An association weight matrix identified biological pathways associated with bull fertility traits in a multi-breed population

Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix-partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with 'regulation of neurotransmitter secretion' and 'chromatin formation'. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes-KDM5C, LRRK2, and PME-was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.

Multi-breed genomic predictions and functional variants for fertility of tropical bulls

Worldwide, most beef breeding herds are naturally mated. As such, the ability to identify and select fertile bulls is critically important for both productivity and genetic improvement. Here, we collected ten fertility-related phenotypes for 6,063 bulls from six tropically adapted breeds. Phenotypes were comprised of four bull conformation traits and six traits directly related to the quality of the bull's semen. We also generated high-density DNA genotypes for all the animals. In total, 680,758 single nucleotide polymorphism (SNP) genotypes were analyzed. The genomic correlation of the same trait observed in different breeds was positive for scrotal circumference and sheath score on most breed comparisons, but close to zero for the percentage of normal sperm, suggesting a divergent genetic background for this trait. We confirmed the importance of a breed being present in the reference population to the generation of accurate genomic estimated breeding values (GEBV) in an across-breed validation scenario. Average GEBV accuracies varied from 0.19 to 0.44 when the breed was not included in the reference population. The range improved to 0.28 to 0.59 when the breed was in the reference population. Variants associated with the gene HDAC4, six genes from the spermatogenesis-associated (SPATA) family of proteins, and 29 transcription factors were identified as candidate genes. Collectively these results enable very early in-life selection for bull fertility traits, supporting genetic improvement strategies currently taking place within tropical beef production systems. This study also improves our understanding of the molecular basis of male fertility in mammals.

A conserved haplotype in Wagyu cattle contains RAB4A whose encoded protein regulates glucose trafficking in muscle and fat cells

The Wagyu breed of taurine cattle possess favourable genetics for intramuscular fat (IMF) but genomic loci associated with the trait remain under characterised. Here, we report the identification of a previously unidentified genomic region possessing a particular haplotype structure in Wagyu. Through deployment of a genome-wide haplotype detection analysis that captures regions conserved in a target population but not other populations we screened 100 individual Wagyu and contrasted them with 100 individuals from two independent comparison breeds, Charolais and Angus, using high-density SNPs. An extreme level of Wagyu conservation was assigned to a single genomic window (spanning genomic coordinates BTA28:41 088-300 265 bp). In fact, a five-SNP region spanning 27 096 bp is almost perfectly conserved among the 100 Wagyu individuals assayed and partially overlaps RAB4A. Focussing in, two consecutive SNPs (genomic coordinates 236 949 and 239 950) are apparently fixed within the Wagyu (BB and AA respectively), but at mixed frequencies in the other two breeds. These SNPs are located in the two introns straddling exon 7. In a separate analysis using the 1000 Bulls database, we found that, coincident with exon 7 of RAB4A first allele frequencies were highest in the high IMF Japanese Native (Wagyu) breeds (0.78) and lowest in the low IMF indicine breeds (Nelore and Brahman), with intermediate marbling breeds (Angus and Charolais) assigned intermediate rankings (0.42). RAB4A is known to encode a protein that regulates intracellular trafficking of the insulin-regulated glucose transporter GLUT4. RAB4A can be considered an attractive new positional candidate for IMF development.

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

Background

Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome.

Results

We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N’Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region.

Conclusions

Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.

RAPID COMMUNICATION: Multi-breed validation study unraveled genomic regions associated with puberty traits segregating across tropically adapted breeds1

An efficient strategy to improve QTL detection power is performing across-breed validation studies. Variants segregating across breeds are expected to be in high linkage disequilibrium (LD) with causal mutations affecting economically important traits. The aim of this study was to validate, in a Tropical Composite cattle (TC) population, QTL associations identified for sexual precocity traits in a Nellore and Brahman meta-analysis genome-wide association study. In total, 2,816 TC, 8,001 Nellore, and 2,210 Brahman animals were available for the analysis. For that, genomic regions significantly associated with puberty traits in the meta-analysis study were validated for the following sexual precocity traits in TC: age at first corpus luteum (AGECL), first postpartum anestrus interval (PPAI), and scrotal circumference at 18 months of age (SC). We considered validated QTL those underpinned by significant markers from the Nellore and Brahman meta-analysis (P ≤ 10-4) that were also significant for a TC trait, i.e., presenting a P-value of ≤10-3 for AGECL, PPAI, or SC. We also considered as validated QTL those regions where significant markers in the reference population were at ±250 kb from significant markers in the validation population. Using this criteria, 49 SNP were validated for AGECL, 4 for PPAI, and 14 for SC, from which 5 were in common with AGECL, totaling 62 validated SNP for these traits and 30 candidate genes surrounding them. Considering just candidate genes closest to the top SNP of each chromosome, for AGECL 8 candidate genes were identified: COL8A1, PENK, ENSBTAG00000047425, BPNT1, ADAMTS17, CCHCR1, SUFU, and ENSBTAG00000046374. For PPAI, 3 genes emerged as candidates (PCBP3, KCNK10, and MRPS5), and for SC 8 candidate genes were identified (SNORA70, TRAC, ASS1, BPNT1, LRRK1, PKHD1, PTPRM, and ENSBTAG00000045690). Several candidate regions presented here were previously associated with puberty traits in cattle. The majority of emerging candidate genes are related to biological processes involved in reproductive events, such as maintenance of gestation, and some are known to be expressed in reproductive tissues. Our results suggested that some QTL controlling early puberty seem to be segregating across cattle breeds adapted to tropical conditions.

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.

