Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle

BACKGROUND

Hoof structure and health are essential for the welfare and productivity of beef cattle. Therefore, we assessed the genetic and genomic background of foot score traits in American (US) and Australian (AU) Angus cattle and investigated the feasibility of performing genomic evaluations combining data for foot score traits recorded in US and AU Angus cattle. The traits evaluated were foot angle (FA) and claw set (CS). In total, 109,294 and ~ 1.12 million animals had phenotypic and genomic information, respectively. Four sets of analyses were performed: (1) genomic connectedness between US and AU Angus cattle populations and population structure, (2) estimation of genetic parameters, (3) single-step genomic prediction of breeding values, and (4) single-step genome-wide association studies for FA and CS.

RESULTS

There was no clear genetic differentiation between US and AU Angus populations. Similar heritability estimates (FA: 0.22-0.24 and CS: 0.22-0.27) and moderate-to-high genetic correlations between US and AU foot scores (FA: 0.61 and CS: 0.76) were obtained. A joint-genomic prediction using data from both populations outperformed within-country genomic evaluations. A genomic prediction model considering US and AU datasets as a single population performed similarly to the scenario accounting for genotype-by-environment interactions (i.e., multiple-trait model considering US and AU records as different traits), even though the genetic correlations between countries were lower than 0.80. Common significant genomic regions were observed between US and AU for FA and CS. Significant single nucleotide polymorphisms were identified on the Bos taurus (BTA) chromosomes BTA1, BTA5, BTA11, BTA13, BTA19, BTA20, and BTA23. The candidate genes identified were primarily from growth factor gene families, including FGF12 and GDF5, which were previously associated with bone structure and repair.

CONCLUSIONS

This study presents comprehensive population structure and genetic and genomic analyses of foot scores in US and AU Angus cattle populations, which are essential for optimizing the implementation of genomic selection for improved foot scores in Angus cattle breeding programs. We have also identified candidate genes associated with foot scores in the largest Angus cattle populations in the world and made recommendations for genomic evaluations for improved foot score traits in the US and AU.

Family climate influences next-generation family business leader effectiveness and work engagement

Effective next-generation leadership is central to the multi-generational survival of family businesses. This study of 100 next-generation family business leaders found that business-owning families that openly express their opinions, take time to listen to each other, and squarely address difficult issues positively influence the development of the emotional and social intelligence competencies in next-generation family leaders that drive their leadership effectiveness. That kind of open and transparent communication in the family also makes it more likely next-generation leaders will be held accountable for their leadership performance by others, which increases the degree to which they are positively engaged with their work in the family firm. On the other hand, the results suggest that senior-generation family leaders who lead autocratically, a leadership style often observed in entrepreneurs who found family firms, make it less likely that next-generation family leaders will learn the emotional and social intelligence competencies that predict their leadership effectiveness. The study also found that autocratic senior-generation leaders negatively affect next-generation leader self-efficacy and make it less likely that others will hold them accountable, which limits their engagement with work in the family business. One of the study's most important findings is that next-generation leader acceptance of personal responsibility for their leadership behaviors and results serves as a mediator through which the nature of the family climate influences their leadership effectiveness and work engagement. This suggests that while the nature of family relationships may make it easier or more difficult, next-generation family leaders have ultimate control over the development of their leadership talent and the inspiration, enthusiasm, energy, and pride they feel when working in the family business.

Unraveling the phenotypic and genomic background of behavioral plasticity and temperament in North American Angus cattle

BACKGROUND

Longitudinal records of temperament can be used for assessing behavioral plasticity, such as aptness to learn, memorize, or change behavioral responses based on affective state. In this study, we evaluated the phenotypic and genomic background of North American Angus cow temperament measured throughout their lifetime around the weaning season, including the development of a new indicator trait termed docility-based learning and behavioral plasticity. The analyses included 273,695 and 153,898 records for yearling (YT) and cow at weaning (CT) temperament, respectively, 723,248 animals in the pedigree, and 8784 genotyped animals. Both YT and CT were measured when the animal was loading into/exiting the chute. Moreover, CT was measured around the time in which the cow was separated from her calf. A random regression model fitting a first-order Legendre orthogonal polynomial was used to model the covariance structure of temperament and to assess the learning and behavioral plasticity (i.e., slope of the regression) of individual cows. This study provides, for the first time, a longitudinal perspective of the genetic and genomic mechanisms underlying temperament, learning, and behavioral plasticity in beef cattle.

RESULTS

CT measured across years is heritable (0.38-0.53). Positive and strong genetic correlations (0.91-1.00) were observed among all CT age-group pairs and between CT and YT (0.84). Over 90% of the candidate genes identified overlapped among CT age-groups and the estimated effect of genomic markers located within important candidate genes changed over time. A small but significant genetic component was observed for learning and behavioral plasticity (heritability = 0.02 ± 0.002). Various candidate genes were identified, revealing the polygenic nature of the traits evaluated. The pathways and candidate genes identified are associated with steroid and glucocorticoid hormones, development delay, cognitive development, and behavioral changes in cattle and other species.

CONCLUSIONS

Cow temperament is highly heritable and repeatable. The changes in temperament can be genetically improved by selecting animals with favorable learning and behavioral plasticity (i.e., habituation). Furthermore, the environment explains a large part of the variation in learning and behavioral plasticity, leading to opportunities to also improve the overall temperament by refining management practices. Moreover, behavioral plasticity offers opportunities to improve the long-term animal and handler welfare through habituation.

Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits

Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen's safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1-6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal-human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.

Haplotype-Based Single-Step GWAS for Yearling Temperament in American Angus Cattle

Behavior is a complex trait and, therefore, understanding its genetic architecture is paramount for the development of effective breeding strategies. The objective of this study was to perform traditional and weighted single-step genome-wide association studies (ssGWAS and WssGWAS, respectively) for yearling temperament (YT) in North American Angus cattle using haplotypes. Approximately 266 K YT records and 70 K animals genotyped using a 50 K single nucleotide polymorphisms (SNP) panel were used. Linkage disequilibrium thresholds (LD) of 0.15, 0.50, and 0.80 were used to create the haploblocks, and the inclusion of non-LD-clustered SNPs (NCSNP) with the haplotypes in the genomic models was also evaluated. WssGWAS did not perform better than ssGWAS. Cattle YT was found to be a highly polygenic trait, with genes and quantitative trait loci (QTL) broadly distributed across the whole genome. Association studies using LD-based haplotypes should include NCSNPs and different LD thresholds to increase the likelihood of finding the relevant genomic regions affecting the trait of interest. The main candidate genes identified, i.e., ATXN10, ADAM10, VAX2, ATP6V1B1, CRISPLD1, CAPRIN1, FA2H, SPEF2, PLXNA1, and CACNA2D3, are involved in important biological processes and metabolic pathways related to behavioral traits, social interactions, and aggressiveness in cattle. Future studies should further investigate the role of these candidate genes.

MRI characterization of hemodynamic patterns of human fetuses with cyanotic congenital heart disease

OBJECTIVES

To characterize, using magnetic resonance imaging (MRI), the distribution of blood flow and oxygen transport in human fetuses with subtypes of congenital heart disease (CHD) that present with neonatal cyanosis.

METHODS

Blood flow was measured in the major vessels of 152 late-gestation human fetuses with CHD and 40 gestational-age-matched normal fetuses, using cine phase-contrast MRI. Oxygen saturation (SaO₂ ) was measured in the major vessels of 57 fetuses with CHD and 40 controls.

RESULTS

Compared with controls, we found lower combined ventricular output in fetuses with single-ventricle physiology, with the lowest being observed in fetuses with severe forms of Ebstein's anomaly. Obstructive lesions of the left or right heart were associated with increased flow across the contralateral side. Pulmonary blood flow was reduced in fetuses with Ebstein's anomaly, while those with Ebstein's anomaly and tricuspid atresia had reduced umbilical flow. Flow in the superior vena cava was elevated in fetuses with transposition of the great arteries, normal in fetuses with hypoplastic left heart, tetralogy of Fallot or tricuspid atresia and reduced in fetuses with Ebstein's anomaly. Umbilical vein SaO₂ was reduced in fetuses with hypoplastic left heart or tetralogy of Fallot. Ascending aorta and superior vena cava SaO₂ were reduced in nearly all CHD subtypes.

