alternative analysis methodologies; including genomic best linear unbiased prediction (GBLUP) with multiple genomic relationship matrices (MGRM) and Bayesian (BayesR) analyses, to determine if prediction accuracy for age at puberty can be improved. METHODS: Genotypes and phenotypes were obtained from two research herds. In total, 868 Brahman and 960 Tropical Composite heifers were recorded in the first population and 3695 Brahman, Santa Gertrudis and Droughtmaster heifers were recorded in the second population. Genotypes were imputed to 23 million whole-genome sequence variants. Eight strategies were used to pre-select variants from genome-wide association study (GWAS) results using conditional or joint (COJO) analyses. Pre-selected variants were included in three models, GBLUP with a single genomic relationship matrix (SGRM), GBLUP MGRM and BayesR. Five-way cross-validation was used to test the effect of marker panel density (6 K, 50 K and 800 K), analysis model, and inclusion of pre-selected WGS variants on prediction accuracy. RESULTS: In all tested scenarios, prediction accuracies for age at puberty were highest in BayesR analyses. The addition of pre-selected WGS variants had little effect on the accuracy of prediction when BayesR was used. The inclusion of WGS variants that were pre-selected using a meta-analysis with COJO analyses by chromosome, fitted in a MGRM model, had the highest prediction accuracies in the GBLUP analyses, regardless of marker density. When the low-density (6 K) panel was used, the prediction accuracy of GBLUP was equal (0.42) to that with the high-density panel when only six additional sequence variants (identified using meta-analysis COJO by chromosome) were included. CONCLUSIONS: While BayesR consistently outperforms other methods in terms of prediction accuracies, reasonable improvements in accuracy can be achieved when using GBLUP and low-density panels with the inclusion of a relatively small number of highly relevant WGS variants.

Multivariate genomic predictions for age at puberty in tropically adapted beef heifers.

Heifers that have an earlier age at puberty often have greater lifetime productivity. Age at puberty is moderately heritable so selection should effectively reduce the number of days to puberty, and improve heifer productivity and profitability as a result. However, recording age at puberty is intensive, requiring repeat ovarian scanning to determine age at first corpus luteum (AGECL). Genomic selection has been proposed as a strategy to select for earlier age at puberty; however, large reference populations of cows with AGECL records and genotypes would be required to generate accurate GEBV for this trait. Reproductive maturity score (RMS) is a proxy trait for age at puberty for implementation in northern Australia beef herds, where large scale recording of AGECL is not feasible. RMS assigns a score of 0 to 5 from a single ovarian scan to describe ovarian maturity at ~600 d. Here we use multivariate genomic prediction to evaluate the value of a large RMS data set to improve accuracy of GEBV for age at puberty (AGECL). There were 882 Brahman and 990 Tropical Composite heifers with AGECL phenotypes, and an independent set of 974 Brahman, 1,798 Santa Gertrudis, and 910 Droughtmaster heifers with RMS phenotypes. All animals had 728,785 real or imputed SNP genotypes. The correlation of AGECL and RMS (h2 = 0.23) was estimated as -0.83 using the genomic information. This result also demonstrates that using genomic information it is possible to estimate genetic correlations between traits collected on different animals in different herds, with minimal or unknown pedigree linkage between them. Inclusion of heifers with RMS in the multi-trait model improved the accuracy of genomic evaluations for AGECL. Accuracy of RMS GEBV generally did not improve by adding heifers with AGECL phenotypes into the reference population. These results suggest that RMS and AGECL may be used together in a multi-trait prediction model to increase the accuracy of prediction for age at puberty in tropically adapted beef cattle.

Towards multi-breed genomic evaluations for female fertility of tropical beef cattle.

