Geoffry Fordyce

Genome-wide association studies of female reproduction in tropically adapted beef cattle

The genetics of reproduction is poorly understood because the heritabilities of traits currently recorded are low. To elucidate the genetics underlying reproduction in beef cattle, we performed a genome-wide association study using the bovine SNP50 chip in 2 tropically adapted beef cattle breeds, Brahman and Tropical Composite. Here we present the results for 3 female reproduction traits: 1) age at puberty, defined as age in days at first observed corpus luteum (CL) after frequent ovarian ultrasound scans (AGECL); 2) the postpartum anestrous interval, measured as the number of days from calving to first ovulation postpartum (first rebreeding interval, PPAI); and 3) the occurrence of the first postpartum ovulation before weaning in the first rebreeding period (PW), defined from PPAI. In addition, correlated traits such as BW, height, serum IGF1 concentration, condition score, and fatness were also examined. In the Brahman and Tropical Composite cattle, 169 [false positive rate (FPR) = 0.262] and 84 (FPR = 0.581) SNP, respectively, were significant (P < 0.001) for AGECL. In Brahman, 41% of these significant markers mapped to a single chromosomal region on BTA14. In Tropical Composites, 16% of these significant markers were located on BTA5. For PPAI, 66 (FPR = 0.67) and 113 (FPR = 0.432) SNP were significant (P < 0.001) in Brahman and Tropical Composite, respectively, whereas for PW, 68 (FPR = 0.64) and 113 (FPR = 0.432) SNP were significant (P < 0.01). In Tropical Composites, the largest concentration of PPAI markers were located on BTA5 [19% (PPAI) and 23% (PW)], and BTA16 [17% (PPAI) and 18% (PW)]. In Brahman cattle, the largest concentration of markers for postpartum anestrus was located on BTA3 (14% for PPAI and PW) and BTA14 (17% PPAI). Very few of the significant markers for female reproduction traits for the Brahman and Tropical Composite breeds were located in the same chromosomal regions. However, fatness and BW traits as well as serum IGF1 concentration were found to be associated with similar genome regions within and between breeds. Clusters of SNP associated with multiple traits were located on BTA14 in Brahman and BTA5 in Tropical Composites.

Genetics of heifer puberty in two tropical beef genotypes in northern Australia and associations with heifer- and steer-production traits

A total of 2115 heifers from two tropical genotypes (1007 Brahman and 1108 Tropical Composite) raised in four locations in northern Australia were ovarian-scanned every 4–6 weeks to determine the age at the first-observed corpus luteum (CL) and this was used to define the age at puberty for each heifer. Other traits recorded at each time of ovarian scanning were liveweight, fat depths and body condition score. Reproductive tract size was measured close to the start of the first joining period. Results showed significant effects of location and birth month on the age at first CL and associated puberty traits. Genotypes did not differ significantly for the age or weight at first CL; however, Brahman were fatter at first CL and had a small reproductive tract size compared with that of Tropical Composite. Genetic analyses estimated the age at first CL to be moderately to highly heritable for Brahman (0.57) and Tropical Composite (0.52). The associated traits were also moderately heritable, except for reproductive tract size in Brahmans (0.03) and for Tropical Composite, the presence of an observed CL on the scanning day closest to the start of joining (0.07). Genetic correlations among puberty traits were mostly moderate to high and generally larger in magnitude for Brahman than for Tropical Composite. Genetic correlations between the age at CL and heifer- and steer-production traits showed important genotype differences. For Tropical Composite, the age at CL was negatively correlated with the heifer growth rate in their first postweaning wet season (–0.40) and carcass marbling score (–0.49), but was positively correlated with carcass P8 fat depth (0.43). For Brahman, the age at CL was moderately negatively genetically correlated with heifer measures of bodyweight, fatness, body condition score and IGF-I, in both their first postweaning wet and second dry seasons, but was positively correlated with the dry-season growth rate. For Brahman, genetic correlations between the age at CL and steer traits showed possible antagonisms with feedlot residual feed intake (–0.60) and meat colour (0.73). Selection can be used to change the heifer age at puberty in both genotypes, with few major antagonisms with steer- and heifer-production traits.

