Novel genetic parameters for genetic residual feed intake in dairy cattle using time series data from multiple parities and countries in North America and Europe

Residual feed intake is viewed as an important trait in breeding programs that could be used to enhance genetic progress in feed efficiency. In particular, improving feed efficiency could improve both economic and environmental sustainability in the dairy cattle industry. However, data remain sparse, limiting the development of reliable genomic evaluations across lactation and parity for residual feed intake. Here, we estimated novel genetic parameters for genetic residual feed intake (gRFI) across the first, second, and third parity, using a random regression model. Research data on the measured feed intake, milk production, and body weight of 7,379 cows (271,080 records) from 6 countries in 2 continents were shared through the Horizon 2020 project Genomic Management Tools to Optimise Resilience and Efficiency, and the Resilient Dairy Genome Project. The countries included Canada (1,053 cows with 47,130 weekly records), Denmark (1,045 cows with 72,760 weekly records), France (329 cows with 16,888 weekly records), Germany (938 cows with 32,614 weekly records), the Netherlands (2,051 cows with 57,830 weekly records), and United States (1,963 cows with 43,858 weekly records). Each trait had variance components estimated from first to third parity, using a random regression model across countries. Genetic residual feed intake was found to be heritable in all 3 parities, with first parity being predominant (range: 22-34%). Genetic residual feed intake was highly correlated across parities for mid- to late lactation; however, genetic correlation across parities was lower during early lactation, especially when comparing first and third parity. We estimated a genetic correlation of 0.77 ± 0.37 between North America and Europe for dry matter intake at first parity. Published literature on genetic correlations between high input countries/continents for dry matter intake support a high genetic correlation for dry matter intake. In conclusion, our results demonstrate the feasibility of estimating variance components for gRFI across parities, and the value of sharing data on scarce phenotypes across countries. These results can potentially be implemented in genetic evaluations for gRFI in dairy cattle.

Endotoxin-induced cytokine, chemokine and white blood cell profiles of variable stress-responding sheep

Individual variation of the hypothalamic-pituitary-adrenal (HPA) axis response to stress could contribute to variable stress resiliency of livestock. During stress events, the innate immune system can also become activated and work in concert with the neuroendocrine system to restore homeostasis, while minimizing tissue damage. The purpose of this study was to assess immune function in variable stress-responding sheep in response to bacterial lipopolysaccharide (LPS) endotoxin immune-challenge. High (HSR, n = 12), middle (MSR, n = 12), and low-stress responders (LSR, n = 12) were selected from a population of 112 female lambs and classified based on serum cortisol concentration after receiving an intravenous bolus of LPS (400 ng/kg). Blood was collected from the jugular vein at 0 and 4 hrs post-LPS challenge to monitor changes in serum pro- and anti-inflammatory cytokines and chemokines, and white blood cell populations. Rectal temperature was recorded hourly to monitor fever. HSR had the greatest increase in rectal temperature and strongest pro-inflammatory IL-6 and IFN-γ cytokine responses compared to MSR and LSR. HSR and MSR had stronger anti-inflammatory IL-10 cytokine and CCL2 chemokine responses than LSR. White blood cell counts changed between 0 and 4 h; however, no differences were detected among the variable stress response groups. The distinct inflammatory response in variable stress responding sheep could contribute to individual differences in stress resiliency and this warrants investigation in the context of other types of stress.

Genetic and genomic analyses of embryo production in dairy cattle

The Canadian dairy industry has been using invivo and invitro assisted reproductive technologies to produce embryos. Technological improvements have helped increase the number and quality of embryos produced, but genetic and genomic tools for improving these traits have yet to be assessed for the Canadian Holstein population. Genetic parameters and a genome-wide association study were performed in Canadian Holstein for the total number of embryos (NE) and the number of viable embryos (VE). Results showed potential for genetic selection for both NE and VE, with heritability estimates (± s.e.) of approximately 0.15±0.01. Genetic correlations between the number of embryos produced using different procedures (invivo and invitro) suggested that a similar number of embryos should be expected from a donor regardless of the procedure used. A region on chromosome 11 of the bovine genome was found to be significantly associated with the number of embryos, indicating a potential regulatory role of this region on embryo production. Overall, these findings are of interest for the Canadian dairy industry because they provide useful information for breeders that are interested in producing embryos from the elite donors in their herds or in the population using assisted reproductive technologies.

