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

BACKGROUND

It has been challenging to implement genomic selection in multi-breed tropical beef cattle populations. If commercial (often crossbred) animals could be used in the reference population for these genomic evaluations, this could allow for very large reference populations. In tropical beef systems, such animals often have no pedigree information. Here we investigate potential models for such data, using marker heterozygosity (to model heterosis) and breed composition derived from genetic markers, as covariates in the model. Models treated breed effects as either fixed or random, and included genomic best linear unbiased prediction (GBLUP) and BayesR. A tropically-adapted beef cattle dataset of 29,391 purebred, crossbred and composite commercial animals was used to evaluate the models.

RESULTS

Treating breed effects as random, in an approach analogous to genetic groups allowed partitioning of the genetic variance into within-breed and across breed-components (even with a large number of breeds), and estimation of within-breed and across-breed genomic estimated breeding values (GEBV). We demonstrate that moderately-accurate (0.30-0.43) GEBV can be calculated using these models. Treating breed effects as random gave more accurate GEBV than treating breed as fixed. A simple GBLUP model where no breed effects were fitted gave the same accuracy (and correlations of GEBV very close to 1) as a model where GEBV for within-breed and the GEBV for (random) across-breed effects were included. When GEBV were predicted for herds with no data in the reference population, BayesR resulted in the highest accuracy, with 3% accuracy improvement averaged across traits, especially when the validation population was less related to the reference population. Estimates of heterosis from our models were in line with previous estimates from beef cattle. A method for estimating the number of effective breed comparisons for each breed combination accumulated across contemporary groups is presented.

CONCLUSIONS

When no pedigree is available, breed composition and heterosis for inclusion in multi-breed genomic evaluation can be estimated from genotypes. When GEBV were predicted for herds with no data in the reference population, BayesR resulted in the highest accuracy.

Proteomic Analysis of Hypothalamus and Pituitary Gland in Pre and Postpubertal Brahman Heifers

The hypothalamus and the pituitary gland are directly involved in the complex systemic changes that drive the onset of puberty in cattle. Here, we applied integrated bioinformatics to elucidate the critical proteins underlying puberty and uncover potential molecular mechanisms from the hypothalamus and pituitary gland of prepubertal (n = 6) and postpubertal (n = 6) cattle. Proteomic analysis in the hypothalamus and pituitary gland revealed 275 and 186 differentially abundant (DA) proteins, respectively (adjusted p-value < 0.01). The proteome profiles found herein were integrated with previously acquired transcriptome profiles. These transcriptomic studies used the same tissues harvested from the same heifers at pre- and post-puberty. This comparison detected a small number of matched transcripts and protein changes at puberty in each tissue, suggesting the need for multiple omics analyses for interpreting complex biological systems. In the hypothalamus, upregulated DA proteins at post-puberty were enriched in pathways related to puberty, including GnRH, calcium and oxytocin signalling pathways, whereas downregulated proteins were observed in the estrogen signalling pathway, axon guidance and GABAergic synapse. Additionally, this study revealed that ribosomal pathway proteins in the pituitary were involved in the pubertal development of mammals. The reported molecules and derived protein-protein networks are a starting point for future experimental approaches that might dissect with more detail the role of each molecule to provide new insights into the mechanisms of puberty onset in cattle.

Environmental variation effects fertility in tropical beef cattle

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

Sustainable Intensification of Beef Production in the Tropics: The Role of Genetically Improving Sexual Precocity of Heifers

Simple Summary

Tropical pasture-based beef production systems play a vital role in global food security. The importance of promoting sustainable intensification of such systems has been debated worldwide. Demand for beef is growing together with concerns over the impact of its production on the environment. Implementing sustainable livestock intensification programs relies on animal genetic improvement. In tropical areas, the lack of sexual precocity is a bottleneck for cattle efficiency, directly impacting the sustainability of production systems. In the present review we present and discuss the state of the art of genetic evaluation for sexual precocity in Bos indicus beef cattle, covering the definition of measurable traits, genetic parameter estimates, genomic analyses, and a case study of selection for sexual precocity in Nellore breeding programs.