Reproductive responses of cattle to GnRH agonists

The response in cattle to treatment with gonadotrophin releasing hormone (GnRH) agonist includes downregulation of GnRH receptors on gonadotrophe cells, desensitisation of the anterior pituitary gland to endogenous GnRH, and the abolition of pulsatile release of LH. In bulls, a tonic pattern of LH release is associated with increased secretion of testosterone, which persists for the duration of treatment with GnRH agonist. The mechanism for this response in bulls has not been elucidated, but clearly pulsatile release of LH is not required to stimulate the synthesis of steroidogenic enzymes that sustain elevated secretion of testosterone. In heifers, desensitisation to endogenous GnRH prevents the occurrence of the pre-ovulatory surge release of LH, thus blocking ovulation. The latter provided the opportunity to evaluate the potential of a GnRH agonist bioimplant to control fertility in heifers under extensive management. Bioimplants that contained graded amounts of GnRH agonist prevented pregnancies in heifers for periods of 3 to 12 months. Zebu crossbred heifers treated with GnRH agonist from 14 to 23 months of age failed to conceive, but showed normal conception patterns when introduced into mating herds at around 26 months of age. After treatment with GnRH agonist for 4 to 6 weeks, ovarian follicular growth in heifers is restricted to relatively small (2-4 mm) antral follicles. Suppressed follicular growth in heifers treated long-term with GnRH agonist is due to a lack of gonadotrophin support, rather than a direct action of agonist at the ovaries. This was demonstrated by the ability to induce apparently normal follicular growth and ovulation by acute treatment with FSH for 4 days, followed by an injection of LH, in heifers that had been exposed to GnRH agonist for around 6 months, and which had only small (2-4 mm) antral follicles at the start of FSH treatment. GnRH agonist bioimplants have been incorporated into new multiple ovulation and embryo transfer protocols that allow control of the time of ovulation subsequent to superstimulation of ovarian follicular growth with FSH. In these protocols, the endogenous surge release of LH is blocked by treatment with agonist and ovulation is timed by injection of exogenous LH, allowing fixed-time AI. It can be concluded from recent studies that GnRH agonist bioimplants have considerable potential for both pro-fertility and anti-fertility applications in cattle. It is likely that commercial bioimplants will be available within the next 3 to 5 years.

Bull selection and use in northern Australia: 1. Physical traits

A systematic breeding soundness examination, including assessment of serving capacity was conducted on 5/8 Brahman, Brahman and Belmont Red bulls, most aged 2-4 years, at 12 different cattle properties across northern Australia. A subset of bulls (n=235) were subsequently mated in various groups, as multiple-sires, to cows and heifers at bull:female ratios of 2.5-6%. The number of calves sired by individual bulls (calf output) was determined by DNA typing for paternity. Overall, the incidence of physical abnormalities that were judged likely to result in reduced reproductive performance was low (5.6-12% of bulls). Measures of key physical traits scrotal circumference, sheath depth (vertical distance from ventral abdominal wall to preputial orifice), and sheath score were moderately to highly repeatable. Except in Belmont Red bulls, liveweight was positively correlated with scrotal circumference (r=0.36-0.78; P<0.01), and both traits increased with age. In 2-year-old Brahman bulls only, percent normal spermatozoa was correlated with scrotal circumference (r=0.34; P<0.05). However, 12 and 15% of Santa Gertrudis and Brahman bulls, respectively, with greater than or equal to the recommended threshold values for scrotal circumferences, had less than 50% morphologically normal spermatozoa. Size and conformation of the umbilicus was associated with conformation of the sheath, and influenced mating ability in 2-year-old Brahman and 3-year-old Santa Gertrudis bulls. In 2-year-old Brahman bulls umbilical cord thickness was positively related (r=0.36; P<0.05) to sheath depth, and negatively related (r=-0.65; P<0.05) to number of mounts and serves in a serving capacity test. In 3-year-old Santa Gertrudis bulls navel (external umbilical scar) score was negatively related to the number of serves (r=-0.53; P<0.01) in a serving capacity test. None of the physical traits measured were consistently included in the final regression model for calf output for each breed.

