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.
Multi-trait assessment of early-in-life female, male and genomic measures for use in genetic selection to improve female reproductive performance of Brahman cattle
Early-in-life female and male measures with potential to be practical genetic indicators were chosen from earlier analyses and examined together with genomic measures for multi-trait use to improve female reproduction of Brahman cattle. Combinations of measures were evaluated on the genetic gains expected from selection of sires and dams for each of age at puberty (AGECL, i.e. first observation of a 'corpus luteum'), lactation anoestrous interval in 3-year-old cows (LAI), and lifetime annual weaning rate (LAWR, i.e. the weaning rate of cows based on the number of annual matings they experienced over six possible matings). Selection was on an index of comparable records for each combination. Selection intensities were less than theoretically possible but assumed a concerted selection effort was able to be made across the Brahman breed. The results suggested that substantial genetic gains could be possible but need to be confirmed in other data. The estimated increase in LAWR in 10 years, for combinations without or with genomic measures, ranged from 8 to 12 calves weaned per 100 cows from selection of sires, and from 12 to 15 calves weaned per 100 cows from selection of sires and dams. Corresponding reductions in LAI were 60-103 days or 94-136 days, and those for AGECL were 95-125 or 141-176 days, respectively. Coat score (a measure of the sleekness or wooliness of the coat) and hip height in females, and preputial eversion and liveweight in males, were measures that may warrant wider recording for Brahman female reproduction genetic evaluation. Pregnancy-test outcomes from Matings 1 and 2 also should be recorded. Percentage normal sperm may be important to record for reducing LAI and scrotal size and serum insulin-like growth factor-I concentration in heifers at 18 months for reducing AGECL. Use of a genomic estimated breeding value (EBV) in combination with other measures added to genetic gains, especially at genomic EBV accuracies of 40%. Accuracies of genomic EBVs needed to approach 60% for the genomic EBV to be the most important contributor to gains in the combinations of measures studied.
Understanding the Genetics of Lactation Anoestrus in Brahman Beef Cattle to Enhance Genetic Evaluation of Female Reproductive Traits
Female reproduction is an important profit driver in northern Australia beef production systems. However low weaning rates are common, and are mainly the result of extended post-partum anoestrus intervals, especially in 'Bos indicus' cattle (Entwistle 1983). Research, mainly in dairy, has established that measures of postpartum anoestrus, such as calving to ovulation interval, are moderately heritable and may offer means to genetically improve female reproduction. Age at puberty has also been shown to be highly heritable in Brahman cattle (Johnston et al. 2006). Currently world-wide, genetic evaluation of female reproduction in beef cattle is limited. In Australia days to calving is used (Graser et al. 2005) and some other countries have analyses for heifer pregnancy. The aim of this work was to determine the amount of genetic variation in measures of lactation anoestrus in Brahmans, and its relationship to age at puberty, and to discuss implications for the genetic evaluation of female reproduction.
Genetic correlations of young bull reproductive traits and heifer puberty traits with female reproductive performance in two tropical beef genotypes in northern Australia
Genetic correlations of young bull and heifer puberty traits with measures of early and lifetime female reproductive performance were estimated in two tropical beef cattle genotypes. Heifer age at puberty was highly (rg = -0.71 ± 0.11) and moderately (rg = -0.40 ± 0.20) genetically correlated with pregnancy rate at first annual mating (mating 1) and lifetime annual calving rate, respectively in Brahman (BRAH). In Tropical Composite (TCOMP), heifer age at puberty was highly correlated with reproductive outcomes from the first re-breed (mating 2), mainly due to its association with lactation anoestrous interval (rg = 0.72 ± 0.17). Scrotal circumference were correlated with heifer age at puberty (rg = -0.41 ± 0.11 at 12 months in BRAH; -0.30 ± 0.13 at 6 months in TCOMP) but correlations were lower with later female reproduction traits. Bull insulin-like growth factor-I was correlated with heifer age at puberty (rg = -0.56 ± 0.11 in BRAH; -0.43 ± 0.11 in TCOMP) and blood luteinising hormone concentration was moderately correlated with lactation anoestrous interval (rg = 0.59 ± 0.23) in TCOMP. Semen quality traits, including mass activity, motility and percent normal sperm were genetically correlated with lactation anoestrus and female lifetime female reproductive traits in both genotypes, but the magnitudes of the relationships differed with bull age at measurement. Preputial eversion and sheath scores were genetically associated with lifetime calving and weaning rates in both genotypes. Several of the early-in-life male and female measures examined were moderately to highly genetically correlated with early and lifetime female reproduction traits and may be useful as indirect selection criteria for improving female reproduction in tropical breeds in northern Australia.