Growth of Brahman cross heifers to 2 years of age in the dry tropics

Growth of 1368 Brahman cross heifers from 6 year cohorts was monitored over the 2 years post-weaning in Australia’s northern forest, a low-animal-growth dry tropical environment. Heifers weighing 47–266 kg at weaning were managed in groups weighing <100 kg, 100–149 kg, 150–199 kg, and >199 kg during the post-weaning dry season. Weaner heifers were allocated to receive 300 g/day of a protein meal during the dry season or to basic nutritional management to sustain health. Heifers in three cohorts were allocated to first mating at 1 or 2 years of age, in four cohorts to vaccination against androstenedione, and in a small proportion of two cohorts to ovariectomy post-weaning. Growth was highly variable between seasons and years; average cohort liveweight by the start of 2-year-old mating was 256–319 kg. Heifer groups not receiving protein supplementation gained –16 to 21 kg (2 kg average) during 6-month dry seasons, and 49–131 kg (101 kg average) during wet seasons to reach an average of two-thirds of mature liveweight (445 kg) and 95% of mature hip height (1350 mm) by the start of mating at 2 years. Average body condition score (1–5) fluctuated by 1–2 units between seasons. Hip height gain continued, irrespective of season, commencing at ~0.60 mm/day at 6 months of age, and decelerating by ~0.00075 mm/day through to 2.5 years of age. Standard errors of predicted means across analyses were ~0.015 for average daily weight gains, 0.4 mm for average monthly height gain and 0.06 score units for average seasonal body condition score change. Post-weaning dry-season supplementation increased gains in liveweight, height and body condition score by an average of 0.1 kg/day, 0.1 mm/day and 0.5 units, respectively, during the supplementation period. Periods of poor nutrition or high nutritional demand secondary to reproduction suppressed daily gains in liveweight and hip height, at which times body condition score was also reduced. Subsequent to this, partial to full compensation occurred for all measures. Ovariectomy had negative effects on growth. Androstenedione vaccination had no effect on growth. The main conclusion is that heifer growth in Australia’s dry tropical northern forest region is highly variable between seasons and years, thus limiting significant proportions of some cohorts from reaching target weights for mating at 2 years of age, even after compensatory growth.

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.

Maternal body composition in seedstock herds. 3. Multivariate analysis using factor analytic models and cluster analysis

Considerable information exists on genetic relationships of body composition and carcass quality of young and finished beef cattle. However, there is a dearth of information on genetic relationships of cow body composition over time and, also, relationships with young-animal body-composition measures. The aim of the present study is to understand genetic relationships among various cow body-composition traits of Angus cows over time, from yearling to weaning of a second calf at ~3.5 years. To determine genetic correlations among various composition traits over time, a multi-trait–multi-time analysis is required. For the Maternal Productivity Project, this necessitates modelling of five traits (namely weight and ultrasound measure for loin eye muscle area (EMA), rib fat, P8 rump fat and intramuscular fat) by five time combinations (recordings at yearling then pre-calving and weaning in first and second parity). The approach was based on including all 25 trait-by-time combinations in an analysis using factor analytic models to approximate the genetic covariance matrix. Various models for the residual covariance structure were investigated. The analyses yielded correlations that could be compared with those of past studies reported in the literature and, also, to a set of bivariate analyses. Clustering of the genetic multi-trait–multi-time correlation structure resulted in a separation of traits (weight and EMA, and the fat traits) and also of time effects into early (heifer = before first lactation) and late (cow = post-first lactation) measurements.

Climate Adaptation of Tropical Cattle

There is sustained growth in the number of tropical cattle, which represent more than half of all cattle worldwide. By and large, most research in tropical areas is still focused on breeds of cattle, their particular advantages or disadvantages in tropical areas, and the tropical forages or feeds that could be usefully fed to them. A consistent issue for adaptation to climate is the heat of tropical environments. Changing the external characteristics of the animal, such as color and coat characteristics, is one way to adapt, and there are several major genes for these traits. However, further improvement in heat tolerance and other adaptation traits will need to use the entire genome and all physical and physiological systems. Apart from the response to heat, climate forcing through methane emission identifies dry season weight loss as an important if somewhat neglected trait in climate adaptation of cattle. The use of genome-estimated breeding values in tropical areas is in its infancy and will be difficult to implement, but will be essential for rapid, coordinated genetic improvement. The difficulty of implementation cannot be exaggerated and may require major improvements in methodology.

Genomic correlation: harnessing the benefit of combining two unrelated populations for genomic selection

BACKGROUND

The success of genomic selection in animal breeding hinges on the availability of a large reference population on which genomic-based predictions of additive genetic or breeding values are built. Here, we explore the benefit of combining two unrelated populations into a single reference population.

METHODS

The datasets consisted of 1829 Brahman and 1973 Tropical Composite cattle with measurements on five phenotypes relevant to tropical adaptation and genotypes for 71,726 genome-wide single nucleotide polymorphisms (SNPs). The underlying genomic correlation for the same phenotype across the two breeds was explored on the basis of consistent linkage disequilibrium (LD) phase and marker effects in both breeds.

RESULTS

The proportion of genetic variance explained by the entire set of SNPs ranged from 37.5 to 57.6 %. Estimated genomic correlations were drastically affected by the process used to select SNPs and went from near 0 to more than 0.80 for most traits when using the set of SNPs with significant effects and the same LD phase in the two breeds. We found that, by carefully selecting the subset of SNPs, the missing heritability can be largely recovered and accuracies in genomic predictions can be improved six-fold. However, the increases in accuracy might come at the expense of large biases.

CONCLUSIONS

Our results offer hope for the effective implementation of genomic selection schemes in situations where the number of breeds is large, the sample size within any single breed is small and the breeding objective includes many phenotypes.

Accuracy of genomic selection for age at puberty in a multi-breed population of tropically adapted beef cattle

Genomic selection is becoming a standard tool in livestock breeding programs, particularly for traits that are hard to measure. Accuracy of genomic selection can be improved by increasing the quantity and quality of data and potentially by improving analytical methods. Adding genotypes and phenotypes from additional breeds or crosses often improves the accuracy of genomic predictions but requires specific methodology. A model was developed to incorporate breed composition estimated from genotypes into genomic selection models. This method was applied to age at puberty data in female beef cattle (as estimated from age at first observation of a corpus luteum) from a mix of Brahman and Tropical Composite beef cattle. In this dataset, the new model incorporating breed composition did not increase the accuracy of genomic selection. However, the breeding values exhibited slightly less bias (as assessed by deviation of regression of phenotype on genomic breeding values from the expected value of 1). Adding additional Brahman animals to the Tropical Composite analysis increased the accuracy of genomic predictions and did not affect the accuracy of the Brahman predictions.