Bull selection and use in northern Australia 4. Calf output and predictors of fertility of bulls in multiple-sire herds

On 10 northern Australian properties, the number of calves sired (calf output) by individual bulls in multiple-sire matings was measured by DNA typing for paternity. There were 235 bulls (92 Santa Gertrudis, 25 5/8 Brahman and 119 Brahman) from 37 multiple-sire mating groups. Number of bulls in groups ranged from 2 to 25 and ages of bulls ranged from 2 to 5 years. Mating periods were for 3-12 months and bull mating percentages were 2.5-6%. In all, there were 4251 calves tested and the resolution of paternity ranged from 92.5 to 100% and averaged 97.7% across all sites. This included 9.9% of calves with no potential sires in any of the mating groups. Of the 235 bulls mated, 58% sired 10% or less calves in each of their respective mating groups with 6% not siring any calves. In contrast, 14% sired over 30% of the calves in each of the respective mating groups. When bulls were mated in groups of 8-24, the maximum percent of calves sired by individual bulls was 26+/-7% (mean+/-S.D.) with a range 11-36%. However, when bulls were mated in groups of 2-7, the maximum percent of calves sired by individual bulls was 59+/-19% with a range 24-94%. Calf output of bulls was moderately repeatable across years at four of five sites. Multiple regression models relating pre-mating measures of physical, seminal and behavioural traits to calf output were developed for the three breed groups. In all, only 138 of the 235 bulls were included in the models (40 Santa Gertrudis, 24 5/8 Brahman and 74 Brahman). Sheath and testicular traits, such as scrotal circumference and testicular tone, were generally not related to calf output, the exceptions being sheath depth in Brahman bulls which was negatively related (P<0.05) and scrotal circumference in 5/8 Brahmans which was positively related (P=0.08) to calf output. Dominance was only included in the 5/8 Brahman model but there was no significant relationship between dominance hierarchy and calf output. Semen motility was only related (P<0.05) to calf output in 5/8 Brahmans. However, measures of semen quality based on spermatozoa morphology were important contributors to calf output in the Santa Gertrudis and Brahman models where percent normal spermatozoa was positively related (P<0.01) to calf output. In Santa Gertrudis and Brahman bulls, measures of sexual behaviour in the serving capacity test were related to calf output. In Santa Gertrudis, these were for the number of displays of sexual interest (P<0.05), and mounts (P<0.01), but not number of serves, whilst in Brahman bulls, libido score was positively related to calf output (P<0.05). The models only explained 35-57% of the variation in calf output.

Genetics of adaptive traits in heifers and their relationship to growth, pubertal and carcass traits in two tropical beef cattle genotypes.

Genetic analyses of tropical adaptive traits were conducted for two tropically adapted genotypes, Brahman (BRAH) and Tropical Composite (TCOMP). Traits included tick scores (TICK), faecal egg counts (EPG), buffalo fly-lesion scores (FLY), rectal temperatures under hot conditions (TEMP), coat scores (COAT), coat colour on a light to dark scale (COLOUR), navel scores (NAVEL) and temperament measured as flight time (FT). The data comprised adaptive measures recorded at specific times on 2071 heifers comprising 966 BRAH and 1105 TCOMP. The genetic correlations of these adaptive traits with heifer growth, scanned carcass, pubertal measures and steer growth and carcass traits were estimated. BRAH recorded significantly (P 50%). In general, phenotypic correlations between these adaptive traits were low and genetic correlations were non-significant, implying trait independence. Genetic correlations between EPG and weight traits (0.29 to 0.44) indicated a positive relationship, implying no deleterious effect of worms on the growth at a genetic level, especially in TCOMP. The negative genetic correlations between COAT and body-condition score across genotypes (–0.33 to –0.48) indicated genetic advantage of sleek coats in tropics. A positive genetic correlation between COAT and the age at the first-observed corpus luteum (0.73) in BRAH indicated that BRAH with sleeker coats were genetically early maturing. Further, sleeker coats were genetically indicative of lower weights and lower fat cover at puberty in BRAH. The scanned fat measures at rump and rib sites for feedlot steers showed strong genetic correlation (0.50–0.58) with heifer TEMP, indicating genetically fatter animals had genetically lower heat tolerance. In BRAH, a positive genetic association between heifer COLOUR and scanned fat measures in steers (0.50–0.54) implied increased fatness in genetically darker animals. Further, in BRAH, a strong negative genetic correlation (–0.97) was observed between steer retail beef yield and heifer TEMP, indicating a favourable genetic association. In general, genetic correlations between adaptive traits and other economic traits were genotype specific. Further, it can be concluded that selection for productive and pubertal traits in tropical beef cattle genotypes would not adversely affect their tropical adaptability.