Symposium review: Exploiting homozygosity in the era of genomics-Selection, inbreeding, and mating programs

The advent of genomic selection paved the way for an unprecedented acceleration in genetic progress. The increased ability to select superior individuals has been coupled with a drastic reduction in the generation interval for most dairy populations, representing both an opportunity and a challenge. Homozygosity is now rapidly accumulating in dairy populations. Currently, inbreeding depression is managed mostly by culling at the farm level and by controlling the overall accumulation of homozygosity at the population level. A better understanding of how homozygosity and recessive load are related will guarantee continued genetic improvement while curtailing the accumulation of harmful recessives and maintaining enough genetic variability to ensure the possibility of selection in the face of changing environmental conditions. In this review, we present a snapshot of the current dairy selection structure as it relates to response to selection and accumulation of homozygosity, briefly outline the main approaches currently used to manage inbreeding and overall variability, and present some approaches that can be used in the short term to control accumulation of harmful recessives while maintaining sustained selection pressure.

Short communication: Characterizing ovine serum stress biomarkers during endotoxemia

Breeding stress-resilient livestock is a potential strategy to help mitigate the negative effect of environmental and pathogenic stressors. The hypothalamic-pituitary-adrenal axis and immune system are activated during stress events and release mediators into the circulation that help restore physiological homeostasis. The purpose of this study was to assess a comprehensive set of circulatory mediators released in response to an acute immune stress challenge to identify candidate biomarkers that can be used for the selection of stress-resilient animals. Fifteen female lambs were stress challenged with an intravenous bolus of lipopolysaccharide (LPS; 400 ng/kg), and blood was collected from the jugular vein at 0, 2, 4, and 6 h after LPS challenge to identify and monitor candidate stress biomarkers; temperature was also recorded over time. Biomarker responses were evaluated with a repeated-measures model to compare time points with baseline values. As expected, all sheep had a monophasic febrile response to LPS challenge, and cortisol increased and returned to baseline by 6 h. The cytokines tumor necrosis factor-α, IL-6, IFN-γ (proinflammatory), and IL-10 (anti-inflammatory) increased, but only tumor necrosis factor-α returned to baseline during the monitoring period. The cytokines IL-1α, IL-1β, IL-17α (proinflammatory), and IL-4 (anti-inflammatory) did not respond to LPS challenge. All chemokines (CCL2, CCL3, CCL4, CXCL10, and IL-8) responded to LPS challenge; however, only CCL2, CCL3, CCL4, and CXCL10 increased over time, and only CCL3, CCL4, and CXCL10 returned to baseline during the monitoring period. MicroRNA (miR-145, miR-233, and miR-1246) also increased and remained elevated during the study. In summary, the LPS challenge induced a strong stress response in Rideau-Dorset sheep that could be monitored with a distinct profile of circulatory biomarkers.

Genetic correlations among selected traits in Canadian Holsteins

In the Canadian dairy industry, there are currently over 80 traits routinely evaluated, and more are considered for potential selection. Particularly, in the last few years, recording has commenced for several new phenotypes required to introduce novel traits with high economic importance into the selection program. However, without a systematic estimation of the genetic correlations that exist among traits, the potential results of indirect selection are unknown. Therefore, 29 traits representative of the trait diversity for first lactation Canadian animals were selected. Their two-by-two genetic correlations were estimated from a dataset of 62 498 first lactation Holstein cows, using a Markov Chain Monte Carlo Gibbs sampling approach. The general tendencies among the groups of traits confirm that production traits are negatively correlated with fertility traits and that functional traits are positively correlated with one another. The association of udder depth with fertility and disease resistance has also been highlighted. This contribution offers a comprehensive overview of current estimates across traits and includes correlations with novel traits that constitute an original addition to the literature. These new estimates can be used for newly developed genomic evaluation models and possibly lead to more accurate estimations of the dairy cows’ overall genetic merit.