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.

A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle

High intramuscular fat (IMF) awards price premiums to beef producers and is associated with meat quality and flavor. Studying gene interactions and pathways that affect IMF might unveil causative physiological mechanisms and inform genomic selection, leading to increased accuracy of predictions of breeding value. To study gene interactions and pathways, a gene network was derived from genetic markers associated with direct measures of IMF, other fat phenotypes, feedlot performance, and a number of meat quality traits relating to body conformation, development, and metabolism that might be plausibly expected to interact with IMF biology. Marker associations were inferred from genomewide association studies (GWAS) based on high density genotypes and 29 traits measured on 10,181 beef cattle animals from 3 breed types. For the network inference, SNP pairs were assessed according to the strength of the correlation between their additive association effects across the 29 traits. The co-association inferred network was formed by 2,434 genes connected by 28,283 edges. Topological network parameters suggested a highly cohesive network, in which the genes are strongly functionally interconnected. Pathway and network analyses pointed towards a trio of transcription factors (TF) as key regulators of carcass IMF: PPARGC1A, HNF4G, and FOXP3. Importantly, none of these genes would have been deemed as significantly associated with IMF from the GWAS. Instead, a total of 313 network genes show significant co-association with the 3 TF. These genes belong to a wide variety of biological functions, canonical pathways, and genetic networks linked to IMF-related phenotypes. In summary, our GWAS and network predictions are supported by the current literature and suggest a cooperative role for the 3 TF and other interacting genes including CAPN6, STC2, MAP2K4, EYA1, COPS5, XKR4, NR2E1, TOX, ATF1, ASPH, TGS1, and TTPA as modulators of carcass and meat quality traits in beef cattle.

Variation in genes involved in epigenetic processes offers insights into tropically adapted cattle diversity

We evaluated the relevance of the BovineHD Illumina SNP chip with respect to genes involved in epigenetic processes. Genotypes for 729,068 SNP on two tropical cattle breeds of Australia were used: Brahman (n = 2112) and Tropical Composite (n = 2550). We used data mining approaches to compile a list of bovine protein-coding genes involved in epigenetic processes. These genes represent 9 functional categories that contain between one (histone demethylases) and 99 (chromatin remodeling factors) genes. A total of 3091 SNP mapped to positions within 3000 bp of the 193 coding regions of those genes, including 113 SNP in transcribed regions, 2738 in intronic regions and 240 in up- or down-stream regions. For all these SNP categories, we observed differences in the allelic frequencies between Brahman and Tropical Composite cattle. These differences were larger than those observed for the entire set of 729,068 SNP (P = 1.79 x 10⁻⁵). A multidimensional scaling analysis using only the 113 SNP in transcribed regions allowed for the separation of the two populations and this separation was comparable to the one obtained with a random set of 113 SNP (Principal Component 1 r² > 0.84). To further characterize the differences between the breeds we defined a gene-differentiation metric based on the average genotypic frequencies of SNP connected to each gene and compared both cattle populations. The 10% most differentiated genes were distributed across 10 chromosomes, with significant (P < 0.05) enrichment on BTA 3 and 10. The 10% most conserved genes were located in 12 chromosomes. We conclude that there is variation between cattle populations in genes connected to epigenetic processes, and this variation can be used to differentiate cattle breeds. More research is needed to fully characterize the use of these SNP and its potential as means to further our understanding of biological variation and epigenetic processes.

The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes

Background

The extent of linkage disequilibrium (LD) between molecular markers impacts genome-wide association studies and implementation of genomic selection. The availability of high-density single nucleotide polymorphism (SNP) genotyping platforms makes it possible to investigate LD at an unprecedented resolution. In this work, we characterised LD decay in breeds of beef cattle of taurine, indicine and composite origins and explored its variation across autosomes and the X chromosome.

Findings

In each breed, LD decayed rapidly and r² was less than 0.2 for marker pairs separated by 50 kb. The LD decay curves clustered into three groups of similar LD decay that distinguished the three main cattle types. At short distances between markers (< 10 kb), taurine breeds showed higher LD (r² = 0.45) than their indicine (r² = 0.25) and composite (r² = 0.32) counterparts. This higher LD in taurine breeds was attributed to a smaller effective population size and a stronger bottleneck during breed formation. Using all SNPs on only the X chromosome, the three cattle types could still be distinguished. However for taurine breeds, the LD decay on the X chromosome was much faster and the background level much lower than for indicine breeds and composite populations. When using only SNPs that were polymorphic in all breeds, the analysis of the X chromosome mimicked that of the autosomes.

Conclusions

The pattern of LD mirrored some aspects of the history of breed populations and showed a sharp decay with increasing physical distance between markers. We conclude that the availability of the HD chip can be used to detect association signals that remained hidden when using lower density genotyping platforms, since LD dropped below 0.2 at distances of 50 kb.

The genetics of cow growth and body composition at first calving in two tropical beef genotypes

