R. G. Holroyd

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.

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.

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.

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.

Male traits and herd reproductive capability in tropical beef cattle. 2. Genetic parameters of bull traits

A total of 4063 young bulls of two tropical genotypes (1639 Brahman and 2424 Tropical Composite) raised in northern Australia were evaluated for a comprehensive range of production and reproduction traits up to 24 months of age. Prior to weaning, peripheral blood concentrations of luteinising hormone (LH) and inhibin were measured at 4 months of age. At weaning (6 months) blood insulin-like growth factor-1 (IGF-I) and flight time were recorded. Body composition traits of fat depth and eye-muscle area were determined by ultrasonography at 15 months of age when additional measurements of liveweight, hip height and body condition score were recorded. Bull breeding soundness was evaluated at ~12, 18 and 24 months of age when measurements of scrotal circumference, sheath score, semen mass activity, progressive motility of individual sperm and percent morphologically normal sperm were recorded. Magnitude of heritability and genetic correlations changed across time for some traits. Heritability of LH, inhibin, IGF-I and of 18-month scrotal circumference, mass activity, progressive motility and percent normal sperm was 0.31, 0.74, 0.44, 0.75, 0.24, 0.15 and 0.25, respectively, for Brahmans and 0.48, 0.72, 0.36, 0.43, 0.13, 0.15 and 0.20, respectively, for Tropical Composites. Inhibin and IGF-I had moderate genetic association with percent normal sperm at 24 months in Brahmans but low to negligible associations in Tropical Composites. Body condition score in Brahmans and sperm motility (mass and individual) traits in both genotypes had moderate to strong genetic correlation with percent normal sperm and may prove useful candidates for indirect selection. There is scope to increase scrotal circumference by selection and this will be associated with favourable correlated responses of improved semen quality in both genotypes. The lack of genetic antagonism among bull traits indicates that selection for improved semen quality will not adversely affect other production traits.

Bull selection and use in northern Australia. 5. Social behaviour and management

Calf output of bulls was derived using DNA typing for paternity following multiple-sire mating at two sites in northern Australia. At Swans Lagoon Beef Cattle Research Station, 12, mixed-age, Brahman cross bulls were continuously mated with an average of 325 females in a 22km2 open-savannah paddock. Water was available in two troughs. Behaviour of the bulls and location of cows were monitored. At Kamilaroi Station, 2- to 2.5-year-old Brahman bulls were introduced to the study. Twenty-four bulls (HIGH%) were mated in an 84km2 paddock for 3.5 months to 411 heifers in 1995/1995 and for 4.5 months to 350 heifers and 320 first-lactation cows in 1995/1996. A second group of 10 bulls (LOW%) selected on reproductive soundness was mated concurrently in a neighbouring 60km2 paddock to 411 heifers in 1995/1995 and to 350 heifers and 298 first-lactation cows in 1995/1996. In each paddock in both years, 300-350 females were expected to cycle during mating. Both paddocks were flat and semi-forested and water was available only at troughs. At both sites, detailed physical and reproductive examinations of all bulls were conducted prior to and post-mating.Calf output of individual bulls was highly variable but repeatable (r=0.6-0.7) between years. Up to 90% of the 270-380 calves resulting from each mating were sired by between 6 and 8 bulls. Reducing from 3.7 to 2.8% bulls:females at Swans Lagoon did not delay conceptions. At Kamilaroi, reproductively sound bulls achieved an estimated 5-6 conceptions per week over the peak mating period when sufficient cycling females were available. Differences in pregnancy rates between paddocks appeared due to differences in nutrition and it appeared that conceptions were not delayed with LOW% vs. HIGH% bulls. Variance between bulls in calf output was substantially lower when fewer bulls were used. Bull attrition occurred each year in the HIGH% paddock but not in the LOW% paddock. Calf output was unrelated to body condition of bulls. Seven of the 12 bulls in one 2-year period at Swans Lagoon appeared to restrict their movement range to 250-750ha for 90-100% of the time. These ranges expanded when the bull:female ratio was reduced. Only one of the nine bulls remained within a 500ha home range for at least 85% of the time during peak mating in 1998 at 2.8% bulls:females. In previous years with 3.7% bulls:females, up to eight of the 12 bulls had remained within a 500ha home range for 85% of the time. Bull behaviour related to high calf output included restricted movement range, grazing with females at a majority of observations, stable social behaviour, and social dominance. These observations demonstrate that multiple-sire mating of reproductively sound Brahman and Brahman-derived bulls at 2.5% of cycling females will not jeopardise herd fertility under extensive management in northern Australia.

The performance of Brahman-Shorthorn and Sahiwal-Shorthorn beef cattle in the dry tropics of northern Queensland. 5. Scrotal circumference, temperament, ectoparasite resistance, and the genetics of growth and other traits in bulls

The genetics of growth to 24 months, scrotal circumference (SC) at 24 months and temperaments at 6, 12 and 18 months in 7 year groups of F2 et seq., 1/2 Brahman, 1/2 Sahiwal, 3/4 Brahman and 3/4 Sahiwal bulls were investigated in the dry tropics of northern Queensland. Cattle tick (Boophilus microplus) and buffalo fly (Haematobia irritans exigua) resistance were also assessed at 24 months. Scrotal circumference at 24 months was highest in 1/2 Sahiwal crosses (28 cm v. 26-27 cm; P 0.9); however, the rG of weaning weight with postweaning seasonal growth rates to 24 months were consistently negative (-0.09 to -0.71; P>0.05). The rG of SC with post-weaning growth rates were negative (-0.4 to -0.8). The rG of SC with weights up to 18 months were not significantly different to zero, but tended to be negative with weight at 24 months.

Genetics of early and lifetime annual reproductive performance in cows of two tropical beef genotypes in northern Australia

Reproduction records from 2137 cows first mated at 2 years of age and recorded through to 8.5 years of age were used to study the genetics of early and lifetime reproductive performance from two genotypes (1020 Brahman and 1117 Tropical Composite) in tropical Australian production systems. Regular ultrasound scanning of the reproductive tract, coupled with full recording of mating, calving and weaning histories, allowed a comprehensive evaluation of a range of reproductive traits. Results showed components traits of early reproductive performance had moderate to high heritabilities, especially in Brahmans. The heritability of lactation anoestrous interval in 3-year-old cows was 0.51 +/- 0.18 and 0.26 +/- 0.11 for Brahman and Tropical Composite, respectively. Heritabilities of binary reproductive output traits (conception rate, pregnancy rate, calving rate and weaning rate) from first and second matings were generally moderate to high on the underlying scale. Estimates ranged from 0.15 to 0.69 in Brahman and 0.15 to 0.34 in Tropical Composite, but were considerably lower when expressed on the observed scale, particularly for those traits with high mean levels. Heritabilities of lifetime reproduction traits were low, with estimates of 0.11 +/- 0.06 and 0.07 +/- 0.06 for lifetime annual weaning rate in Brahman and Tropical Composite, respectively. Significant differences in mean reproductive performance were observed between the two genotypes, especially for traits associated with anoestrus in first-lactation cows. Genetic correlations between early-in-life reproductive measures and lifetime reproduction traits were moderate to high. Genetic correlations between lactation anoestrous interval and lifetime annual weaning rate were -0.62 +/- 0.24 in Brahman and -0.87 +/- 0.32 in Tropical Composite. The results emphasise the substantial opportunity that exists to genetically improve weaning rates in tropical beef cattle breeds by focusing recording and selection on early-in-life female reproduction traits, particularly in Brahman for traits associated with lactation anoestrus.