Developing accurate genomic evaluations of fertility for tropical beef cattle must deal with at least two major challenges (i) recording cow fertility traits in extensive production systems on large numbers of cows and (ii) the genomic evaluations should work across the breeds, crossbreds, and composites used in tropical beef production. Here, we assess accuracy of genomic evaluations for a trait which can be collected on a large scale in extensive conditions, corpus luteum score (CLscore), which is 1 if ovarian scanning indicates a heifer has cycled by 600 d and 0 if not, in a multi-breed population. A total of 3,696 heifers, including 979 Brahmans, 914 Droughtmasters, and 1,803 Santa Gertrudis in seven herds across 3-yr cohorts with CLscores, were genotyped for 24,211 SNPs. Genotypes were imputed to 728,785 SNPs. GBLUP and BayesR were used to predict GEBV. Accuracy of GEBV was evaluated with two validation strategies. In the first strategy, the last year cohort of heifers from each herd was used for validation, such that every herd had heifers in both reference and validation populations. In the second validation strategy, each herd in turn was removed in its entirety from the reference population, and was used for validation. For both validation strategies, accuracy of GEBV for single breed and multi-breed reference populations was assessed. For the first validation strategy, accuracy of GEBV ranged from 0.2 for Brahmans to 0.4 for Droughtmasters. Increasing marker density from 24K SNPs to 728K SNPs resulted in a small increase in accuracy, and including multiple-breeds in the reference did not help improve accuracy. These results suggest that provided a herd has animals in the reference population, the accuracy of the GEBV is largely determined by within herd (linkage) information. The situation was very different when entire herds were predicted in the second validation. In this case accuracy of GEBV using only 24K SNPs and only a within breed reference was close to zero for all breeds. Accuracy increased substantially when 728K SNPs, BayesR, and a multi-breed reference were used, from 0.15 for Brahmans to 0.35 for Santa Gertrudis. Given the second validation strategy is more likely to reflect the situation for many herds in tropical beef production (no animals in the reference), genomic evaluations for fertility in tropical beef cattle should be based on high-density markers (728K SNPs) and should be multi-breed.

Ultrasonographic measurements in first trimester concepti identify predictors of birth weight and postnatal development in cattle.

The placenta is a major driver of prenatal growth and involved in programming of postnatal performance. We therefore determined placental and embryo-fetal ultrasonographic parameters in early pregnancy and their relationships with birth weight and postnatal weights in a Bos indicus-Bos taurus composite beef cattle population. Pregnancies were generated in 2-yr-old Droughtmaster heifers by artificial insemination after estrus synchronization in 2 consecutive years (2009, n = 36 and 2010, n = 57), with a subset of 2010 heifers used again as lactating 3-yr-old cows in 2011 (n = 24). Each cohort was managed as 1 contemporary group for measurements of Corpus luteum diameter, amnion length and width, placentome width and thickness, and embryo-fetal crown-rump length, at 7 and 8 wk of gestation. This was followed by recordings of birth weight, branding weight at 5 to 6 mo of age and weaning weight 2 mo later. At a significance threshold of P < 0.05, placentome thickness at week 7 was negatively correlated with weights at birth (r = -0.23), branding (r = -0.25), and weaning (r = -0.35), whereas placentome width at week 7 (r = 0.24) and thickness at week 8 (r = 0.29) were positively correlated with birth weight. Thicker placentomes in males at week 7 (7%) difference mirrored sex differences in weights at birth (7%), branding (10%), and weaning (6%). The sex difference trend for birth weight was not consistent across sire-year combinations, ranging from -3.2 to +4.7 kg (birth weight of males - females per sire). These results support the hypothesis that placental parameters at the transition from embryo to fetal stage are major predictors of fetal and postnatal growth, albeit with significant environmentally induced plasticity, in stabilized B. indicus-B. taurus composite populations, and suggest that elements of B. indicus-B. taurus reciprocal differences in birth weight persist in composite populations.

The genetic architecture of climatic adaptation of tropical cattle.

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.

Scrotal circumference of Australian beef bulls.