The genetics of cow growth and body composition traits, measured before first calving (pre-calving: in females before calving following their first 3-month annual mating period, at an average age of 34 months) and at the start of the subsequent mating period (Mating 2: on average 109 days later), were evaluated in 1016 Brahman (BRAH) and 1094 Tropical Composite (TCOMP) cows. Measurements analysed were liveweight, ultrasound-scanned measurements of P8 and 12/13th rib fat depth and eye muscle area, body condition score and hip height. Traits describing the change in these from pre-calving to Mating 2 were also included in the analysis. The maternal genetic component of weaning weight was estimated from weaning-weight records on these cows, their steer half-sibs and their progeny generated from up to six matings (n = 12 528). Within pregnant cows at pre-calving, BRAH were significantly lighter, leaner at the P8 site and taller than their TCOMP contemporaries, and these differences were also significant at Mating 2. There was a genetic basis for variation in growth and body composition traits measured at pre-calving and Mating 2 in BRAH (h2 = 0.27–0.67) and TCOMP (h2 = 0.25–0.87). Traits describing the change from pre- calving to Mating 2 were also moderately heritable for both genotypes (h2 = 0.17–0.54), except for change in hip height (h2 = 0.00 and 0.10 for BRAH and TCOMP, respectively). Genetic correlations between measurements of the same trait at pre-calving and Mating 2 were consistently positive and strong (rg = 0.75–0.98) and similar for both genotypes. In lactating cows, genetic correlations of growth and body composition traits with their change from pre-calving to Mating 2 showed that when animals had low levels of P8 and rib fat at Mating 2, change in eye muscle area was an important descriptor of genetic body condition score (rg = 0.63). This was supported by moderate genetic relationships, which suggested that lactating cows that were genetically predisposed to lose less eye muscle area were those that ended the period with higher P8 fat (rg = 0.66), rib fat (rg = 0.72) and body condition score (rg = 0.61). Change in liveweight, body condition score and, in particular, eye muscle area was significantly related to the maternal genetic component of weaning weight (rg = from –0.40 to –0.85) in both genotypes, suggesting that cows with higher genetic milk-production potential were those with the propensity for greater loss of these traits over the period from pre-calving to Mating 2. These results showed that for tropically adapted cows, the change in eye muscle area from pre-calving to Mating 2 was a more important descriptor of body condition at Mating 2 than was change in fat depth, and that higher genetic milk-production potential, measured as maternal weaning weight, was genetically related to higher mobilisation of muscle, and therefore body condition, over this period.

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.

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.

Genetic relationships between steer performance and female reproduction and possible impacts on whole herd productivity in two tropical beef genotypes

Steer growth and carcass composition, and female reproductive performance have been identified as key aspects of productivity by breeders of tropically adapted beef cattle in Australia. Research has also demonstrated that traits describing meat quality and feed intake and efficiency are of economic importance to Australia’s beef industry. The present study aimed to determine genetic relationships of traits describing steer growth, feed intake and efficiency, carcass composition and meat quality with female reproductive performance in two genotypes of tropically adapted beef cattle. Female reproduction traits describing outcomes of first (Mating 1) and second (Mating 2) annual matings and lifetime reproduction (averaged over 6 matings) were analysed for 1020 Brahman (BRAH) and 1117 Tropical Composite (TCOMP) females. Steer traits were available for 1007 BRAH and 1210 TCOMP half-sibs of the females evaluated for reproductive performance, and measurements of liveweight and body composition for 1025 BRAH and 1520 TCOMP bull progeny of the same females were included in the analysis. Results demonstrated that selection to increase steer carcass weight and eye muscle area and decrease carcass fat depth would have no significant unfavourable impact on female reproductive performance for both genotypes. Measures of liveweight, eye muscle area and P8 fat depth in young BRAH bulls, however, were only moderately correlated with steer carcass equivalents (rg = 0.28 to 0.55) and results showed that selection on the basis of bull measurements alone may negatively affect female lifetime annual calving rate (rg = –0.44 to –0.75) if both were not included in a multi-trait genetic evaluation and considered when making selection decisions. More favourable (lower) net feed intake in BRAH steers was genetically associated with lower Mating 1 weaning rate (rg = 0.76) and higher days to calving (rg = –0.50), although this did not significantly affect lifetime annual calving or weaning rate (rg = 0.10 and 0.29, respectively). For TCOMP, higher steer carcass P8 fat depth was unfavourably genetically associated with female Mating 2 weaning rate (rg = –0.76), although these relationships were not as strong for weaning rate at Mating 1 or when averaged over the animals lifetime (rg = 0.43 and –0.13, respectively). Lower (more favourable) shear force (a measure of tenderness) also displayed a significant genetic association with higher (less favourable) Mating 1 days to calving in TCOMP and, while standard errors were high, tended to be unfavourably associated with other measures of female reproduction evaluated for the present study. Steer growth, carcass composition, meat quality and residual feed intake and female reproduction could be improved simultaneously if measurements describing both are included in a multi-trait genetic evaluation. Results of the present study also showed that expanding female reproduction traits to include descriptors of first and second mating outcomes, as well as lifetime reproductive performance, would allow a fuller account to be taken of genetic relationships of male traits with female reproduction.

Genetic relationships of female reproduction with growth, body composition, maternal weaning weight and tropical adaptation in two tropical beef genotypes

The genetic relationships of female reproduction with growth and body composition, tropical adaptation traits and maternal weaning weight (descriptive of genetic potential milk production) were estimated in 1027 Brahman (BRAH) and 1132 Tropical Composite (TCOMP) females. Female reproduction was evaluated at puberty, as outcomes of the first and second annual mating periods (Mating 1 and Mating 2, which commenced when females averaged 27 and 39 months of age, respectively), as well as annual averages over up to six matings. Traits evaluated included age at puberty, Mating 1 and 2 pregnancy rate, weaning rate and days to calving, and lifetime annual calving and weaning rate. Traits describing growth and body composition (liveweight, hip height, ultrasound-scanned P8 fat depth and eye muscle area, subjective body condition score and blood IGF-I concentration) were measured in the animals as heifers (at ~18 months of age), and again at the start of Mating 2. Traits describing tropical adaptation included coat-length scores in both genotypes and, in BRAH, buffalo fly lesion scores. Previously reported analyses of these data identified heifer IGF-I and coat and buffalo-fly-lesion scores as potential genetic indicators for age at puberty in BRAH. The results of the present study found that exploiting these relationships would have no unfavourable genetic consequences for later female reproduction and, in some cases, may be indicators of female reproduction, when evaluated as outcomes of Matings 1 or 2, or as lifetime annual calving or weaning rates. For BRAH, heifer liveweight was a genetic indicator for Mating 1 weaning rate (rg = 0.70), and, while standard errors were high, there were also positive genetic correlations of heifer hip height, eye muscle area and blood IGF-I concentration with Mating 1 weaning rate (rg = 0.61, 0.58 and 0.43, respectively). For TCOMP, significant genetic relationships of heifer growth, body composition and tropical adaptation traits with female reproduction were virtually absent, suggesting that there is less opportunity to identify earlier in life measures as genetic indicators of reproduction for this genotype. Higher maternal weaning weight was significantly genetically related to lower lifetime annual weaning rate (rg = –0.50) in BRAH, and with lower Mating 2 calving and weaning rate (rg = –0.72 and –0.59, respectively) in TCOMP, which will need to be considered when making selection decisions that affect genetic milk in these genotypes. Importantly, the results presented revealed no strong genetic antagonisms of heifer growth and body composition traits with female reproduction, suggesting that selection could be undertaken to improve these simultaneously.