Abstract

Increasing productivity through continued animal genetic improvement is a crucial part of implementing sustainable livestock intensification programs. In Zebu cattle, the lack of sexual precocity is one of the main obstacles to improving beef production efficiency. Puberty-related traits are complex, but large-scale data sets from different “omics” have provided information on specific genes and biological processes with major effects on the expression of such traits, which can greatly increase animal genetic evaluation. In addition, genetic parameter estimates and genomic predictions involving sexual precocity indicator traits and productive, reproductive, and feed-efficiency related traits highlighted the feasibility and importance of direct selection for anticipating heifer reproductive life. Indeed, the case study of selection for sexual precocity in Nellore breeding programs presented here show that, in 12 years of selection for female early precocity and improved management practices, the phenotypic means of age at first calving showed a strong decreasing trend, changing from nearly 34 to less than 28 months, with a genetic trend of almost −2 days/year. In this period, the percentage of early pregnancy in the herds changed from around 10% to more than 60%, showing that the genetic improvement of heifer’s sexual precocity allows optimizing the productive cycle by reducing the number of unproductive animals in the herd. It has a direct impact on sustainability by better use of resources. Genomic selection breeding programs accounting for genotype by environment interaction represent promising tools for accelerating genetic progress for sexual precocity in tropical beef cattle.

Genetic Parameters for Maternal Performance Traits in Commercially Farmed New Zealand Beef Cattle

Simple Summary

Enhancing maternal performance in a beef cattle enterprise can increase overall profitability. Knowledge of the degree of genetic variation in relevant traits is required to inform breeding decisions in commercial environments. The objective of this research was to examine the inheritance of maternal performance traits and to evaluate the trait complementarity among reproduction, live weight, hip height, body condition score and maternal weaning weight in 15-month-old heifers, 2-year-old cows and mature cows using data collected on commercial New Zealand hill country farms. Results from this study indicate that almost no genetic variation exists for pregnancy outcomes in 15-month-old heifers and mature cows under New Zealand farming conditions but there is potential to improve reproductive performance in 2-year-old cows through genetic selection. Cows with greater genetic potential for rebreeding performance after their first calving season were more likely to have greater live weight, hip height and body condition score as heifers but were unlikely to become larger cows at maturity. Cows with genetics for greater maternal weaning weight were more likely to carry lower body condition and those animals tended to show greater reproductive performance.

Abstract

Maternal performance is a major driver of profitability in cow-calf beef cattle enterprises. The aim of this research was to evaluate the inheritance of maternal performance traits and examine the intercorrelation among reproduction, live weight, hip height, body condition and maternal contribution to calf weaning weight in 15-month-old heifers, 2-year-old cows and mature cows in New Zealand beef herds. Data were collected on a total of 14,241 cows and their progeny on five commercial New Zealand hill country farms. Heritabilities were low for reproductive traits in heifers and mature cows (0–0.06) but were greater in 2-year-old cows (0.12–0.21). Body condition scores were lowly (0.15–0.26) and live weights (0.42–0.48) and hip heights (0.47–0.65) highly heritable in heifers, 2-year-old cows and mature cows. Results indicate that 2-year-old cows with higher genetic potential for rebreeding ability may have greater genetic merit for live weight, hip height and body condition as heifers (r_g = 0.19–0.54) but are unlikely to be larger cows at maturity (r_g = −0.27–−0.10). The maternal genetic effect on weaning weight had a heritability of 0.20 and was negatively genetically correlated with body condition score in lactating cows (r_g = −0.55–−0.40) but positively genetically correlated with rebreeding performance (r_g = 0.48).

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

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

Meta-Analysis of Heifer Traits Identified Reproductive Pathways in Bos indicus Cattle