Bull traits measured early in life as indicators of herd fertility
This study investigated the genetic relationships of blood hormones, scrotal size, body weight, condition score and flight time measured on young bulls to 12 months of age with key reproductive traits in Brahman and Tropical Composite breeds (n=4079). Heritability of the traits ranged from 0.17 to 0.72 indicating potential for genetic change in both populations. Genetic correlations with presence of sperm in the ejaculate at 12 months of age, percent normal sperm at 2 years old, and heifer age at puberty were moderate, in some cases up to 0.61, indicating a potential to improve the efficiency of selection of breeding replacements.
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.
Male traits and herd reproductive capability in tropical beef cattle. 1. Experimental design and animal measures
Research into the genetics of whole herd profitability has been a focus of the Beef Cooperative Research Centre for Beef Genetic Technologies over the past decade and it has been identified that measures of male reproduction may offer a potential indirect means of selecting for improved female reproduction. This paper describes the experimental design and provides a descriptive analysis of an array of male traits in Brahman and Tropical Composite genotypes managed under the medium to high stress, semi-extensive to extensive production systems of northern Australia. A total of 1639 Brahman and 2424 Tropical Composite bulls with known pedigrees, bred and raised in northern Australia, were evaluated for a comprehensive range of productive and reproductive traits. These included blood hormonal traits (luteinising hormone, inhibin and insulin-like growth factor-I); growth and carcass traits (liveweight, body condition score, ultrasound scanned 12-13th rib fat, rump P8 fat, eye muscle area and hip height); adaptation traits (flight time and rectal temperature); and a bull breeding soundness evaluation (leg and hoof conformation, sheath score, length of everted prepuce, penile anatomy, scrotal circumference, semen mass activity, sperm motility and sperm morphology). Large phenotypic variation was evident for most traits, with complete overlap between genotypes, indicating that there is likely to be a significant opportunity to improve bull fertility traits through management and bull selection.
Female, Male and Genomic Measures for Use in Genetic Selection to Improve Lifetime Weaning Rate of Brahman Cattle
Female and male measures with potential to be practical, early-in-life genetic indicators of female reproduction in Brahmans were chosen from earlier reports and compared, along with genomic measures, for multi-trait use to improve Brahman lifetime annual weaning rate ('LAWR'). Results suggested substantial genetic gains in 'LAWR' may be possible in 10 years using these measures, but need confirming in other data. Female hip height and coat score and male preputial eversion and liveweight were measures that could warrant wider recording for 'LAWR' improvement. Recording of pregnancy test outcomes from matings 1 and 2 should also be encouraged. A genomic EBV in combination with other measures added to the gain in 'LAWR', but needed an accuracy approaching 60% to be the most important contributor to gains in the combinations of measures studied.
Genetic variation in growth, hormonal and seminal traits of young tropically adapted bulls
Except for scrotal circumference there is little published information on the genetic variation of traits measured on young tropical breed bulls. The current study assesses growth, hormonal and seminal traits measured in Brahman and tropical Composite bulls (n=2212) from weaning through to 2 years. Heritability of scrotal size (39 to 75%), prepubertal serum concentration of inhibin (40 to 71%) and semen quality traits (19 to 27%) indicated potential to genetically improve these traits in both Brahman and tropical Composite populations. Genetic correlations between male traits varied (-46 to 78%), some suggesting antagonism between traits while others indicated that some traits measured in bulls early in life could potentially be indicators of post-pubertal semen quality.
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 live weight, 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.