Genetic parameters for calf mortality and correlated cow and calf traits in tropically adapted beef breeds managed in extensive Australian production systems

The genetic associations between cow teat and udder traits with maternal contributions to calf mortality were studied in Brahman (BRAH) and Tropical Composite (TCOMP) cattle managed in extensive production systems of northern Australia. Data from 9286 purebred and crossbred calves, progeny of 2076 cows and 149 sires, were recorded from 2003 to 2011. Calf weights at birth (BWT) and weaning (WWT) were routinely recorded. The event of calf death before weaning (DWEAN) was analysed as a repeated-measure of the cow. Cows were also scored at each calving for front- and back-teat size and udder size (US) on an ascending five-point scale. Heritabilities for front-teat size, back-teat size and US were 0.38 ± 0.05, 0.31 ± 0.05 and 0.49 ± 0.01, and estimates were the same for BRAH and TCOMP. The heritability of DWEAN was higher in BRAH (0.09 ± 0.02) than in TCOMP (0.02 ± 0.01). Variance ratios for maternal genetic effects contributing to variation in BWT and WWT were 0.13 ± 0.02 and 0.18 ± 0.05, and tended to be larger in TCOMP than in BRAH. Teat and udder scores were moderately correlated phenotypically (0.37 ± 0.01) and genetically (0.53 ± 0.04) with each other. Both traits were uncorrelated genetically with calf birthweight but positively correlated with WWT and DWEAN. The genetic correlation between average teat score at calving and DWEAN was larger (0.54 ± 0.05) than that between US and DWEAN (0.33 ± 0.06), whereas the genetic correlation between US and maternal effects for WWT was larger (0.60 ± 0.08) than the corresponding value for average teat score with maternal WWT (0.37 ± 0.13). Correlations between BWT and WWT were high for both direct (0.63 ± 0.07) and maternal (0.50 ± 0.09) genetic effects. Genetic correlations between maternal effects for BWT or WWT with DWEAN were both negative (–0.23 ± 0.10 and –0.21 ± 0.04), while the correlation between BWT and WWT for maternal effects was positive (0.54 ± 0.09), showing that larger calves at birth are less likely to die before weaning and have heavier weaning weights from maternal genetic contributions to these traits. Selection on maternal components of BWT and WWT should be accompanied by recording for teat and udder characteristics to assist in preventing any undesired correlated response in teat or udder size, which can have detrimental outcomes for calf survival, despite expectations of higher milk yield.

Factors associated with calf mortality in tropically adapted beef breeds managed in extensive Australian production systems

Data from 9296 calves born to 2078 dams over 9 years across five sites were used to investigate factors associated with calf mortality for tropically adapted breeds (Brahman and Tropical Composite) recorded in extensive production systems, using multivariate logistic regression. The average calf mortality pre-weaning was 9.5% of calves born, varying from 1.5% to 41% across all sites and years. In total, 67% of calves that died did so within a week of their birth, with cause of death most frequently recorded as unknown. The major factors significantly (P < 0.05) associated with mortality for potentially large numbers of calves included the specific production environment represented by site-year, low calf birthweight (more so than high birthweight) and horn status at branding. Almost all calf deaths post-branding (assessed from n = 8348 calves) occurred in calves that were dehorned, totalling 2.1% of dehorned calves and 15.9% of all calf deaths recorded. Breed effects on calf mortality were primarily the result of breed differences in calf birthweight and, to a lesser extent, large teat size of cows; however, differences in other breed characteristics could be important. Twin births and calves assisted at birth had a very high risk of mortality, but <1% of calves were twins and few calves were assisted at birth. Conversely, it could not be established how many calves would have benefitted from assistance at birth. Cow age group and outcome from the previous season were also associated with current calf mortality; maiden or young cows (<4 years old) had increased calf losses overall. More mature cows with a previous outcome of calf loss were also more likely to have another calf loss in the subsequent year, and this should be considered for culling decisions. Closer attention to the management of younger cows is warranted to improve calf survival.

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.

Evidence for pleiotropism and recent selection in the PLAG1 region in Australian Beef cattle

A putative functional mutation (rs109231213) near PLAG1 (BTA14) associated with stature was studied in beef cattle. Data from 8199 Bos taurus, Bos indicus and Tropical Composite cattle were used to test the associations between rs109231213 and various phenotypes. Further, 23 496 SNPs located on BTA14 were tested for association with these phenotypes, both independently and fitted together with rs109231213. The C allele of rs109231213 significantly increased hip height, weight, net food intake, age at puberty in males and females and decreased IGF-I concentration in blood and fat depth. When rs109231213 was fitted as a fixed effect in the model, there was an overall reduction in associations between other SNPs and these traits but some SNPs remained associated (P < 10(-4) ). Frequency of the mutant C allele of rs109231213 differed among B. indicus (0.52), B. taurus (0.96) and Tropical Composite (0.68). Most chromosomes carrying the C allele had the same surrounding 10 SNP haplotype, probably because the C allele was introgressed into Brahman from B. taurus cattle. A region of reduced heterozygosity surrounds the C allele; this is small in B. taurus but 20 Mb long in Brahmans, indicating recent and strong selection for the mutant allele. Thus, the C allele appears to mark a mutation that has been selected almost to fixation in the B. taurus breeds studied here and introduced into Brahman cattle during grading up and selected to a frequency of 0.52 despite its negative effects on fertility.