Fertility traits measured early in life define the reproductive potential of heifers. Knowledge of genetics and biology can help devise genomic selection methods to improve heifer fertility. In this study, we used ~2400 Brahman cattle to perform GWAS and multi-trait meta-analysis to determine genomic regions associated with heifer fertility. Heifer traits measured were pregnancy at first mating opportunity (PREG1, a binary trait), first conception score (FCS, score 1 to 3) and rebreeding score (REB, score 1 to 3.5). The heritability estimates were 0.17 (0.03) for PREG1, 0.11 (0.05) for FCS and 0.28 (0.05) for REB. The three traits were highly genetically correlated (0.75-0.83) as expected. Meta-analysis was performed using SNP effects estimated for each of the three traits, adjusted for standard error. We identified 1359 significant SNPs (p-value < 9.9 × 10-6 at FDR < 0.0001) in the multi-trait meta-analysis. Genomic regions of 0.5 Mb around each significant SNP from the meta-analysis were annotated to create a list of 2560 positional candidate genes. The most significant SNP was in the vicinity of a genomic region on chromosome 8, encompassing the genes SLC44A1, FSD1L, FKTN, TAL2 and TMEM38B. The genomic region in humans that contains homologs of these genes is associated with age at puberty in girls. Top significant SNPs pointed to additional fertility-related genes, again within a 0.5 Mb region, including ESR2, ITPR1, GNG2, RGS9BP, ANKRD27, TDRD12, GRM1, MTHFD1, PTGDR and NTNG1. Functional pathway enrichment analysis resulted in many positional candidate genes relating to known fertility pathways, including GnRH signaling, estrogen signaling, progesterone mediated oocyte maturation, cAMP signaling, calcium signaling, glutamatergic signaling, focal adhesion, PI3K-AKT signaling and ovarian steroidogenesis pathway. The comparison of results from this study with previous transcriptomics and proteomics studies on puberty of the same cattle breed (Brahman) but in a different population identified 392 genes in common from which some genes-BRAF, GABRA2, GABR1B, GAD1, FSHR, CNGA3, PDE10A, SNAP25, ESR2, GRIA2, ORAI1, EGFR, CHRNA5, VDAC2, ACVR2B, ORAI3, CYP11A1, GRIN2A, ATP2B3, CAMK2A, PLA2G, CAMK2D and MAPK3-are also part of the above-mentioned pathways. The biological functions of the positional candidate genes and their annotation to known pathways allowed integrating the results into a bigger picture of molecular mechanisms related to puberty in the hypothalamus-pituitary-ovarian axis. A reasonable number of genes, common between previous puberty studies and this study on early reproductive traits, corroborates the proposed molecular mechanisms. This study identified the polymorphism associated with early reproductive traits, and candidate genes that provided a visualization of the proposed mechanisms, coordinating the hypothalamic, pituitary, and ovarian functions for reproductive performance in Brahman cattle.

Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle

Context Studies have shown that favourable genetic correlations exist between female and male fertility traits. However, investigations regarding these correlations in Australian tropical beef cattle are limited to either pedigree or single-breed analysis. Aim The study aims to use genomic information to estimate genetic parameters of six female and seven male fertility traits measured during the first 2 years of life, in two tropical breeds. Methods Single-, bivariate and multi-trait models were used to analyse fertility data from Brahman (BB; 996 cows and 1022 bulls); and Tropical Composite (TC; 1091 cows and 998 bulls) cattle genotyped with high-density single-nucleotide polymorphism chip assay. Key results Heritability estimates in BB cows ranged from low (0.07 ± 0.04) for days to calving at the first calving opportunity (DC1, days) to high (0.57 ± 0.08) for age at first corpus luteum (AGECL, days). In BB bulls, estimates varied from low (0.09 ± 0.05) for sperm motility (score 1–5) to high (0.64 ± 0.06) for scrotal circumference (SC) measured at 24 months (SC24, cm). Similarly, heritability estimates in TC cows were low (0.04 ± 0.03) for DC1 and high (0.69 ± 0.02) for AGECL. In TC bulls, the heritability was low (0.09 ± 0.05) for sperm motility and high (0.69 ± 0.07) for SC24. Within-sex for both breeds, blood concentrations of insulin growth-factor 1 (IGF1) measured in cows at 18 months (IGF1c) were negatively correlated with female fertility phenotypes. In BB, across-sex, bulls’ blood concentration of IGF1 measured at 6 months (IGF1b) was a good indicator trait for the following four female traits: AGECL, the first postpartum anoestrus interval, age at first calving and DC1. In TC, IGF1b and percentage normal sperm were good predictors of female fertility phenotypes. Conclusions The heritability estimates and genomic correlations from the present study generally support and confirmed the earlier estimates from pedigree analyses. The findings suggest that selection for female fertility traits will benefit male fertility, and vice versa. Implications Heritability estimates and genomic correlations suggest that we can select for fertility traits measured early in life, with benefits within and across sex. Using traits available through veterinary assessment of bull fertility as selection indicators will enhance bull and cow fertility, which can lead to better breeding rates in tropical herds.