CONCLUSIONS

Fetuses with cyanotic CHD exhibit profound changes in the distribution of blood flow and oxygen transport, which result in changes in cerebral, pulmonary and placental blood flow and oxygenation. These alterations of fetal circulatory physiology may influence the neonatal course and help account for abnormalities of prenatal growth and development that have been described in newborns with cyanotic CHD. © 2021 International Society of Ultrasound in Obstetrics and Gynecology.

PSXV-1 Genetic evaluation of longevity of cows culled due to fertility-related problems using random regression models and censored data

A recent study showed that longevity based on different culling reasons should be considered as different traits in genetic evaluations. However, it is still necessary to create a pipeline that avoid including/excluding animals culled for different reasons in every genetic evaluation run. This study aimed to: 1) perform a genetic evaluation of the longevity of cows culled due to fertility-related problems including records of animals culled for other reasons (i.e., age, structural problems, disease, and performance) as censored records; and, 2) identify the impact of censored data in the genetic parameters and breeding values estimated. Two longevity indicators were evaluated: traditional (TL; time from first calving to culling) and functional (FL; time period in which the cow was alive and also calving after its first calving) longevity. Both TL and FL were evaluated from 2 to 15 years-old, and codified as binary traits for each age (0 = culled and 1 = alive/calved). Both trait definitions were analyzed using a Bayesian random regression linear model. Animals culled for reasons other than fertility were either excluded from the data (standard) or had their records censored after the culling date reported in the dataset (censored). After the quality control, 154,419 and 450,124 animals had uncensored and censored records, respectively. Heritabilities estimated for TL over the ages ranged from 0.02 to 0.13 for standard, and from 0.01 to 0.12 for censored datasets. Heritabilities estimated for FL ranged from 0.01 to 0.14 (standard), and from 0.01 to 0.13 (censored). Average (SD) correlation of breeding values predicted over all ages, using the standard and censored datasets, was 0.77 (0.16) for TL, and 0.83 (0.11) for FL. Our findings suggest that including censored data in the analyses might impact the genomic evaluations and further work is need to determine the optimal predictive approach.

PSVIII-4 Genetic evaluation of functional heifer longevity in north American angus cattle

The goals of this study were to develop a genetic evaluation system for a novel trait called functional heifer longevity (FHL), and determine if this novel trait is heritable. The FHL trait was defined as binary, in which the heifers received the code 1 if they had calved by the end of their third year (n = 377,938), or 0 if they were culled/sold during this period (n = 368,308). Analysis were performed using linear animal models and Bayesian inference. The significant systematic effects included in the statistical models are born by embryo transfer, year-season of birth, and age at calving (in months). Three models, differing according to their random effects (i.e., reduced model, which included only herd-year-season and additive genetic random effects; maternal genetic model, which added maternal genetic effects; and complete model, which further added maternal permanent environmental effects), were compared based on the deviance information criterion (DIC) and the estimates of genetic parameters. The reduced model was preferred according to the DIC values. However, high maternal heritabilities were estimated using the maternal genetic (0.51) and complete (0.36) models, indicating that maternal effects can impact the selection of heifers for breeding. Similar additive genetic heritabilities were estimated among the three models (0.24, 0.27, and 0.25 using the reduced, maternal genetic, and complete models, respectively), and no significant re-ranking of selection candidates were observed based on their additive genetic breeding values. Total heritabilities and correlations estimated between additive genetic and maternal genetic effects were 0.37 and -0.28 for the maternal genetic, and 0.31 and -0.27 for the complete model, respectively. This study shows that FHL is heritable, and that including maternal effects in the statistical models might be important. These results contribute to a larger project studying the genetics of female longevity in Angus cattle.

29 Effects of Recent and Ancient Inbreeding on Growth in American Angus Cattle

The accumulation of inbreeding can lead to an unfavorable change in the phenotypic value of individuals for traits related to fitness, also known as inbreeding depression. However, inbreeding accumulated at a more distant past (ancient inbreeding) is expected to have a smaller depressive effect than that accumulated more recently due to the loss of detrimental alleles caused by purifying selection. Therefore, the aim of this study was to quantify the inbreeding depression caused by recent and ancient inbreeding for birth weight, weaning weight, and post-weaning gain. Pedigree and genomic information were obtained from Angus Genetics, Inc. (St. Joseph, MO) for 569,364 individuals from the American Angus breed. Pedigree inbreeding and genomic inbreeding based on runs of homozygosity (ROH) were estimated using the SNP1101 software. Model-based genomic inbreeding based on the probability a marker is part of a homozygous-by-descent segment (HBD) was estimated using the RZooROH in R. The generational cutoffs for designating inbreeding as recent was that acquired 5 generations ago or sooner for pedigree, 6.25 generations ago or sooner for ROH, and 8 generations ago or sooner for HBD inbreeding. The effect of a 1% increase in inbreeding was modeled in males and females using a linear mixed model approach. Recent pedigree inbreeding was found to decrease birth weight by 0.04 and 0.03 kg, decrease weaning weight by 0.50 and 0.48 kg, and decrease post-weaning gain by 0.62 and 0.32 kg, in males and females respectively. Ancient pedigree inbreeding was generally found to have no effect on growth. For genomic inbreeding, when both recent and ancient inbreeding had a detrimental effect on growth, recent inbreeding generally had a larger effect. The results of this study demonstrate that inbreeding accumulated recently should be quantified and managed in beef cattle populations to avoid economic losses.

Survival of the first rather than the fittest in a Shewanella electrode biofilm

For natural selection to operate there must exist heritable variation among individuals that affects their survival and reproduction. Among free-living microbes, where differences in growth rates largely define selection intensities, competitive exclusion is common. However, among surface attached communities, these dynamics become less predictable. If extreme circumstances were to dictate that a surface population is immortal and all offspring must emigrate, the offspring would be unable to contribute to the composition of the population. Meanwhile, the immortals, regardless of reproductive capacity, would remain unchanged in relative abundance. The normal cycle of birth, death, and competitive exclusion would be broken. We tested whether conditions required to set up this idealized scenario can be approximated in a microbial biofilm. Using two differentially-reproducing strains of Shewanella oneidensis grown on an anode as the sole terminal electron acceptor - a system in which metabolism is obligately tied to surface attachment - we found that selection against a slow-growing competitor is drastically reduced. This work furthers understanding of natural selection dynamics in sessile microbial communities, and provides a framework for designing stable microbial communities for industrial and experimental applications.

A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders

Simple Summary

This study is a comprehensive review of genomic regions associated with animal behavior in farmed mammals (beef and dairy cattle, pigs, and sheep) which contributes to a better understanding of the biological mechanisms influencing the target indicator trait and to gene expression studies by suggesting genes likely controlling the trait, and it will be useful in optimizing genomic predictions of breeding values incorporating biological information. Behavioral mechanisms are complex traits, genetically controlled by multiple genes spread across the whole genome. The majority of the genes identified in cattle, pigs, and sheep in association with a plethora of behavioral measurements (e.g., temperament, terrain use, milking speed, tail biting, and sucking reflex) are likely controlling stimuli reception (e.g., olfactory), internal recognition of stimuli (e.g., neuroactive ligand–receptor interaction), and body response to a stimulus (e.g., blood pressure, fatty acidy metabolism, hormone signaling, and inflammatory pathways). Six genes were commonly identified between cattle and pigs. About half of the genes for behavior identified in farmed mammals were also identified in humans for behavioral, mental, and neuronal disorders. Our findings indicate that the majority of the genes identified are likely controlling animal behavioral outcomes because their biological functions as well as potentially differing allele frequencies between two breed groups (subjectively) clustered based on their temperament characteristics.

Abstract

The main objectives of this study were to perform a systematic review of genomic regions associated with various behavioral traits in the main farmed mammals and identify key candidate genes and potential causal mutations by contrasting the frequency of polymorphisms in cattle breeds with divergent behavioral traits (based on a subjective clustering approach). A total of 687 (cattle), 1391 (pigs), and 148 (sheep) genomic regions associated with 37 (cattle), 55 (pigs), and 22 (sheep) behavioral traits were identified in the literature. In total, 383, 317, and 15 genes overlap with genomic regions identified for cattle, pigs, and sheep, respectively. Six common genes (e.g., NR3C2, PITPNM3, RERG, SPNS3, U6, and ZFAT) were found for cattle and pigs. A combined gene-set of 634 human genes was produced through identified homologous genes. A total of 313 out of 634 genes have previously been associated with behavioral, mental, and neurologic disorders (e.g., anxiety and schizophrenia) in humans. Additionally, a total of 491 candidate genes had at least one statistically significant polymorphism (p-value < 0.05). Out of those, 110 genes were defined as having polymorphic regions differing in greater than 50% of exon regions. Therefore, conserved genomic regions controlling behavior were found across farmed mammal species and humans.