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.

Liveweight prediction from hip height, condition score, fetal age and breed in tropical female cattle

Hip height, body condition, subcutaneous fat, eye muscle area, percentage Bos taurus, fetal age and diet digestibility data were collected at 17 372 assessments on 2181 Brahman and tropical composite (average 28% Brahman) female cattle aged between 0.5 and 7.5 years of age at five sites across Queensland. The study validated the subtraction of previously published estimates of gravid uterine weight to correct liveweight to the non-pregnant status. Hip height and liveweight were linearly related (Brahman: P < 0.001, R2 = 58%; tropical composite P < 0.001, R2 = 67%). Liveweight varied by 12–14% per body condition score (5-point scale) as cows differed from moderate condition (P < 0.01). Parallel effects were also found due to subcutaneous rump fat depth and eye muscle area, which were highly correlated with each other and body condition score (r = 0.7–0.8). Liveweight differed from average by 1.65–1.66% per mm of rump fat depth and 0.71–0.76% per cm2 of eye muscle area (P < 0.01). Estimated dry matter digestibility of pasture consumed had no consistent effect in predicting liveweight and was therefore excluded from final models. A method developed to estimate full liveweight of post-weaning age female beef cattle from the other measures taken predicted liveweight to within 10 and 23% of that recorded for 65 and 95% of cases, respectively. For a 95% chance of predicted group average liveweight (body condition score used) being within 5, 4, 3, 2 and 1% of actual group average liveweight required 23, 36, 62, 137 and 521 females, respectively, if precision and accuracy of measurements matches that used in the research. Non-pregnant Bos taurus female cattle were calculated to be 10–40% heavier than Brahmans at the same hip height and body condition, indicating a substantial conformational difference. The liveweight prediction method was applied to a validation population of 83 unrelated groups of cattle weighed in extensive commercial situations on 119 days over 18 months (20 917 assessments). Liveweight prediction in the validation population exceeded average recorded liveweight for weigh groups by an average of 19 kg (~6%) demonstrating the difficulty of achieving accurate and precise animal measurements under extensive commercial grazing conditions.

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.

Genetic parameters of infectious bovine keratoconjunctivitis and its relationship with weight and parasite infestations in Australian tropical Bos taurus cattle

Background

Infectious bovine keratoconjunctivitis (IBK) or ‘pinkeye’ is an economically important ocular disease that significantly impacts animal performance. Genetic parameters for IBK infection and its genetic and phenotypic correlations with cattle tick counts, number of helminth (unspecified species) eggs per gram of faeces and growth traits in Australian tropically adapted Bos taurus cattle were estimated.

Methods

Animals were clinically examined for the presence of IBK infection before and after weaning when the calves were 3 to 6 months and 15 to 18 months old, respectively and were also recorded for tick counts, helminth eggs counts as an indicator of intestinal parasites and live weights at several ages including 18 months.

Results

Negative genetic correlations were estimated between IBK incidence and weight traits for animals in pre-weaning and post-weaning datasets. Genetic correlations among weight measurements were positive, with moderate to high values. Genetic correlations of IBK incidence with tick counts were positive for the pre-weaning and negative for the post-weaning datasets but negative with helminth eggs counts for the pre-weaning dataset and slightly positive for the post-weaning dataset. Genetic correlations between tick and helminth eggs counts were moderate and positive for both datasets. Phenotypic correlations of IBK incidence with helminth eggs per gram of faeces were moderate and positive for both datasets, but were close to zero for both datasets with tick counts.

Conclusions

Our results suggest that genetic selection against IBK incidence in tropical cattle is feasible and that calves genetically prone to acquire IBK infection could also be genetically prone to have a slower growth. The positive genetic correlations among weight traits and between tick and helminth eggs counts suggest that they are controlled by common genes (with pleiotropic effects). Genetic correlations between IBK incidence and tick and helminth egg counts were moderate and opposite between pre-weaning and post-weaning datasets, suggesting that the environmental and (or) maternal effects differ between these two growth phases. This preliminary study provides estimated genetic parameters for IBK incidence, which could be used to design selection and breeding programs for tropical adaptation in beef cattle.

The IGF1 pathway genes and their association with age of puberty in cattle

Insulin-like growth factor I (somatomedin C) (IGF1) influences gonadotrophin-releasing hormone (GnRH) neurons during puberty, and GnRH release guides pubertal development. Therefore, genes of the IGF1 pathway are biological candidates for the identification of single-nucleotide polymorphisms (SNPs) affecting age of puberty. In a genome-wide association study, genotyped heifers were Tropical Composite (TCOMP, n = 866) or Brahman (BRAH, n = 843), with observation of age at first corpus luteum defining puberty. We examined SNPs in or near genes of the IGF1 pathway and report seven genes associated with age at puberty in cattle: IGF1R, IGFBP2, IGFBP4, PERK (HUGO symbol EIF2AK3), PIK3R1, GSK3B and IRS1. SNPs in the IGF1 receptor (IGF1R) showed the most promising associations: two SNPs were associated with puberty in TCOMP (P < 0.05) and one in BRAH (P = 0.00009). This last SNP explained 2% of the genetic variation (R(2) = 2.04%) for age of puberty in BRAH. Hence, IGF1R was examined further. Additional SNPs were genotyped, and haplotypes were analysed. To test more SNPs in this gene, four new SNPs from dbSNP were selected and genotyped. Single SNP and haploytpe analysis revealed associations with age of puberty in both breeds. There were two haplotypes of 12 IGF1R SNPs associated with puberty in BRAH (P < 0.05) and one in TCOMP (P < 0.05). One haplotype of two SNPs was associated (P < 0.01) with puberty in BRAH, but not in TCOMP. In conclusion, the IGF1 pathway appeared more relevant for age of puberty in Brahman cattle, and IGF1R showed higher significance when compared with other genes from the pathway.