Normal range for scrotal circumference in Australian beef bulls was established using more than 300,000 measurements of breed, management group, age, liveweight, and scrotal circumference. The data used were derived from Australian bull breeders and two large research projects in northern Australia. Most bulls were within 250 to 750 kg liveweight and 300 to 750 days of age. The differences between breeds and variances within breeds were higher when scrotal circumference was predicted from age rather than liveweight, because of variance in growth rates. The average standard deviation for predicted scrotal circumference from liveweight and age was 25 and 30 mm, respectively. Scrotal circumference by liveweight relationships have a similar pattern across all breeds, except in Waygu, with a 50 to 70 mm range in average scrotal circumference at liveweights between 250 and 750 kg. Temperate breed bulls tended to have higher scrotal circumference at the same liveweight than tropically adapted breeds. Five groupings of common beef breeds in Australian were identified, within which there were similar predictions of scrotal circumference from liveweight. It was concluded that liveweight and breed are required to identify whether scrotal circumference is within normal range for Australian beef bulls that experience a wide range of nutritional conditions.

Sperm chromatin in beef bulls in tropical environments.

Sperm chromatin status was assessed in 565 Zebu and Zebu crossbred beef bulls in extensive tropical environments using the sperm chromatin structure assay (SCSA). The SCSA involved exposure of sperm to acid hydrolysis for 0.5 or 5.0 minutes, followed by flow cytometry to ascertain relative amounts of double-stranded (normal) and single-stranded (denatured) DNA, which was used to generate a DNA fragmentation index (%DFI). With conventional SCSA (0.5-minute SCSA), 513 bulls (91%) had <15 %DFI, 24 bulls (4%) had 15 to 27 %DFI, and 28 bulls (5%) had >27 %DFI. In 5.0-minute SCSA, 432 bulls (76%) had <15 %DFI, 68 bulls (12%) had 15 to 27 %DFI and 65 bulls (12%) had >27 %DFI. For most bulls, the SCSA was repeatable on two to four occasions; however, because most bulls had <15 %DFI, repeatability of the SCSA will need to be determined in a larger number of bulls in the 15 to 27 %DFI and >27 %DFI categories. The %DFI was negatively correlated with several bull semen parameters and the strongest negative correlation was with normal sperm. There was a strong positive correlation between %DFI and sperm head abnormalities. Based on these findings, most Zebu beef bulls in extensive tropical environments had relatively stable sperm chromatin. Based on the apparent negative correlations with conventional semen parameters, we inferred that the SCSA measured a unique feature of sperm quality, which has also been suggested for other species. Further studies on the relationships between sperm chromatin stability and fertility are required in beef bulls before chromatin status can be used as an additional predictor of the siring capacity of individual bulls in extensive multiple-sire herds.

Standardising bull breeding soundness evaluations and reporting in Australia.

There is substantial variation in bull breeding soundness evaluation procedures and reports in Australia; the situation is compounded by difficulties in interpretation and the validity of many reports. In an effort to overcome this, the scientific literature was reviewed [Fordyce G. In: Fordyce G, editor. Bull fertility: selection and management in Australia. Eight Mile Plains, Australia: Australian Cattle Vets; 2002] and the needs of stakeholders were considered in preparing a manual, Evaluating and Reporting Bull Fertility [Entwistle KW, Fordyce G. Evaluating and reporting bull fertility. Eight Mile Plains, Australia: Australian Cattle Vets; 2003.] that outlined standards for assessing and reporting bull breeding soundness. A new recording and reporting system, called Bull Reporter, is based on standards from this manual and groups bull fertility traits into five summary categories: Scrotum, Physical, Crush-side Semen, Sperm Morphology, and Serving. The client will generally select which categories they wish to have included in the evaluation to suit their specific purposes. While there is adequate room for comments, the veterinarian is not required to make an overall judgment of whether the bull has normal capacity to sire calves under natural mating management, but ensures the standards for each selected category are met. Professional, standardised, easy-to-read reports are produced either electronically [Entwistle KW, Fordyce G. Evaluating and reporting bull fertility. Eight Mile Plains, Australia: Australian Cattle Vets; 2003.] or manually. A bull owner or their agent signs the certificate to affirm that bulls have not undergone procedures to rectify faults which may have otherwise caused them to fail the standards. An accreditation system for assessing sperm morphology was established because of its demonstrated relationship with pregnancy rates and because of the difficulties in achieving consistent and accurate assessments among laboratories. It is considered that Bull Reporter is applicable to beef and dairy bulls across all levels of management, genotypes and environments throughout Australia, with substantial potential for application elsewhere in the world.