A review of factors that impact on the capacity of beef cattle females to conceive, maintain a pregnancy and wean a calf—Implications for reproductive efficiency in northern Australia ☆

Abstract A review of factors that may impact on the capacity of beef cattle females, grazing semi-extensive to extensive pastures in northern Australia, to conceive, maintain a pregnancy and wean a calf was conducted. Pregnancy and weaning rates have generally been used to measure the reproductive performance of herds. However, this review recognises that reproductive efficiency and the general measures associated with it more effectively describe the economic performance of beef cattle enterprises. More specifically, reproductive efficiency is influenced by (1) pregnancy rate which is influenced by (i) age at puberty; (ii) duration of post-partum anoestrus; (iii) fertilisation failure and (iv) embryo survival; while (2) weight by number of calves per breeding female retained for mating is influenced by (i) cow survival; (ii) foetal survival; and (iii) calf survival; and (3) overall lifetime calf weight weaned per mating. These measures of reproductive efficiency are discussed in depth. Further, a range of infectious and non-infectious factors, namely, environmental, physiological, breed and genetic factors and their impact on these stages of the reproductive cycle are investigated and implications for the northern Australian beef industry are discussed. Finally, conclusions and recommendations to minimise reproductive inefficiencies based on current knowledge are presented.

Finding genes for economically important traits: Brahman cattle puberty

Age at puberty is an important component of reproductive performance in beef cattle production systems. Brahman cattle are typically late-pubertal relative to Bos taurus cattle and so it is of economic relevance to select for early age at puberty. To assist selection and elucidate the genes underlying puberty, we performed a genome-wide association study (GWAS) using the BovineSNP50 chip (similar to 54 000 polymorphisms) in Brahman bulls (n = 1105) and heifers (n = 843) and where the heifers were previously analysed in a different study. In a new attempt to generate unbiased estimates of single-nucleotide polymorphism (SNP) effects and proportion of variance explained by each SNP, the available data were halved on the basis of year and month of birth into a calibration and validation set. The traits that defined age at puberty were, in heifers, the age at which the first corpus luteum was detected (AGECL, h(2) = 0.56 +/- 0.11) and in bulls, the age at a scrotal circumference of 26 cm (AGE26, h(2) = 0.78 +/- 0.10). At puberty, heifers were on average older (751 +/- 142 days) than bulls (555 +/- 101 days), but AGECL and AGE26 were genetically correlated (r = 0.20 +/- 0.10). There were 134 SNPs associated with AGECL and 146 SNPs associated with AGE26 (P < 0.0001). From these SNPs, 32 (similar to 22%) were associated (P < 0.0001) with both traits. These top 32 SNPs were all located on Chromosome BTA 14, between 21.95 Mb and 28.4 Mb. These results suggest that the genes located in that region of BTA 14 play a role in pubertal development in Brahman cattle. There are many annotated genes underlying this region of BTA 14 and these are the subject of current research. Further, we identified a region on Chromosome X where markers were associated (P < 1.00E-8) with AGE26, but not with AGECL. Information about specific genes and markers add value to our understanding of puberty and potentially contribute to genomic selection. Therefore, identifying these genes contributing to genetic variation in AGECL and AGE26 can assist with the selection for early onset of puberty.

Bull selection and use in northern Australia. Part 2. Semen traits

Detailed semen evaluations were carried out on approximately 363 Santa Gertrudis, 5/8 Brahman and Brahman bulls on 12 different properties across northern Australia, as part of systematic breeding soundness examinations. A subset of bulls (n=245) were subsequently mated in groups, to cows and heifers at bull:female ratios of 2.5-6.0%, with the paternity of resulting calves being determined by microsatellite DNA testing. Motility traits of semen and spermatozoa were moderately repeatable and correlated with each other, but were unrelated to calf output. The percentage of morphologically normal spermatozoa in ejaculates was moderately to highly repeatable (e.g. r=0.10-0.64). The most common morphological abnormalities seen were mid-piece abnormalities, in particular, distal mid-piece reflex associated with a cytoplasmic droplet. Semen quality, particularly percent normal spermatozoa, was consistently related to calf output. In general, bulls with <50% normal spermatozoa sired few calves while bulls with the highest calf outputs had >70% normal spermatozoa. The presence or absence of heparin binding proteins in semen did not influence calf output. Semen from 93% of tested bulls was positive for heparin binding proteins. These results confirm that examination of semen, in particular, evaluation of percent morphologically normal spermatozoa, should be included in the breeding soundness examination of bulls.

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

ABSTRACT 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 (χ2 = 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.