The Effect of Stress on Reproduction and Reproductive Technologies in Beef Cattle-A Review

Researchers have contributed by increasing our understanding of the factors affecting reproduction in beef, mainly physical health and nutrition aspects, which have been main concerns during decades. Animal welfare is of outmost relevance in all animal production systems and it is strongly associated to stress. Stress responses involve endocrine, paracrine and neural systems and the consequences of this stress on the reproductive efficiency of specifically, beef cattle and bulls, need to be highlighted. We, therefore, describe the fundamentals of stress and its quantification, focusing in beef herds, reviewing the highly valuable pieces of research, already implemented in this field. We examine major factors (stressors) contributing to stress in beef cattle and their effects on the animals, their reproductive performance and the success of reproductive biotechnologies. We include terms such as acclimatization, acclimation or temperament, very relevant in beef systems. We examine specifically the management stress due to handling, social environment and hierarchy or weaning effects; nutritional stress; and thermal stress (not only heat stress) and also review the influence of these stressors on reproductive performance and effectiveness of reproductive biotechnologies in beef herds. A final message on the attention that should be devoted to these factors is highlighted.

Gene regulation could be attributed to TCF3 and other key transcription factors in the muscle of pubertal heifers

Puberty is a whole-body event, driven by the hypothalamic integration of peripheral signals such as leptin or IGF-1. In the process of puberty, reproductive development is simultaneous to growth, including muscle growth. To enhance our understanding of muscle function related to puberty, we performed transcriptome analyses of muscle samples from six pre- and six post-pubertal Brahman heifers (Bos indicus). Our aims were to perform differential expression analyses and co-expression analyses to derive a regulatory gene network associate with puberty. As a result, we identified 431 differentially expressed (DEx) transcripts (genes and non-coding RNAs) when comparing pre- to post-pubertal average gene expression. The DEx transcripts were compared with all expressed transcripts in our samples (over 14,000 transcripts) for functional enrichment analyses. The DEx transcripts were associated with "extracellular region," "inflammatory response" and "hormone activity" (adjusted p < .05). Inflammatory response for muscle regeneration is a necessary aspect of muscle growth, which is accelerated during puberty. The term "hormone activity" may signal genes that respond to progesterone signalling in the muscle, as the presence of this hormone is an important difference between pre- and post-pubertal heifers in our experimental design. The DEx transcript with the highest average expression difference was a mitochondrial gene, ENSBTAG00000043574 that might be another important link between energy metabolism and puberty. In the derived co-expression gene network, we identified six hub genes: CDC5L, MYC, TCF3, RUNX2, ATF2 and CREB1. In the same network, 48 key regulators of DEx transcripts were identified, using a regulatory impact factor metric. The hub gene TCF3 was also a key regulator. The majority of the key regulators (22 genes) are members of the zinc finger family, which has been implicated in bovine puberty in other tissues. In conclusion, we described how puberty may affect muscle gene expression in cattle.

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

Background

In tropically-adapted beef heifers, application of genomic prediction for age at puberty has been limited due to low prediction accuracies. Our aim was to investigate novel methods of pre-selecting whole-genome sequence (WGS) variants and alternative analysis methodologies; including genomic best linear unbiased prediction (GBLUP) with multiple genomic relationship matrices (MGRM) and Bayesian (BayesR) analyses, to determine if prediction accuracy for age at puberty can be improved.

Methods

Genotypes and phenotypes were obtained from two research herds. In total, 868 Brahman and 960 Tropical Composite heifers were recorded in the first population and 3695 Brahman, Santa Gertrudis and Droughtmaster heifers were recorded in the second population. Genotypes were imputed to 23 million whole-genome sequence variants. Eight strategies were used to pre-select variants from genome-wide association study (GWAS) results using conditional or joint (COJO) analyses. Pre-selected variants were included in three models, GBLUP with a single genomic relationship matrix (SGRM), GBLUP MGRM and BayesR. Five-way cross-validation was used to test the effect of marker panel density (6 K, 50 K and 800 K), analysis model, and inclusion of pre-selected WGS variants on prediction accuracy.

Results

In all tested scenarios, prediction accuracies for age at puberty were highest in BayesR analyses. The addition of pre-selected WGS variants had little effect on the accuracy of prediction when BayesR was used. The inclusion of WGS variants that were pre-selected using a meta-analysis with COJO analyses by chromosome, fitted in a MGRM model, had the highest prediction accuracies in the GBLUP analyses, regardless of marker density. When the low-density (6 K) panel was used, the prediction accuracy of GBLUP was equal (0.42) to that with the high-density panel when only six additional sequence variants (identified using meta-analysis COJO by chromosome) were included.