47 Distortion of Mendelian segregation across Angus cattle genome reveal novel lethal haplotype affecting reproduction

The rapid development of DNA technologies, together with the adoption and daily routine use of commercial SNP arrays in livestock industries, provided a valuable resource of large and powerful data that can be explored for innovative applications for animal breeding purposes. Thus, the current availability of trios (i.e., sire-dam-offspring) of genotyped families enables the implementation of the transmission ratio distortion (TRD) approach to discover lethal alleles. Lethal alleles, which are crucial genetic determinants for reproduction, do not follow Mendelian principles but deviate from inheritance expectations, displaying signals of TRD. In this research, TRD was characterized using allelic (specific- and unspecific-parent TRD) and genotypic parameterizations (additive- and dominance-TRD) using both SNP- and haplotype-based methods. The analyses were performed using 258,140 Angus animals with 92,942 autosomal SNP genotypes, including 7,486 sires, 72,688 dams and 205,966 offspring. Across the whole genome, 852 regions displaying TRD were identified with different statistical significance. Among these findings, 19 haplotypes with recessive patterns (potential lethality for homozygote individuals) and 52 genomic regions with allelic patterns exhibiting complete or quasi-complete absence for homozygous individuals in addition to under-representation (potentially reduced viability) of heterozygous offspring were found. The average number of under-represented offspring (i.e., expected but not observed) across 52 allelic TRD regions ranged from 5,000 to 41,008. In contrast, the number of non-observed homozygous offspring for the 19 regions with recessive pattern ranges from 10 to 564. In addition, 64 and 20 genomic regions with TRD showed significant effects on the trait heifer pregnancy P &lt; 0.05 and P &lt; 0.01, respectively, reducing the progeny rate up to 15%. These novel findings in Angus present new candidate genomic regions putatively carrying lethal and semi-lethal alleles providing opportunities to reduce the rates of embryonic losses or death of offspring which could improve fertility and fitness in beef cattle populations.

30 Inbreeding in American Angus cattle before and after the implementation of genomic selection

The aim of this study was to characterize the American Angus cattle population in terms of changes to the inbreeding rate (ΔF) and effective population size (Ne) before and after the implementation of genomic selection (GS). Genomic information (89,206 SNPs) was obtained for 25,960 bulls and 134,962 cows born between the years 2000 and 2017. Bulls and cows were independently grouped into two groups based on year of birth, pre-GS (2000–2009), and post-GS (2010–2017). Genomic inbreeding (FGRM) was calculated assuming fixed allele frequencies (0.5). Inbreeding based on runs of homozygosity (FROH) was calculated using software SNP1101 (Sargolzaei, 2014). The yearly ΔF for each group was estimated by regressing the inbreeding coefficients on year of birth. The generation intervals (L) were calculated for each of the four pathways of selection at both time periods (pre-GS and post-GS), where the mean of the sires of sires and dams of sires pathways was taken to be the generation interval for the bulls and the mean of the sires of dams and dams of dams pathways was taken to be the generation interval for the cows. The L and ΔF of the three inbreeding coefficients were used to estimate the Ne. Estimates of ΔF and Ne for both sexes at the two time periods can be found in table 1. In both sexes, ΔFROH decreased and NeROH increased from pre-GS to post-GS. For bulls, ΔFGRM and NeGRM did not change, and for cows, ΔFGRM decreased and NeGRM increased from pre-GS to post-GS. These results suggest that the implementation of genomic selection in Angus cattle has not caused the increased inbreeding rates and reduced effective population sizes seen in other species, but instead has been beneficial for the preservation of genetic diversity.

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31 Changes in genomic predictions when new data is included

Persistence of genomic evaluations depends on the amount of data and population parameters. When the data are large enough to estimate nearly all chromosome segments (about 10,000 in Angus), the persistence can be high. Subsequently, the regular evaluations can be run less often, and indirect predictions based on backsolved SNP effects may be accurate over an extended period as full predictions. The objective of this study was to investigate changes in GEBV across monthly genomic evaluations in a large genotyped population. A dataset from American Angus that contained 8,186,503 records for birth weight, 8,881,124 for weaning weight, and 4,386,184 for post-weaning gain was used. A total of 10,129,980 animals born up to December of 2017 had pedigree information, of which 484,074 were genotyped. A truncated dataset kept animals that were born up to December of 2016 (Dec2016). To mimic a scenario where evaluations are run every 30 days, the 2017 data was added month by month and new GEBV were computed using ssGBLUP. Genomic predictions from the Dec2016 evaluation were contrasted to the monthly evaluations for all genotyped animals, genotyped animals with or without phenotypes, genotyped animals with or without new phenotypes after Dec2016 and for young genotyped animals (born in 2016, with no phenotypes or progeny). The average number of animals added by month was 26,225, with a larger concentration from January to April. The correlations between GEBV from Dec2016 and all the 12 consecutive evaluations were greater or equal than 0.99 in all cases. The average (maximum) changes for young animals from Dec2016 to January and December of 2017 ranged from 0.05 (0.25) to 0.10 (0.53) additive standard deviations. The same changes for animals with records past Dec2016 were from 0.05 (0.11) to 0.88 (1.59). Genomic evaluations have high persistence over a year; however, outliers show larger changes.

22 Accuracy of indirect predictions for large datasets based on prediction error covariance of SNP effects from single-step GBLUP

With an ever-increasing number of genotyped animals, there is a question of whether to include all genotypes into single-step GBLUP (ssGBLUP) evaluations or to include only genotyped animals with phenotypes and use indirect predictions (IP) for the remaining young genotyped animals. Under ssGBLUP, SNP effects can be backsolved from GEBV, and IP can be calculated as the sum of SNP effects weighted by the gene content. To publish IP, a measure of accuracy that reflects the standard error of prediction, and that is comparable to GEBV accuracy, is needed. Our first objective was to test formulas to compute accuracy of IP by backsolving prediction error covariance (PEC) of GEBV into PEC of SNP effects. The second objective was to investigate the number of genotyped animals needed to obtain robust IP accuracy. Data were provided by the American Angus Association, with 38,000 post-weaning gain phenotypes and 60,000 genotyped animals. Correlations between GEBV and IP were ≥0.99. When all genotyped animals were used for PEC computations, accuracy correlations were also ≥0.99. Additionally, GEBV and IP accuracies were compatible, with both direct inversion of the genomic relationship matrix (G) or using the algorithm for proven and young (APY) to obtain G inverse. As the number of genotyped animals in PEC computations decreased to 15,000, accuracy correlations were still high (≥0.96), but IP accuracies were biased downwards. Indirect prediction accuracy can be successfully obtained from ssGBLUP without running an extra SNP-BLUP evaluation to compute SNP PEC. It is possible to reduce the number of genotyped animals in PEC computations, but accuracies may be slightly underestimated. When the amount of genomic and phenotypic data is large, the polygenic part of GEBV becomes small and IP can be very accurate. Further research is needed to approximate SNP PEC with a large number of genotyped animals.

Development of a genetic evaluation for hair shedding in American Angus cattle to improve thermotolerance

BACKGROUND

Heat stress and fescue toxicosis caused by ingesting tall fescue infected with the endophytic fungus Epichloë coenophiala represent two of the most prevalent stressors to beef cattle in the United States and cost the beef industry millions of dollars each year. The rate at which a beef cow sheds her winter coat early in the summer is an indicator of adaptation to heat and an economically relevant trait in temperate or subtropical parts of the world. Furthermore, research suggests that early-summer hair shedding may reflect tolerance to fescue toxicosis, since vasoconstriction induced by fescue toxicosis limits the ability of an animal to shed its winter coat. Both heat stress and fescue toxicosis reduce profitability partly via indirect maternal effects on calf weaning weight. Here, we developed parameters for routine genetic evaluation of hair shedding score in American Angus cattle, and identified genomic loci associated with variation in hair shedding score via genome-wide association analysis (GWAA).

RESULTS

Hair shedding score was moderately heritable (h2 = 0.34 to 0.40), with different repeatability estimates between cattle grazing versus not grazing endophyte-infected tall fescue. Our results suggest modestly negative genetic and phenotypic correlations between a dam's hair shedding score (lower score is earlier shedding) and the weaning weight of her calf, which is one metric of performance. Together, these results indicate that economic gains can be made by using hair shedding score breeding values to select for heat-tolerant cattle. GWAA identified 176 variants significant at FDR < 0.05. Functional enrichment analyses using genes that were located within 50 kb of these variants identified pathways involved in keratin formation, prolactin signalling, host-virus interaction, and other biological processes.