Animal-level factors affecting ovarian function in Bos indicus heifers treated to synchronize ovulation with intravaginal progesterone-releasing devices and oestradiol benzoate

The primary objective of this study was to investigate the impact of animal-level factors including energy balance and environmental/management stress, on the ovarian function of Bos indicus heifers treated to synchronize ovulation. Two-year-old Brahman (BN) (n = 30) and BN-cross (n = 34) heifers were randomly allocated to three intravaginal progesterone-releasing device (IPRD) treatment groups: (i) standard-dose IPRD [Cue-Mate(®) (CM) 1.56 g; n = 17]; (ii) half-dose IPRD [0.78 g progesterone (P(4)); CM 0.78 g; n = 15]; (iii) half-dose IPRD + 300 IU equine chorionic gonadotrophin at IPRD removal (CM 0.78 g + G; n = 14); (iv) and a control group, 2× PGF(2α) [500 μg prostaglandin F(2α) (PGF(2α))] on Day -16 and -2 (n = 18). Intravaginal progesterone-releasing device-treated heifers received 250 μg PGF(2α) at IPRD insertion (Day -10) and IPRD removal (Day -2) and 1 mg oestradiol benzoate on Day -10 and -1. Heifers were managed in a small feedlot and fed a defined ration. Ovarian function was evaluated by ultrasonography and plasma P(4) throughout the synchronized and return cycles. Energy balance was evaluated using plasma insulin-like growth factor 1 (IGF-I) and glucose concentrations. The impact of environmental stressors was evaluated using plasma cortisol concentration. Heifers that had normal ovarian function had significantly higher IGF-I concentrations at commencement of the experiment (p = 0.008) and significantly higher plasma glucose concentrations at Day -2 (p = 0.040) and Day 4 (p = 0.043), than heifers with abnormal ovarian function. There was no difference between the mean pre-ovulatory cortisol concentrations of heifers that ovulated or did not ovulate. However, heifers that ovulated had higher cortisol concentrations at Day 4 (p = 0.056) and 6 (p = 0.026) after ovulation than heifers that did not ovulate.

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.

Genotype by environment interaction in Nelore cattle from five Brazilian states

Records from 75,941 Nelore cattle were used to determine the importance of genotype by environment interaction (GEI) in five Brazilian states. (Co)variance components were estimated by single-trait analysis (with yearling weight, W450, considered to be the same trait in all states) and multiple-trait analysis (with the record from each state considered to be a different trait). The direct heritability estimates for yearling weight were 0.51, 0.39, 0.44, 0.37 and 0.41 in the states of Goiás, Mato Grosso, São Paulo, Mato Grosso do Sul and Minas Gerais, respectively. The across-state genetic correlation estimates between Goiás and Mato Grosso, Goiás and Minas Gerais, São Paulo and Minas Gerais, and Mato Grosso do Sul and Minas Gerais ranged from 0.67 to 0.75. These estimates indicate that GEIs are biologically important. No interactions were observed between Goiás and São Paulo, Goiás and Mato Grosso do Sul, Mato Grosso and São Paulo, Mato Grosso and Mato Grosso do Sul, Mato Grosso and Minas Gerais, or São Paulo and Mato Grosso do Sul (0.82 to 0.97). Comparison of single and multiple-trait analyses showed that selection based on the former was less efficient in the presence of GEI, with substantial losses (up to 10%) during selection.

A single nucleotide polymorphism-derived regulatory gene network underlying puberty in 2 tropical breeds of beef cattle

Harsh tropical environments impose serious challenges on poorly adapted species. In beef cattle, tropical adaptation in the form of temperature and disease resistance, coupled with acclimatization to seasonal and limited forage, comes at a cost to production efficiency. Prominent among these costs is delayed onset of puberty, a challenging phenotype to manipulate through traditional breeding mechanisms. Recently, system biology approaches, including gene networks, have been applied to the genetic dissection of complex phenotypes. We aimed at developing and studying gene networks underlying cattle puberty. Our starting material comprises the association results of ~50,000 SNP on 22 traits, including age at puberty, and 2 cattle breed populations: Brahman (n = 843) and Tropical Composite (n = 866). We defined age at puberty as the age at first corpus luteum (AGECL). By capturing the genes harboring mutations minimally associated (P < 0.05) to AGECL or to a set of traits related with AGECL, we derived a gene network for each breed separately and a third network for the combined data set. At the intersection of the 3 networks, we identified candidate genes and pathways that were common to both breeds. Resulting from these analyses, we identified an enrichment of genes involved in axon guidance, cell adhesion, ErbB signaling, and glutamate activity, pathways that are known to affect pulsatile release of GnRH, which is necessary for the onset of puberty. Furthermore, we employed network connectivity and centrality parameters along with a regulatory impact factor metric to identify the key transcription factors (TF) responsible for the molecular regulation of puberty. As a novel finding, we report 5 TF (HIVEP3, TOX, EYA1, NCOA2, and ZFHX4) located in the network intersecting both breeds and interacting with other TF, forming a regulatory network that harmonizes with the recent literature of puberty. Finally, we support our network predictions with evidence derived from gene expression in hypothalamic tissue of adult cows.

Detection of chromosome segments of zebu and taurine origin and their effect on beef production and growth

Cattle in breeds formed by recent crossing of Bos taurus (Bt) and Bos indicus (Bi) subspecies should contain chromosomes that are a composite of Bt and Bt segments. Using data from a 50K SNP chip, we were able to identify whether a chromosome segment of 11 SNP in a composite animal descended from a Bt or a Bi ancestor. When the method was tested in purebred Bt or Brahman cattle, about 94% of segments were assigned correctly. About 10% of the genome in Australian Brahman cattle appears to be of Bt origin, as might be expected from their history. We then examined the effect of the origin of each chromosome segment on BW in a population of 515 Bt × Bi composite cattle and found 67 chromosome segments with a significant (P<0.01) effect. We confirmed these effects by examining these 67 segments in a population of Brahman cattle and in a population of mixed breeds including composite breeds such as Santa Gertrudis and Brahman cattle. About 66% of the 67 segments had an effect in the same direction in the confirmation analyses as in the discovery population. However, the effect on BW and other traits of chromosome segment origin is small, indicating that we had low power to detect these effects with the number of animals available. Consequently, when chromosome segment origin was used in genomic selection to predict BW, the accuracy was low (0.08). Chromosome segments that had a positive effect on BW tend to be at greater frequency in composite breeds than chromosome segments with a negative effect on BW.