Conclusions

While BayesR consistently outperforms other methods in terms of prediction accuracies, reasonable improvements in accuracy can be achieved when using GBLUP and low-density panels with the inclusion of a relatively small number of highly relevant WGS variants.

Calf loss in northern Australia: a systematic review

Calf mortality is a key issue for the north Australian beef industry; however, the sector faces several challenges that preclude the detection and reduction of calf mortality rates. A systematic literature review methodology was employed to explore scientific literature describing the scope of calf loss in northern Australia. Online databases were used to locate articles reporting on beef calf mortality rates within the north Australian region. Articles (n=43) consisting of 668 beef cattle cohorts were retrieved that reported calf mortality between 1936 and 2014. Of these, 13 different observation periods were identified. Most cohorts (n=201) examined mortality between the pregnancy to weaning period, whereas only 20 cohorts in four studies were located that investigated calf mortality in the perinatal and postnatal periods. A broad seasonal and regional influence was identified, however, the dilution of the datasets due to the high number of timeline variations, prevented robust statistical analysis and the further examination of influential factors, such as breed. The results of the systematic literature review indicate that the resolution of the data available does not allow for producers or researchers to accurately target the occurrence or cause of calf mortality. Experimental protocols for future research pertaining to reproductive efficiency and calf loss in northern Australia should be standardised. Consistency in reporting factors and periods must first occur for robust statistical analyses to be achieved.

Animal science Down Under: a history of research, development and extension in support of Australia’s livestock industries

This account of the development and achievements of the animal sciences in Australia is prefaced by a brief history of the livestock industries from 1788 to the present. During the 19th century, progress in industry development was due more to the experience and ingenuity of producers than to the application of scientific principles; the end of the century also saw the establishment of departments of agriculture and agricultural colleges in all Australian colonies (later states). Between the two world wars, the Council for Scientific and Industrial Research was established, including well supported Divisions of Animal Nutrition and Animal Health, and there was significant growth in research and extension capability in the state departments. However, the research capacity of the recently established university Faculties of Agriculture and Veterinary Science was limited by lack of funding and opportunity to offer postgraduate research training. The three decades after 1945 were marked by strong political support for agricultural research, development and extension, visionary scientific leadership, and major growth in research institutions and achievements, partly driven by increased university funding and enrolment of postgraduate students. State-supported extension services for livestock producers peaked during the 1970s. The final decades of the 20th century featured uncertain commodity markets and changing public attitudes to livestock production. There were also important Federal Government initiatives to stabilise industry and government funding of agricultural research, development and extension via the Research and Development Corporations, and to promote efficient use of these resources through creation of the Cooperative Research Centres program. These initiatives led to some outstanding research outcomes for most of the livestock sectors, which continued during the early decades of the 21st century, including the advent of genomic selection for genetic improvement of production and health traits, and greatly increased attention to public interest issues, particularly animal welfare and environmental protection. The new century has also seen development and application of the ‘One Health’ concept to protect livestock, humans and the environment from exotic infectious diseases, and an accelerating trend towards privatisation of extension services. Finally, industry challenges and opportunities are briefly discussed, emphasising those amenable to research, development and extension solutions.

Genomic clues of the evolutionary history of Bos indicus cattle

Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.

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

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

STAT6, PBX2, and PBRM1 Emerge as Predicted Regulators of 452 Differentially Expressed Genes Associated With Puberty in Brahman Heifers

The liver plays a central role in metabolism and produces important hormones. Hepatic estrogen receptors and the release of insulin-like growth factor 1 (IGF1) are critical links between liver function and the reproductive system. However, the role of liver in pubertal development is not fully understood. To explore this question, we applied transcriptomic analyses to liver samples of pre- and post-pubertal Brahman heifers and identified differentially expressed (DE) genes and genes encoding transcription factors (TFs). Differential expression of genes suggests potential biological mechanisms and pathways linking liver function to puberty. The analyses identified 452 DE genes and 82 TF with significant contribution to differential gene expression by using a regulatory impact factor metric. Brain-derived neurotrophic factor was observed as the most down-regulated gene (P = 0.003) in post-pubertal heifers and we propose this gene influences pubertal development in Brahman heifers. Additionally, co-expression network analysis provided evidence for three TF as key regulators of liver function during pubertal development: the signal transducer and activator of transcription 6, PBX homeobox 2, and polybromo 1. Pathway enrichment analysis identified transforming growth factor-beta and Wnt signaling pathways as significant annotation terms for the list of DE genes and TF in the co-expression network. Molecular information regarding genes and pathways described in this work are important to further our understanding of puberty onset in Brahman heifers.