CONCLUSIONS

This work contributes to a continuing trend in the development of genetic evaluations for environmental adaptation. Our results will aid beef cattle producers in selecting more sustainable and climate-adapted cattle, as well as enable the development of similar routine genetic evaluations in other breeds.

A comprehensive comparison of high-density SNP panels and an alternative ultra-high-density panel for genomic analyses in Nellore cattle

There is evidence that some genotyping platforms might not work very well for Zebu cattle when compared with Taurine breeds. In addition, the availability of panels with low to moderate number of overlapping markers is a limitation for combining datasets for genomic evaluations, especially when animals are genotyped using different SNP panels. In the present study, we compared the performance of medium- and high-density (HD) commercially available panels and investigated the feasibility of developing an ultra-HD panel (SP) containing markers from an Illumina (HD_I) and an Affymetrix (HD_A) panels. The SP panel contained 1123442 SNPs. After performing SNP pruning on the basis of linkage disequilibrium, HD_A, HD_I and SP contained 429624, 365225 and 658770 markers distributed across the whole genome. The overall mean proportion of markers pruned out per chromosome for HD_A, HD_I and SP was 15.17%, 43.18%, 38.63% respectively. The HD_I panel presented the highest mean number of runs-of-homozygosity segments per animal (45.48%, an increment of 5.11% compared with SP) and longer segments, on average (3057.95 kb per segment), than did both HD_A and SP. HD_I also showed the highest mean number of SNPs per run-of-homozygosity segment. Consequently, the majority of animals presented the highest genomic inbreeding levels when genotyped using HD_I. The visual examination of marker distribution along the genome illustrated uncovered regions among the different panels. Haplotype-block comparison among panels and the average haplotype size constructed on the basis of HD_A were smaller than those from HD_I. The average number of SNPs per haplotype was different between HD_A and HD_I. Both HD_A and HD_I panels achieved high imputation accuracies when used as the lower-density panels for imputing to SP. However, imputation accuracy from HD_A to SP was greater than was imputation from HD_I to SP. Imputation from one HD panel to the other is also feasible. Low- and medium-density panels, composed of markers that are subsets of both HD_A and HD_I panels, should be developed to achieve better imputation accuracies to both HD levels. Therefore, the genomic analyses performed in the present study showed significant differences among the SNP panels used.

332 Indirect predictions based on SNP effects from GBLUP with increasing number of genotyped animals

With the increasing number of genotyped animals, the algorithm for proven and young (APY) can be used to compute the inverse of the genomic relationship matrix (G-1apy) in genomic BLUP (GBLUP) and single-step GBLUP (ssGBLUP). This algorithm also allows the use of all genotyped animals to calculate SNP effects from genomic EBV (GEBV), which can then be used to obtain indirect predictions (IP) for interim evaluations, or as genomic prediction for animals not included in official evaluations. The objective of the study was to evaluate the quality of IP from GBLUP with increasing number of genotyped animals. Birth weight, weaning weight and post-wearing gain phenotypes and genotypes were provided by the American Angus Association. Phenotypes and genotypes were divided in 3 scenarios based on birth year: genotyped animals born up to 2013 (114,937), 2014 (183,847) and 2015 (280,506). A 3-trait model was fit and GBLUP with APY was used to calculate GEBV and SNP effects. To calculate G-1apy, 19,021 core animals were randomly sampled from animals born up to 2013. Core animals remained the same, whereas the number of non-core animals increased as more genotyped animals were added. Additional analyses had updated core animals for each scenario. SNP effects were also calculated based on G-1apy and G-1 only for core animals (G-1core). IP were computed for all animals in each scenario by multiplying the centered genotypes by the SNP effects. To access the quality of IP, correlation between IP and GEBV was calculated. The Correlations were greater than 0.99 for all traits in all scenarios. Despite the increase of non-core animals in APY, GEBV were successfully retrieved from SNP effects using IP. When SNP effects were calculated based on G-1core, updating the core animals as the number of genotyped animals increase seems to be the best choice.

52 Genomic selection in the beef industry: Current achievements and future directions

In the past decade, genomic testing of beef cattle has evolved from applications in research to a routine practice for many beef cattle seedstock breeders. Testing for lethal genetic conditions or parentage was many breeders’ first experience with genomic testing. While the American Angus Association (AAA) began utilizing 384 SNP genotypes in genetic evaluations in 2009, the adoption of genotyping with higher density (~50,000 SNP) arrays by AAA in 2010 launched large-scale genotyping of Angus cattle for genetic evaluation. AAA transitioned from semi-annual to weekly genetic evaluations in 2010, and cost of genotyping decreased from $139 per animal in 2011, to $37 in 2017. In fiscal year 2018, AAA members genotyped over 160,000 animals for genetic evaluation, and as of April 2019, the AAA and Canadian Angus Association joint genetic evaluation includes over 635,000 genotyped animals. Now genotyping arrays with Angus-specific SNP content are used. The primary benefit to Angus breeders has been increased accuracy of genetic prediction for young animals, especially for traits with limited phenotypic information such as carcass traits, feed intake and mature cow size. Future benefits from genotyping include identification and selection against embryonic lethal alleles, better characterization of inbreeding, and selection tools for additional traits relevant to or measured in unique environments. Electronic sensors and other novel approaches may yield previously unmeasurable phenotypes for health and efficiency traits, which can be extended to wider populations for selection using genomics. New techniques such as DNA pooling and genotyping by sequencing may reduce costs enabling widespread testing in commercial cow-calf and cattle feeding enterprises. The application of genomic selection has clearly been a significant advancement in genetic selection in Angus cattle in the past ten years. This early adoption will expedite subsequent genomic tools at an increasing rate and will foster innovation.

Assessing genetic diversity of various Canadian sheep breeds through pedigree analyses

The loss of genetic variability in a population will drastically affect the success of a breeding program by reducing selection response and fitness and, consequently, affecting reproduction, resilience, and production efficiency. The objective of this study was to perform an in-depth analysis of the pedigree of the Canadian sheep breeds to assess the levels of inbreeding, effective population size, and other metrics of genetic diversity, which included the five most important sheep breeds in Canada: Dorset, Polypay (PO), Rideau-Arcott, Romanov (RV), and Suffolk, using a large dataset (1 336 926 animals). As measures of genetic diversity, effective population size, inbreeding coefficient, effective number of founders, effective number of founder genomes, effective number of nonfounders, and effective number of ancestors were estimated. The completeness and depth of the Canadian sheep pedigree datasets were reasonably high, with <20% parental information missing. More attention should be given to PO breed, which was found to have the smallest effective population size (55), and RV breed, which had the highest average level of inbreeding (4.8%). Techniques such as optimum contribution selection and minimum coancestry mating could be used to minimize the inbreeding of future generations, while maintaining genetic progress at a desirable level.

Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

Background

Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genotyped using the Illumina Bovine 50 K BeadChip and imputed to the Illumina BovineHD BeadChip (HD). GWAS were performed on 601,717 real and imputed single nucleotide polymorphism (SNP) genotypes using a single-SNP mixed linear model on 4841 Holstein bulls with breeding value predictions and followed by gene identification and in silico functional analyses. The association results were further validated using five scenarios with different numbers of SNPs.

Results

Seven hundred and eighty-two SNPs were significantly associated with calving performance at a genome-wise false discovery rate (FDR) of 5%. Most of these significant SNPs were on chromosomes 18 (71.9%), 17 (7.4%), 5 (6.8%) and 7 (2.4%) and mapped to 675 genes, among which 142 included at least one significant SNP and 532 were nearby one (100 kbp). For body conformation traits, 607 SNPs were significant at a genome-wise FDR of 5% and most of them were located on chromosomes 5 (30%), 18 (27%), 20 (13%), 6 (6%), 7 (5%), 14 (5%) and 13 (3%). SNP enrichment functional analyses for calving traits at a FDR of 1% suggested potential biological processes including musculoskeletal movement, meiotic cell cycle, oocyte maturation and skeletal muscle contraction. Furthermore, pathway analyses suggested potential pathways associated with calving performance traits including tight junction, oxytocin signaling, and MAPK signaling (P < 0.10). The prediction ability of the 1206 significant SNPs was between 78 and 83% of the prediction ability of the BovineSNP50 SNPs for calving performance traits and between 35 and 79% for body conformation traits.