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

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

Polymorphic regions affecting human height also control stature in cattle

Orthologous positions of 55 genes associated with height in four human populations were located on the bovine genome. Single nucleotide polymorphisms close to eight of these genes were significantly associated with stature in cattle (Bos taurus and Bos indicus). This suggests that these genes may contribute to controlling stature across mammalian species.

Association weight matrix for the genetic dissection of puberty in beef cattle

We describe a systems biology approach for the genetic dissection of complex traits based on applying gene network theory to the results from genome-wide associations. The associations of single-nucleotide polymorphisms (SNP) that were individually associated with a primary phenotype of interest, age at puberty in our study, were explored across 22 related traits. Genomic regions were surveyed for genes harboring the selected SNP. As a result, an association weight matrix (AWM) was constructed with as many rows as genes and as many columns as traits. Each {i, j} cell value in the AWM corresponds to the z-score normalized additive effect of the ith gene (via its neighboring SNP) on the jth trait. Columnwise, the AWM recovered the genetic correlations estimated via pedigree-based restricted maximum-likelihood methods. Rowwise, a combination of hierarchical clustering, gene network, and pathway analyses identified genetic drivers that would have been missed by standard genome-wide association studies. Finally, the promoter regions of the AWM-predicted targets of three key transcription factors (TFs), estrogen-related receptor gamma (ESRRG), Pal3 motif, bound by a PPAR-gamma homodimer, IR3 sites (PPARG), and Prophet of Pit 1, PROP paired-like homeobox 1 (PROP1), were surveyed to identify binding sites corresponding to those TFs. Applied to our case, the AWM results recapitulate the known biology of puberty, captured experimentally validated binding sites, and identified candidate genes and gene-gene interactions for further investigation.

Haplotypes that include the integrin alpha 11 gene are associated with tick burden in cattle

BACKGROUND

Infestations on cattle by the ectoparasite Boophilus (Rhipicephalus) microplus (cattle tick) impact negatively on animal production systems. Host resistance to tick infestation has a low to moderate heritability in the range 0.13 - 0.64 in Australia. Previous studies identified a QTL on bovine chromosome 10 (BTA10) linked to tick burden in cattle.

RESULTS

To confirm these associations, we collected genotypes of 17 SNP from BTA10, including three obtained by sequencing part of the ITGA11 (Integrin alpha 11) gene. Initially, we genotyped 1,055 dairy cattle for the 17 SNP, and then genotyped 557 Brahman and 216 Tropical Composite beef cattle for 11 of the 17 SNP. In total, 7 of the SNP were significantly (P < 0.05) associated with tick burden tested in any of the samples. One SNP, ss161109814, was significantly (P < 0.05) associated with tick burden in both the taurine and the Brahman sample, but the favourable allele was different. Haplotypes for three and for 10 SNP were more significantly (P < 0.001) associated with tick burden than SNP analysed individually. Some of the common haplotypes with the largest sample sizes explained between 1.3% and 1.5% of the residual variance in tick burden.

CONCLUSIONS

These analyses confirm the location of a QTL affecting tick burden on BTA10 and position it close to the ITGA11 gene. The presence of a significant association in such widely divergent animals suggests that further SNP discovery in this region to detect causal mutations would be warranted.

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.

Genetics of meat quality and carcass traits and the impact of tenderstretching in two tropical beef genotypes

Meat quality and carcass traits were measured for 2180 feedlot finished Brahman (BRAH) and Tropical Composite (TCOMP) steers to investigate genetic and non-genetic influences on shear force, and other meat quality traits. Genetic and phenotypic correlations were estimated between carcass and meat quality traits, and with live animal measurements collected in steers from weaning to feedlot exit, and their heifer half-sibs up to their first mating, which were managed in Australia’s tropical or subtropical environments. Left sides of carcasses were tenderstretched (hung by the aitch-bone) while right sides were conventionally hung (by the Achilles tendon). Tenderstretching reduced mean shear force by 1.04 kg, and phenotypic variance by 77% of that observed in conventionally hung sides. Genotype differences existed for carcass traits, with TCOMP carcasses significantly heavier, fatter, with greater eye muscle area, and lower retail beef yield than BRAH. TCOMP had lower shear force, and higher percent intramuscular fat. Meat quality and carcass traits were moderately heritable, with estimates for shear force and compression of 0.33 and 0.19 for BRAH and 0.32 and 0.20 for TCOMP respectively. In both genotypes, estimates of heritability for carcass traits (carcass weight, P8 and rib fat depths, eye muscle area and retail beef yield) were consistently moderate to high (0.21 to 0.56). Shear force and compression were genetically correlated with percent intramuscular fat (r g = –0.26 and –0.57, respectively), and meat colour (r g = –0.41 and –0.68, respectively). For TCOMP, lower shear force was genetically related to decreased carcass P8 fat depth (r g = 0.51). For BRAH steers and heifers measured at pasture, fatness traits and growth rates were genetically correlated with shear force, although the magnitude of these relationships varied with time of measurement. Net feed intake was significantly genetically correlated with carcass rib fat depth (r g = 0.49), eye muscle area (r g = –0.42) and retail beef yield (r g = –0.61). These results demonstrate that selection to improve production and carcass traits can impact meat quality traits in tropically adapted cattle, and that genotype specific evaluations will be necessary to accommodate different genetic relationships between meat quality, carcass and live animal traits.

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 < 0.05) lower TICK, EPG, FLY and TEMP than did TCOMP. BRAH also had significantly sleeker coats, lighter coat colour, more pendulous navels and more docile temperament than did TCOMP. The heritability of TICK and FLY was low (<20%), that of EPG, TEMP, NAVEL and FT was moderate (20–50%) and that of COAT and COLOUR high (>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.