Using ultrasound to derive new reproductive traits in tropical beef breeds: implications for genetic evaluation

Key components of female fertility in tropically adapted beef breeds are age at puberty and interval from calving to conception. Presence of an ovarian corpus luteum or stage of pregnancy were recorded using trans-rectal ultrasonography in 4649 heifers and 2925 first-lactation cows in seven herds of either Brahman, Droughtmaster or Santa Gertrudis tropical beef cattle breeds in northern Australia. The traits derived from a single ultrasonographic examination were incidence of corpus luteum at ~600 days of age in heifers, and weeks pregnant 5 weeks post-mating in heifers at ~2.5 years of age and in first-lactation cows at either 2.5 or 3.5 years of age. At 600 days of age, the bodyweight of heifers averaged 340 kg and 40% had a corpus luteum. At 2.5 years of age bodyweight of heifers averaged 452 kg and 80% were pregnant. First-lactation cows averaged 473 kg and 64% were pregnant. Considerable between-herd variation in traits reflected differences in climate and management at each site. However, estimates of heritability of incidence of corpus luteum at 600 days (0.18–0.32) and weeks pregnant in lactating cows (0.11–0.20) suggested that a significant proportion of the variation was due to additive gene action. Small to moderate genetic correlations with other economically important traits and the range in estimated breeding values indicate substantial opportunity for genetic improvement of the traits. The study provided evidence to accept the hypothesis that strategically timed ultrasound examinations can be adopted to derive useful traits for genetic evaluation.

Using Walk-over-Weighing technology for parturition date determination in beef cattle

The northern Australian beef industry is dominated by cow-calf operations where reproductive efficiency is a major profit driver. The postpartum anoestrus interval is a major contributor to an animal’s reproductive efficiency and is influenced by genetic selection. The genetic trait that measures an animal’s postpartum anoestrus interval is the days to calving estimated breeding value and a key requirement is knowledge of the cow’s calving date. Traditionally calving date is recorded using laborious and costly methods that are impeding the recording and hence the accuracy of genetic predictions for this trait by the northern Australian seedstock industry. The present experiment used Walk-over-Weighing technology to automatically record animal weights as cattle enter a restricted area where they access water. With the use of a novel method to accurately assess weights, the growth paths of cows were tracked from late gestation to post-calving. The calving date was visualised in the growth paths of most cows (78.3%) and a custom algorithm was able to automatically detect the calving date within 10 days of the observed calving period for 63% of cows. The use of Walk-over-Weighing to record calving date provides the opportunity to increase the recording of the days to calving estimated breeding value in the northern seedstock industry, thereby increasing reproductive efficiency and improving the profitability of northern beef producers.

Using temporal associations to determine postpartum oestrus in tropical beef cows

The radio frequency identification (RFID) technology introduced with the National Livestock Identification System has increased the precision of livestock management. Tag readers incorporated in walk-over-weighing systems have enabled automated collection of daily RFID sequential data as cattle access water. The temporal sequence of individuals accessing a watering point in a rangeland grazing system could potentially provide knowledge of key aspects of animal behaviour. The current study investigated the use of the shortest daily average interval of time from cow to bull (TTB) coming to water over a 29-day period to predict postpartum oestrus events. Fifteen Brahman and 15 Belmont Red cows mated to bulls of the same breed in separate paddocks were fitted with proximity loggers, heat-mount detectors and were ovarian-scanned with ultrasonics to determine the timing of postpartum oestrus. The data collected from these devices were compared with RFID sequence data of the bulls following cows to water to evaluate whether TTB alone could predict oestrus activity. At the start of the experimental period, mean (±s.d.) weight and days postpartum of the Brahman cows were 527 (±43.4) kg and 89 (±18.4) days respectively, and of the Belmont Red cows 513 (±54.1) kg and averaged 66 (±19.6) days postpartum. Six of the 15 Brahman cows and 9 of the 15 Belmont Red cows displayed oestrus activity, as indicated by increased contact with the bull, an activated heat-mount detector and the presence of an ovarian corpus luteum. The sensitivity and specificity of TTB as an indicator of oestrus events across the groups were 0.65 and 0.60 respectively. Temporal sequence data have the potential to contribute to the determination of oestrus and date of conception.