Conclusions

Various SNPs that are significantly associated with calving performance are located within or nearby genes with potential roles in tight junction, oxytocin signaling, and MAPK signaling. Combining the significant SNPs or SNPs within or nearby gene(s) from the HD panel with the BovineSNP50 panel yielded a marginal increase in the accuracy of prediction of genomic estimated breeding values for all traits compared to the use of the BovineSNP50 panel alone.

Electronic supplementary material

The online version of this article (10.1186/s12711-017-0356-8) contains supplementary material, which is available to authorized users.

Maternal nutrient restriction in mid-to-late gestation influences fetal mRNA expression in muscle tissues in beef cattle

BACKGROUND

Manipulating maternal nutrition during specific periods of gestation can result in re-programming of fetal and post-natal development. In this experiment we investigated how a feed restriction of 85% compared with 140% of total metabolizable energy requirements, fed to cows during mid-to-late gestation, influences phenotypic development of fetuses and mRNA expression of growth (Insulin-Like Growth Factor family and Insulin Receptor (INSR)), myogenic (Myogenic Differentiation 1 (MYOD1), Myogenin (MYOG), Myocyte Enhancer Factor 2A (MEF2A), Serum Response Factor (SRF)) and adipogenic (Peroxisome Proliferator Activated Receptor Gamma (PPARG)) genes in fetal longissimus dorsi (LD) and semitendinosus (ST) muscle. DNA methylation of imprinted genes, Insulin Like Growth Factor 2 (IGF2) and Insulin Like Growth Factor 2 Receptor (IGF2R), and micro RNA (miRNA) expression, were also examined as potential consequences of poor maternal nutrition, but also potential regulators of altered gene expression patterns.

RESULTS

While the nutrient restriction impacted dam body weight, no differences were observed in phenotypic fetal measurements (weight, crown-rump length, or thorax circumference). Interestingly, LD and ST muscles responded differently to the differential pre-natal nutrient levels. While LD muscle of restricted fetal calves had greater mRNA abundances for Insulin Like Growth Factor 1 and its receptor (IGF1 and IGF1R), IGF2R, INSR, MYOD1, MYOG, and PPARG, no significant differences were observed for gene expression in ST muscle. Similarly, feed restriction had a greater impact on the methylation level of IGF2 Differentially Methylated Region 2 (DMR2) in LD muscle as compared to ST muscle between treatment groups. A negative correlation existed between IGF2 mRNA expression and IGF2 DMR2 methylation level in both LD and ST muscles. Differential expression of miRNAs 1 and 133a were also detected in LD muscle.

CONCLUSIONS

Our data suggests that a nutrient restriction of 85% as compared to 140% of total metabolizable energy requirements during the 2nd half of gestation can alter the expression of growth, myogenic and adipogenic genes in fetal muscle without apparent differences in fetal phenotype. It also appears that the impact of feed restriction varies between muscles suggesting a priority for nutrient partitioning depending on muscle function and/or fiber composition. Differences in the methylation level in IGF2, a well-known imprinted gene, as well as differences in miRNA expression, may be functional mechanisms that precede the differences in gene expression observed, and could lead to trans-generational epigenetic programming.

Evaluation of blood metabolites reflects presence or absence of liver abscesses in beef cattle

Liver abscesses constitute a prominent concern regarding animal health and profitability of the beef industry. Our objective was to evaluate potential biliary and blood indicators of liver abscesses. Twenty-nine beef bulls (initially averaging 356±70.5 kg and 253±30 days of age) were fed a high-concentrate diet during a performance test of 112 days, during which blood was collected at nine time points spaced 0.5-13 days apart within 56 days before slaughter. At the abattoir, blood and bile were collected and livers were inspected for liver abscesses. Results indicated that liver abscesses are associated with elevated levels of plasma cortisol and aspartate aminotransferase, and decreased levels of albumin, cholesterol and testosterone over the period before slaughter. Based on the blood samples collected during exsanguination, the presence of liver abscesses was associated with lower concentrations of thyroxine, albumin, cholesterol and alkaline phosphatase, and is suggested to be associated with lower blood carbon dioxide (P=0.08) and lower biliary cortisol metabolites (P=0.07). Albumin and cholesterol are established indicators of hepatic function and are consistently related to the presence of liver abscesses. Identifying blood parameters that predict liver abscesses has practical implications for cattle husbandry and for ensuring food safety.

Genetic diversity of a New Zealand multi-breed sheep population and composite breeds' history revealed by a high-density SNP chip

Background

Knowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the implementation of genomic selection in a composite Terminal sheep breeding scheme by providing consolidated linkage disequilibrium (LD) measures across SNP markers, estimating consistency of gametic phase between breed-groups, and assessing genetic diversity measures, such as effective population size (N_e), and population structure parameters, using a large number of animals (n = 14,845) genotyped with a high density SNP chip (606,006 markers). Information generated in this research will be useful for optimizing molecular breeding values predictions and managing the available genetic resources.

Results

Overall, as expected, levels of pairwise LD decreased with increasing distance between SNP pairs. The mean LD r² between adjacent SNP was 0.26 ± 0.10. The most recent effective population size for all animals (687) and separately per breed-groups: Primera (974), Lamb Supreme (380), Texel (227) and Dual-Purpose (125) was quite variable. The genotyped animals were outbred or had an average low level of inbreeding. Consistency of gametic phase was higher than 0.94 for all breed pairs at the average distance between SNP on the chip (~4.74 kb). Moreover, there was not a clear separation between the breed-groups based on principal component analysis, suggesting that a mixed-breed training population for calculation of molecular breeding values would be beneficial.

Conclusions

This study reports, for the first time, estimates of linkage disequilibrium, genetic diversity and population structure parameters from a genome-wide perspective in New Zealand Terminal Sire composite sheep breeds. The levels of linkage disequilibrium indicate that genomic selection could be implemented with the high density SNP panel. The moderate to high consistency of gametic phase between breed-groups and overlapping population structure support the pooling of the animals in a mixed training population for genomic predictions. In addition, the moderate to high N_e highlights the need to genotype and phenotype a large training population in order to capture most of the haplotype diversity and increase accuracies of genomic predictions. The results reported herein are a first step toward understanding the genomic architecture of a Terminal Sire composite sheep population and for the optimal implementation of genomic selection and genome-wide association studies in this sheep population.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-017-0492-8) contains supplementary material, which is available to authorized users.

Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip

Background

New Zealand has some unique Terminal Sire composite sheep breeds, which were developed in the last three decades to meet commercial needs. These composite breeds were developed based on crossing various Terminal Sire and Maternal breeds and, therefore, present high genetic diversity compared to other sheep breeds. Their breeding programs are focused on improving carcass and meat quality traits. There is an interest from the industry to implement genomic selection in this population to increase the rates of genetic gain. Therefore, the main objectives of this study were to determine the accuracy of predicted genomic breeding values for various growth, carcass and meat quality traits using a HD SNP chip and to evaluate alternative genomic relationship matrices, validation designs and genomic prediction scenarios. A large multi-breed population (n = 14,845) was genotyped with the HD SNP chip (600 K) and phenotypes were collected for a variety of traits.

Results

The average observed accuracies (± SD) for traits measured in the live animal, carcass, and, meat quality traits ranged from 0.18 ± 0.07 to 0.33 ± 0.10, 0.28 ± 0.09 to 0.55 ± 0.05 and 0.21 ± 0.07 to 0.36 ± 0.08, respectively, depending on the scenario/method used in the genomic predictions. When accounting for population stratification by adjusting for 2, 4 or 6 principal components (PCs) the observed accuracies of molecular breeding values (mBVs) decreased or kept constant for all traits. The mBVs observed accuracies when fitting both G and A matrices were similar to fitting only G matrix. The lowest accuracies were observed for k-means cross-validation and forward validation performed within each k-means cluster.

Conclusions

The accuracies observed in this study support the feasibility of genomic selection for growth, carcass and meat quality traits in New Zealand Terminal Sire breeds using the Ovine HD SNP chip. There was a clear advantage on using a mixed training population instead of performing analyzes per genomic clusters. In order to perform genomic predictions per breed group, genotyping more animals is recommended to increase the size of the training population within each group and the genetic relationship between training and validation populations. The different scenarios evaluated in this study will help geneticists and breeders to make wiser decisions in their breeding programs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-017-0476-8) contains supplementary material, which is available to authorized users.