Comparison of culture and a novel 5' Taq nuclease assay for direct detection of Campylobacter fetus subsp. venerealis in clinical specimens from cattle.

A Campylobacter fetus subsp. venerealis-specific 5' Taq nuclease PCR assay using a 3' minor groove binder-DNA probe (TaqMan MGB) was developed based on a subspecies-specific fragment of unknown identity (S. Hum, K. Quinn, J. Brunner, and S. L. On, Aust. Vet. J. 75:827-831, 1997). The assay specifically detected four C. fetus subsp. venerealis strains with no observed cross-reaction with C. fetus subsp. fetus-related Campylobacter species or other bovine venereal microflora. The 5' Taq nuclease assay detected approximately one single cell compared to 100 and 10 cells in the conventional PCR assay and 2,500 and 25,000 cells from selective culture from inoculated smegma and mucus, respectively. The respective detection limits following the enrichments from smegma and mucus were 5,000 and 50 cells/inoculum for the conventional PCR compared to 500 and 50 cells/inoculum for the 5' Taq nuclease assay. Field sampling confirmed the sensitivity and the specificity of the 5' Taq nuclease assay by detecting an additional 40 bulls that were not detected by culture. Urine-inoculated samples demonstrated comparable detection of C. fetus subsp. venerealis by both culture and the 5' Taq nuclease assay; however, urine was found to be less effective than smegma for bull sampling. Three infected bulls were tested repetitively to compare sampling tools, and the bull rasper proved to be the most suitable, as evidenced by the improved ease of specimen collection and the consistent detection of higher levels of C. fetus subsp. venerealis. The 5' Taq nuclease assay demonstrates a statistically significant association with culture (chi2 = 29.8; P < 0.001) and significant improvements for the detection of C. fetus subsp. venerealis-infected animals from crude clinical extracts following prolonged transport.

Use of GnRH agonist implants for long-term suppression of fertility in extensively managed heifers and cows.

The ability of gonadotrophin releasing hormone (GnRH) agonist implants to suppress ovarian activity and prevent pregnancies, long-term, was examined in heifers and cows maintained under extensive management. At three cattle stations, heifers (2-year-old) and older cows (3- to 16-year-old) were assigned to a control group that received no treatment, or were treated with high-dose (12 mg, Station A) or low-dose (8 mg, Station B and Station C) GnRH agonist implants. The respective numbers of control and GnRH agonist-treated animals (heifers + cows) at each station were: Station A, 20 and 99; Station B, 19 and 89; Station C, 20 and 76. Animals were maintained with 4% bulls and monitored for pregnancy at 2-monthly intervals for approximately 12 months. Pregnancy rates for control heifers and control cows ranged from 60-90% and 80-100%, respectively, depending on the study site. The respective number of animals (heifers + cows) treated with GnRH agonist that conceived, and days to first conception, were: Station A, 9 (9%) and 336 +/- 3 days; Station B, 8 (10%) and 244 +/- 13 days; Station C, 20 (26%) and 231 +/- 3 days. Treatment with high-dose GnRH agonist prevented pregnancies for longer (approximately 300 days) than treatment with low-dose GnRH agonist (approximately 200 days). In the majority of heifers and cows treated with GnRH agonist, ovarian follicular growth was restricted to early antral follicles (2-4mm). The findings indicate that GnRH agonist implants have considerable potential as a practical technology to suppress ovarian activity and control reproduction in female cattle maintained in extensive rangelands environments. The technology also has broader applications in diverse cattle production systems.