Genomic analyses of tropical beef cattle fertility based on genotyping pools of Brahman cows with unknown pedigree

We introduce an innovative approach to lowering the overall cost of obtaining genomic EBV (GEBV) and encourage their use in commercial extensive herds of Brahman beef cattle. In our approach, the DNA genotyping of cow herds from 2 independent properties was performed using a high-density bovine SNP chip on DNA from pooled blood samples, grouped according to the result of a pregnancy test following their first and second joining opportunities. For the DNA pooling strategy, 15 to 28 blood samples from the same phenotype and contemporary group were allocated to pools. Across the 2 properties, a total of 183 pools were created representing 4,164 cows. In addition, blood samples from 309 bulls from the same properties were also taken. After genotyping and quality control, 74,584 remaining SNP were used for analyses. Pools and individual DNA samples were related by means of a "hybrid" genomic relationship matrix. The pooled genotyping analysis of 2 large and independent commercial populations of tropical beef cattle was able to recover significant and plausible associations between SNP and pregnancy test outcome. We discuss 24 SNP with significant association ( < 1.0 × 10) and mapped within 40 kb of an annotated gene. We have established a method to estimate the GEBV in young herd bulls for a trait that is currently unable to be predicted at all. In summary, our novel approach allowed us to conduct genomic analyses of fertility in 2 large commercial Brahman herds managed under extensive pastoral conditions.

The use of walk over weigh to predict calving date in extensively managed beef herds

Beef cattle reproductive rate in northern Australia is low and substantial effort is underway to make improvements. Collection of calf birth date to inform female reproductive rate data is often not practical. Therefore, there is a need to find alternative methods for collecting birth date data. The aim of the project was to trial an automated animal weighing technology (walk over weigh) to estimate calving date for cows in a northern breeding herd grazing in an extensive pasture system. Two-hundred and thirty-two Wagyu cows from a herd of 1195 with confirmed pregnancy tests were stocked in a paddock with a walk over weigh unit at the entry point of the water yard. Each calf born in the paddock was weighed, ear-tagged and a DNA sample collected. After processing, cleaning and smoothing the data, weight profiles of the 232 cows over a 119-day period were analysed. From the weight profiles and confirmed DNA parentage, 96 out of a possible 162 (59%) cows that calved had a correct calving date prediction. It is proposed that improvements in calving date prediction could be increased through engineering changes designed to slow cow movement over the walk over weigh unit. The trial demonstrated with the proposed changes that walk over weigh could be used to estimate calving date in extensive beef herds, with the expectation that this information could be used in genetic evaluation to improve reproductive rate in northern Australia.

Effect of previous reproductive performance on current reproductive rate in South Australian Merino ewes

Reproductive performance of ewes in the current year may be influenced by their performance in the previous year and by the ability of seasonal and management conditions to facilitate full recovery before the next breeding cycle. This possibility was tested by analysing reproductive data from 2100 South Australian Merino ewes mated to Merino rams annually from 1991 to 1997. The model fitted to the data included the fixed effects of previous reproductive performance (PRP) (no lambs born; single or multiple lambs born, none reared; single lambs born, singles reared; multiples born, singles reared; multiples born, multiples reared), age of ewe (2.5, 3.5, 4.5 years), year (1992–1997), bloodline (A, B, L, X) and all two-way interactions. Current-year parameters were net reproduction rate (NRR, lambs weaned of ewes joined) and its components of fertility (ewes lambing of ewes joined), fecundity (lambs born of ewes lambing) and lamb survival (lambs weaned of lambs born). Other parameters were lamb liveweight at weaning per ewe joined and pre-mating liveweight. In addition, repeatability values were calculated across ages for these parameters. NRR was higher in the current year for those groups of ewes that reared lambs in the previous year; this was associated with the highly productive multiple-bearing and -rearing groups having a liveweight at the next mating similar compared to that of groups that did not rear lambs. Repeatability values of 0.27 for NRR and 0.40 for fertility suggest there are genetic and permanent environmental components contributing to the differences observed among the PRP groups for NRR, particularly so for fertility. Selecting ewes after their first lambing opportunity on fertility alone at a rate of 90% would give a non-cumulative increase in fertility of 3.4% at subsequent lambing opportunities. Hence, improvements in the current ewe flock for NRR by graziers managing flocks of the South Australian Merino strain are likely to come from (1) identifying and selecting those ewes of high fertility from early records and (2) attending to management factors impacting on fecundity and lamb survival.

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 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.