History of the Hays Converter

The Hays Converter breed of beef cattle was developed in Alberta, Canada, by Harry Hays in the 1950s. Hays combined specific individuals of the Hereford, Holstein, and Brown Swiss breeds to create an animal with exceptional growth and maternal abilities. In 1975, it became the first breed of cattle developed in Canada to be recognized under the Canadian Livestock Pedigree Act. The breed still exists in small numbers across Canada and represents an important part of Canadian agriculture history.

Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population

BACKGROUND

Genotype imputation is a key element of the implementation of genomic selection within the New Zealand sheep industry, but many factors can influence imputation accuracy. Our objective was to provide practical directions on the implementation of imputation strategies in a multi-breed sheep population genotyped with three single nucleotide polymorphism (SNP) panels: 5K, 50K and HD (600K SNPs).

RESULTS

Imputation from 5K to HD was slightly better (0.6 %) than imputation from 5K to 50K. Two-step imputation from 5K to 50K and then from 50K to HD outperformed direct imputation from 5K to HD. A slight loss in imputation accuracy was observed when a large fixed reference population was used compared to a smaller within-breed reference (including all 50K genotypes on animals from different breeds excluding those in the validation set i.e. to be imputed), but only for a few animals across all imputation scenarios from 5K to 50K. However, a major gain in imputation accuracy for a large proportion of animals (purebred and crossbred), justified the use of a fixed and large reference dataset for all situations. This study also investigated the loss in imputation accuracy specifically for SNPs located at the ends of each chromosome, and showed that only chromosome 26 had an overall imputation (5K to 50K) accuracy for 100 SNPs at each end higher than 60 % (r²). Most of the chromosomes displayed reduced imputation accuracy at least at one of their ends. Prediction of imputation accuracy based on the relatedness of low-density genotypes to those of the reference dataset, before imputation (without running an imputation software) was also investigated. FIMPUTE V2.2 outperformed BEAGLE 3.3.2 across all imputation scenarios.

CONCLUSIONS

Imputation accuracy in sheep breeds can be improved by following a set of recommendations on SNP panels, software, strategies of imputation (one- or two-step imputation), and choice of the animals to be genotyped using both high- and low-density SNP panels. We present a method that predicts imputation accuracy for individual animals at the low-density level, before running imputation, which can be used to restrict genomic prediction only to the animals that can be imputed with sufficient accuracy.

Improved Stability of Treprostinil Sodium with Proper Vial Puncture Technique and Adapter Use

Background:

Treprostinil sodium has an expiration date of 14 days following initial vial puncture.

Objective:

To extend the expiration date of treprostinil sodium after initial vial entry and determine its stability after daily versus every 3-day vial entry. Stability and compatibility of treprostinil sodium with a Clave connector device was assessed.

Methods:

An initial study considered treprostinil vials punctured daily without regard to proper vial puncture technique. A second study considered treprostinil sodium vials punctured every 3 days with proper technique. Vials in these studies were stored in a stability chamber at 25 °C and 60% relative humidity up to 30 days. Treprostinil stability was assessed with a Clave connector adapter up to 84 days with the vials inverted. Vials were analyzed for treprostinil and m-cresol content, pH, appearance, particulate matter, and sterility.

Results:

Initial data indicated 14 days as the expiration date after initial vial entry and daily vial puncture. The parameter influencing stability was particulate matter, which was significantly reduced with proper vial puncture technique and vial entry every 3 days. Particulate matter counts remained low up to 84 days using a Clave adaptor and withdrawal every 7 days. Other stability parameters were acceptable throughout the stability study.

Conclusions:

These data indicate that the number of vial entries influenced treprostinil stability rather than time after initial vial entry. Two methods were identified to extend the expiration date of treprostinil sodium after initial vial puncture: proper vial puncture technique and use of a Clave adapter to withdraw the vial contents.

Genomic clustering helps to improve prediction in a multibreed population

Genomic prediction for crossbred beef cattle has shown limited results using low- to moderate-density SNP panels. The relationship between the training and validation populations, as well as the size of the reference population, affects the prediction accuracy for genomic selection. Rotational crossbreeding systems require the usage of crossbred animals as sires and dams of future generations, so crossbred animals require accurate evaluation. Here, a novel method for grouping of purebred and crossbred animals (based exclusively on genotypes) for genomic selection was investigated. Clustering of animals to investigate the genetic similarity among different groups was performed using several genomic relationship criteria between individuals. Hierarchical clusters based on average-link criteria (computed as the mean distance between elements of each subcluster) were formed. The accuracy of genomic prediction was assessed using 1,500 bulls genotyped for 54,609 markers. Estimated breeding values based on all available phenotypic records for birth weight, weaning gain, postweaning gain, and yearling gain were calculated using BLUP methodologies and deregressed to ensure unbiased comparisons could be made across populations. A 5-fold validation technique was used to calculate direct genomic values for all genotyped bulls; the addition of unrelated animals in the reference population was also investigated. We demonstrate a decrease in genomic selection accuracy after including animals from disconnected clusters. A method to improve genomic selection for crossbred and purebred animals by clustering animals based on their genotype is suggested. Unlike traditional approaches for genomic selection with a fixed reference population, genomic prediction using clusters (GPC) chooses the best reference population for better accuracy of genomic prediction of crossbred and purebred animals using clustering methods based on genotypes. An overall average gain in accuracy of 1.30% was noted over all scenarios across all traits investigated when the GPC approach was implemented. Further investigation is required to assess this difference in accuracy when a larger genotyped population is available, especially for the comparison of groups with higher genetic dissimilarity, such as those found in industry-wide across-breed genetic evaluations.

Utilization of macrominerals and trace elements in pregnant heifers with distinct feed efficiencies

The objective of the study was to evaluate utilization of dietary minerals and trace elements in pregnant heifers with distinct residual feed intakes (RFI). Feed intake, body weight (BW), and body composition traits were recorded in 36 crossbred heifers over a period of 37 wk, starting shortly after weaning at 8.3 (0.10; standard deviation) mo of age with an average BW of 276 (7.8) kg. Both BW and body composition were monitored regularly throughout the study, whereas individual feed intake was assessed during the last 84 d of the trial. Data recorded were used to calculate RFI for each heifer. Heifers were ranked based on RFI and assigned to high (n=14) or low (n=10) RFI groups. After the RFI study, 24 selected heifers [age 18.2 (0.14) mo; 87.5 (4.74) d in gestation; 497 (8.5) kg of BW] were used in an indirect digestibility trial (lignin as internal marker). Heifers were fed a ration containing corn silage, haylage, and a mineral premix in which Ca, P, K, Na, Mg, S, Cu, Fe, Mn, Mo, Se, Zn, and Co were provided in the diet according to National Research Council requirements of pregnant replacement heifers. The digestibility trial lasted 1 wk, during which samples of feces were gathered twice daily, and blood and liver biopsy samples were collected on the last day. We noted no significant differences between low- and high-RFI heifers in dry matter digestibility. Apparent absorption of Cu, Zn, and Mn was increased in heifers with low RFI, and apparent absorption of Co tended to be greater for these animals. Concentrations of macrominerals and trace elements in serum of pregnant heifers were similar for both groups except for Se, which was increased in the serum of low-RFI heifers. Liver concentrations of Cu, Fe, Mn, Mo, Se, and Zn did not differ between low- and high-RFI heifers. In conclusion, whereas improved absorption of some trace elements (Cu, Zn, Mn, and Co) and increased Se serum concentration appear to be associated with superior feed efficiency in pregnant heifers, further studies are needed to investigate the causality of such relationships.

Estimation of genomic breeding values for residual feed intake in a multibreed cattle population

Residual feed intake (RFI) is a measure of the efficiency of animals in feed utilization. The accuracies of GEBV for RFI could be improved by increasing the size of the reference population. Combining RFI records of different breeds is a way to do that. The aims of this study were to 1) develop a method for calculating GEBV in a multibreed population and 2) improve the accuracies of GEBV by using SNP associated with RFI. An alternative method for calculating accuracies of GEBV using genomic BLUP (GBLUP) equations is also described and compared to cross-validation tests. The dataset included RFI records and 606,096 SNP genotypes for 5,614 Bos taurus animals including 842 Holstein heifers and 2,009 Australian and 2,763 Canadian beef cattle. A range of models were tested for combining genotype and phenotype information from different breeds and the best model included an overall effect of each SNP, an effect of each SNP specific to a breed, and a small residual polygenic effect defined by the pedigree. In this model, the Holsteins and some Angus cattle were combined into 1 "breed class" because they were the only cattle measured for RFI at an early age (6-9 mo of age) and were fed a similar diet. The average empirical accuracy (0.31), estimated by calculating the correlation between GEBV and actual phenotypes divided by the square root of estimated heritability in 5-fold cross-validation tests, was near to that expected using the GBLUP equations (0.34). The average empirical and expected accuracies were 0.30 and 0.31, respectively, when the GEBV were estimated for each breed separately. Therefore, the across-breed reference population increased the accuracy of GEBV slightly, although the gain was greater for breeds with smaller number of individuals in the reference population (0.08 in Murray Grey and 0.11 in Hereford for empirical accuracy). In a second approach, SNP that were significantly (P < 0.001) associated with RFI in the beef cattle genomewide association studies were used to create an auxiliary genomic relationship matrix for estimating GEBV in Holstein heifers. The empirical (and expected) accuracy of GEBV within Holsteins increased from 0.33 (0.35) to 0.39 (0.36) and improved even more to 0.43 (0.50) when using a multibreed reference population. Therefore, a multibreed reference population is a useful resource to find SNP with a greater than average association with RFI in 1 breed and use them to estimate GEBV in another breed.

A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project

BACKGROUND

The Canadian Cattle Genome Project is a large-scale international project that aims to develop genomics-based tools to enhance the efficiency and sustainability of beef and dairy production. Obtaining DNA sequence information is an important part of achieving this goal as it facilitates efforts to associate specific DNA differences with phenotypic variation. These associations can be used to guide breeding decisions and provide valuable insight into the molecular basis of traits.

FINDINGS

We describe a dataset of 379 whole-genome sequences, taken primarily from key historic Bos taurus animals, along with the analyses that were performed to assess data quality. The sequenced animals represent ten populations relevant to beef or dairy production. Animal information (name, breed, population), sequence data metrics (mapping rate, depth, concordance), and sequence repository identifiers (NCBI BioProject and BioSample IDs) are provided to enable others to access and exploit this sequence information.

CONCLUSIONS

The large number of whole-genome sequences generated as a result of this project will contribute to ongoing work aiming to catalogue the variation that exists in cattle as well as efforts to improve traits through genotype-guided selection. Studies of gene function, population structure, and sequence evolution are also likely to benefit from the availability of this resource.

Genome-wide association for heifer reproduction and calf performance traits in beef cattle

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5-7, 9, 13-16, 19-21, 24, 25, and 27-29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

Technological, environmental and biological factors: referent variance values for infrared imaging of the bovine

Background

Despite its variety of potential applications, the wide implementation of infrared technology in cattle production faces technical, environmental and biological challenges similar to other indicators of metabolic state. Nine trials, divided into three classes (technological, environmental and biological factors) were conducted to illustrate the influence of these factors on body surface temperature assessed through infrared imaging.

Results

Evaluation of technological factors indicated the following: measurements of body temperatures were strongly repeatable when taken within 10 s; appropriateness of differing infrared camera technologies was influenced by distance to the target; and results were consistent when analysis of thermographs was compared between judges. Evaluation of environmental factors illustrated that wind and debris caused decreases in body surface temperatures without affecting metabolic rate; additionally, body surface temperature increased due to sunlight but returned to baseline values within minutes of shade exposure. Examination/investigation/exploration of animal factors demonstrated that exercise caused an increase in body surface temperature and metabolic rate. Administration of sedative and anti-sedative caused changes on body surface temperature and metabolic rate, and during late pregnancy a foetal thermal imprint was visible through abdominal infrared imaging.

Conclusion

The above factors should be considered in order to standardize operational procedures for taking thermographs, thereby optimizing the use of such technology in cattle operations.

Tract-Based Spatial Statistics in Preterm-Born Neonates Predicts Cognitive and Motor Outcomes at 18 Months

BACKGROUND AND PURPOSE

Adverse neurodevelopmental outcome is common in children born preterm. Early sensitive predictors of neurodevelopmental outcome such as MR imaging are needed. Tract-based spatial statistics, a diffusion MR imaging analysis method, performed at term-equivalent age (40 weeks) is a promising predictor of neurodevelopmental outcomes in children born very preterm. We sought to determine the association of tract-based spatial statistics findings before term-equivalent age with neurodevelopmental outcome at 18-months corrected age.

MATERIALS AND METHODS

Of 180 neonates (born at 24-32-weeks' gestation) enrolled, 153 had DTI acquired early at 32 weeks' postmenstrual age and 105 had DTI acquired later at 39.6 weeks' postmenstrual age. Voxelwise statistics were calculated by performing tract-based spatial statistics on DTI that was aligned to age-appropriate templates. At 18-month corrected age, 166 neonates underwent neurodevelopmental assessment by using the Bayley Scales of Infant Development, 3rd ed, and the Peabody Developmental Motor Scales, 2nd ed.

RESULTS

Tract-based spatial statistics analysis applied to early-acquired scans (postmenstrual age of 30-33 weeks) indicated a limited significant positive association between motor skills and axial diffusivity and radial diffusivity values in the corpus callosum, internal and external/extreme capsules, and midbrain (P < .05, corrected). In contrast, for term scans (postmenstrual age of 37-41 weeks), tract-based spatial statistics analysis showed a significant relationship between both motor and cognitive scores with fractional anisotropy in the corpus callosum and corticospinal tracts (P < .05, corrected). Tract-based spatial statistics in a limited subset of neonates (n = 22) scanned at <30 weeks did not significantly predict neurodevelopmental outcomes.

CONCLUSIONS

The strength of the association between fractional anisotropy values and neurodevelopmental outcome scores increased from early-to-late-acquired scans in preterm-born neonates, consistent with brain dysmaturation in this population.

Next-generation leadership development in family businesses: the critical roles of shared vision and family climate

The multigenerational survival rate for family-owned businesses is not good. Lack of a shared vision for the family enterprise and weak next-generation leadership are often cited as two of the leading reasons for the failure of family firms to successfully transition from one generation of family ownership to the next. The climate of the business-owning family has also been suggested as important to the performance of the family enterprise. Despite these commonly held tenets, there is a lack of rigorous quantitative research that explores the relationships among these three factors. To address this gap, a quantitative study of 100 next-generation family firm leaders and 350 family and non-family leaders and employees with whom they work was conducted. The results demonstrate that a shared vision for the family business has a strong effect on the leadership effectiveness of next-generation family leaders and a moderate effect on the degree to which they are positively engaged with their work. The findings also show that two dimensions of family climate significantly influence the likelihood that a shared vision for the family firm has been created. Open communication in the family is positively related to the presence of a shared vision for the business. Intergenerational authority, which refers to a senior generation that exercises unquestioned authority and sets the rules, is negatively related to the presence of a shared vision. Surprisingly, a third dimension of family climate, cognitive cohesion, which includes shared values in the family, had no relationship with the degree to which there was a shared vision for the family business. The implications for family business owners is that they would be wise to spend as much time on fostering a positive family climate characterized by open communication as they do on creating and executing a successful business strategy if their goal is to pass the business from one generation of family owners to the next.

A meta-analysis of the effects of dietary copper, molybdenum, and sulfur on plasma and liver copper, weight gain, and feed conversion in growing-finishing cattle

The minerals Cu, Mo, and S are essential for metabolic functions related to cattle health and performance. The interaction between Cu, Mo, and S can determine the utilization of each mineral, in particular Cu, by ruminants. A meta-analysis was performed to evaluate the effects of dietary Cu, Mo, and S and their interactions on plasma and liver Cu, ADG, and G:F in growing-finishing cattle. Data were collated from 12 published studies. The model with the best fit to data indicated plasma Cu was positively affected by dietary Cu (P < 0.01) and negatively affected by both dietary Mo (P < 0.01) and S (P < 0.01). Another model also indicated that plasma Cu concentration is positively related to Cu:Mo ratio in the diet (P < 0.01). Dietary Cu had a positive effect on liver Cu (P < 0.01), whereas Mo showed a negative effect (P < 0.05), and no effect of dietary S on liver Cu was observed (P > 0.05). Average daily gain was negatively affected by dietary Mo (P < 0.05) and S (P < 0.01) and positively affected by Cu:Mo ratio (P < 0.01), likely because an increased Cu:Mo ratio minimizes the antagonistic effect of Mo on Cu. The feed conversion ratio was negatively affected by Mo (P < 0.05) and S (P < 0.01), whereas effects of the Cu:Mo ratio and dietary Cu were not significant (P > 0.05). The interaction between S and Mo affected (P < 0.01) G:F, which was likely related to a positive response with the proper balance between these minerals. In conclusion, dietary Cu, Mo, and S and the Cu:Mo ratio caused changes in plasma Cu. Only dietary Mo and S led to a negative response in the performance of growing-finishing cattle, whereas the diet Cu:Mo ratio has a linear and quadratic effect on ADG. Nutritionists and producers need to consider with caution the supplementation of growing-finishing cattle diets with Mo and S because of their potentially adverse effects on animal performance. An appropriate Cu:Mo ratio is desirable to minimize the effects of an impaired supply of Mo on Cu metabolism and ADG.

Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing

A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea—Hanwoo, Jeju Heugu, and Korean Holstein—using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions–deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.

Evolution of a transition state: role of Lys100 in the active site of isocitrate dehydrogenase

An active site lysine essential to catalysis in isocitrate dehydrogenase (IDH) is absent from related enzymes. As all family members catalyze the same oxidative β-decarboxylation at the (2R)-malate core common to their substrates, it seems odd that an amino acid essential to one is not found in all. Ordinarily, hydride transfer to a nicotinamide C4 neutralizes the positive charge at N1 directly. In IDH, the negatively charged C4-carboxylate of isocitrate stabilizes the ground state positive charge on the adjacent nicotinamide N1, opposing hydride transfer. The critical lysine is poised to stabilize-and perhaps even protonate-an oxyanion formed on the nicotinamide 3-carboxamide, thereby enabling the hydride to be transferred while the positive charge at N1 is maintained. IDH might catalyze the same overall reaction as other family members, but dehydrogenation proceeds through a distinct, though related, transition state. Partial activation of lysine mutants by K(+) and NH4 (+) represents a throwback to the primordial state of the first promiscuous substrate family member.

Impact of reference population on accuracy of imputation from 6K to 50K single nucleotide polymorphism chips in purebred and crossbreed beef cattle

Genotyping with lower density but lower cost panels enables more animals to be genotyped for genomic selection. Imputation enables the determination of missing SNP genotypes in animals genotyped with a low-density panel by using information from a reference population genotyped with a higher density panel, which should increase accuracy of genomic EBV. In this study, population imputation, using linkage disequilibrium among markers, was implemented using the software BEAGLE, FIMPUTE 2.2, and IMPUTE2 in a multibreed, crossbred taurine beef cattle population genotyped with the Illumina SNP50. Different combinations of reference populations and imputed animals were defined based on breed composition. Number of animals (n = 250 to 4,932) and the presence of closer relatives in the reference population (only for Angus animals) were investigated. The overall average imputation accuracy for purebred animals ranged from 94.20 to 97.93% using FIMPUTE, from 95.35 to 98.31% using IMPUTE2, and from 90.02 to 96.38% when BEAGLE software was used. Imputation accuracy of crossbred animals ranged from 54.15 to 97.53% (FIMPUTE), from 57.04 to 97.46% (IMPUTE2), and from 54.35 to 95.64% (BEAGLE). Higher imputation accuracies were obtained when closer relatives along with the breed composition of imputed animals was well represented in the reference population. Within breed imputation from 6K to 50K did not improve when an additional purebred population was added to the reference population. FIMPUTE reduced the run time by 13 to 52 times compared to BEAGLE and 51 to 108 times compared to IMPUTE2.

Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

Background

This study was conducted to: (1) identify new SNPs for residual feed intake (RFI) and performance traits within candidate genes identified in a genome wide association study (GWAS); (2) estimate the proportion of variation in RFI explained by the detected SNPs; (3) estimate the effects of detected SNPs on carcass traits to avoid undesirable correlated effects on these economically important traits when selecting for feed efficiency; and (4) map the genes to biological mechanisms and pathways. A total number of 339 SNPs corresponding to 180 genes were tested for association with phenotypes using a single locus regression (SLRM) and genotypic model on 726 and 990 crossbred animals for feed efficiency and carcass traits, respectively.

Results

Strong evidence of associations for RFI were located on chromosomes 8, 15, 16, 18, 19, 21, and 28. The strongest association with RFI (P = 0.0017) was found with a newly discovered SNP located on BTA 8 within the ELP3 gene. SNPs rs41820824 and rs41821600 on BTA 16 within the gene HMCN1 were strongly associated with RFI (P = 0.0064 and P = 0.0033, respectively). A SNP located on BTA 18 within the ZNF423 gene provided strong evidence for association with RFI (P = 0.0028). Genomic estimated breeding values (GEBV) from 98 significant SNPs were moderately correlated (0.47) to the estimated breeding values (EBVs) from a mixed animal model. The significant (P < 0.05) SNPs (98) explained 26% of the genetic variance for RFI. In silico functional analysis for the genes suggested 35 and 39 biological processes and pathways, respectively for feed efficiency traits.

Conclusions

This study identified several positional and functional candidate genes involved in important biological mechanisms associated with feed efficiency and performance. Significant SNPs should be validated in other populations to establish their potential utilization in genetic improvement programs.

Association analysis for feed efficiency traits in beef cattle using preserved haplotypes

This study reports a genome wide scan for chromosome regions and their haplotypes that significantly associated with average daily gain (ADG), dry matter intake (DMI), and residual feed intake (RFI) in beef cattle. The study used data from 597 Angus, 450 Charolais, and 616 crossbred beef cattle, and the Illumina Bovine SNP50 beadchip. Extended haplotype homozygosity was used to identify chromosome regions that had been recently selected for in the three groups of animals. Such regions in the crossbreds were tested for association with ADG, DMI, and RFI. At false discovery rates of 5% and 10%, there were six and eight chromosome regions showing significant associations with the traits, respectively. At nominal significance levels (at least P < 0.05), 23 regions with a total number of 31 haplotypes were found significantly associated with at least one of the three traits. The proportion of phenotypic variance explained by these 23 regions varied depending on the trait; the highest proportion for ADG, DMI, and RFI was 13.50%, 9.92%, and 2.64%, respectively. Most of the haplotypes affected single traits, except for GAA (BTA4), GCG (BTA7), and TAGT (BTA12) that affected multiple traits. Thirty-six quantitative trait loci for 16 production traits, from the current literature, covered fully or in part the 23 chromosome regions. The findings from this study might be an important contribution to the current knowledge of the beef cattle genome and to the effective identification of causative genes associated with important traits in cattle.

Effect of moderate dietary restriction on visceral organ weight, hepatic oxygen consumption, and metabolic proteins associated with energy balance in mature pregnant beef cows

Twenty-two nonlactating multiparous pregnant beef cows (639 ± 68 kg) were used to investigate the effect of dietary restriction on the abundance of selected proteins regulating cellular energy metabolism. Cows were fed at either 85% (n = 11; LOW) or 140% (n = 11; HIGH) of total NE requirements. The diet consisted of a haylage-based total mixed ration containing 20% wheat straw. Cows were slaughtered by block (predicted date of parturition), beginning 83 d after the initiation of dietary treatments and every week thereafter for 6 wk, such that each block was slaughtered at approximately 250 d of gestation. Tissue samples from liver, kidney, sternomandibularis muscle, ruminal papilli (ventral sac), pancreas, and small intestinal muscosa were collected at slaughter and snap frozen in liquid N2. Western blots were conducted to quantify abundance of proliferating cell nuclear antigen (PCNA), ATP synthase, ubiquitin, and Na/K+ ATPase for all tissues; PPARγ, PPARγ coactivator 1 α (PGC-1α), and 5´-adenosine monophosphate-activated protein kinase (AMPK) and the activated form phosphorylated-AMPK (pAMPK) for liver, muscle, and rumen; phosphoenolpyruvate carboxykinase (PEPCK) for liver and kidney; and uncoupling protein 2 (UCP2) for liver. Statistical analysis was conducted using Proc Mixed in SAS and included the fixed effects of dietary treatment, cow age, block, and the random effect of pen. Dietary treatments resulted in cows fed HIGH having greater (P ≤ 0.04) ADG and final BW than cows fed LOW. Abundance of ubiquitin in muscle was greater (P = 0.009) in cows fed LOW, and PCG-1 α in liver was greater (P = 0.03) in cows fed HIGH. Hepatic O2 consumption was greater in HIGH (P ≤ 0.04). Feed intake can influence the abundance of important metabolic proteins and suggest that protein degradation may increase in muscle from moderately nutrient restricted cows and that energy metabolism in liver increases in cows fed above NE requirements.