Genome-wide association analysis for β-hydroxybutyrate concentration in Milk in Holstein dairy cattle

BACKGROUND

Ketosis in dairy cattle has been shown to cause a high morbidity in the farm and substantial financial losses to dairy farmers. Ketosis symptoms, however, are difficult to identify, therefore, the amount of ketone bodies (mainly β-hydroxybutyric acid, BHB) is used as an indicator of subclinical ketosis in cows. It has also been shown that milk BHB concentrations have a strong correlation with ketosis in dairy cattle. Mid-infrared spectroscopy (MIR) has recently became a fast, cheap and high-throughput method for analyzing milk components. The aim of this study was to perform a genome-wide association study (GWAS) on the MIR-predicted milk BHB to identify genomic regions, genes and pathways potentially affecting subclinical ketosis in North American Holstein dairy cattle.

RESULTS

Several significant regions were identified associated with MIR-predicted milk BHB concentrations (indicator of subclinical ketosis) in the first lactation (SCK1) and second and later lactations (SCK2) in Holstein dairy cows. The strongest association was located on BTA6 for SCK1 and BTA14 on SCK2. Several SNPs on BTA6 were identified in regions and variants reported previously to be associated with susceptibility to ketosis and clinical mastitis in Jersey and Holstein dairy cattle, respectively. One highly significant SNP on BTA14 was found within the DGAT1 gene with known functions on fat metabolism and inflammatory response in dairy cattle. A region on BTA6 and three SNPs on BTA20 were found to overlap between SCK1 and SCK2. However, a novel region on BTA20 (55-63 Mb) for SCK2 was also identified, which was not reported in previous association studies. Enrichment analysis of the list of candidate genes within the identified regions for MIR-predicted milk BHB concentrations yielded molecular functions and biological processes that may be involved in the inflammatory response and lipid metabolism in dairy cattle.

CONCLUSIONS

The results of this study confirmed several SNPs and genes identified in previous studies as associated with ketosis susceptibility and immune response, and also found a novel region that can be used for further analysis to identify causal variations and key regulatory genes that affect clinical/ subclinical ketosis.

Genetic analysis for quality of frozen embryos produced by Holstein cattle donors in Canada

The number of embryos produced by Holstein donors has been shown to be heritable, so it could be possible to genetically select for this trait to improve the efficiency of the assisted reproductive technology (ART) in dairy cattle. Another important parameter to consider for achieving good results from ART is embryo quality because embryos of good quality have more chance of producing live offspring. The possibility of using genetic selection for increasing the quality of embryo produced from ART has yet to be assessed. The objective of this study was, therefore, to perform a genetic analysis of embryo quality of Holstein donors in Canada using data recorded by Holstein Canada. The data set used was missing quality score data for embryos transferred fresh into a recipient, so the analyses were only performed for frozen embryos. With most traits in the Canadian dairy industry being evaluated with linear models, embryo quality was also evaluated with this class of models. However, considering the categorical nature of embryo quality, a threshold model was also evaluated. Embryo quality data were analyzed with either a univariate linear animal model or a univariate binomial threshold animal model. Genetic parameters estimated from the different models were comparable. A low heritability was found for the donor (0.04 ± <0.01) and the service sire (0.02 ± <0.01), but the repeatability estimate for the donor was higher (0.17), indicating that it was worthwhile to use a repeated records model. Overall, considering the low genetic parameters estimated, slow genetic progress is expected for the quality of frozen embryos produced by Canadian Holstein donors. Rank correlations were calculated between breeding values estimated from different models. High correlations were found between all models, indicating that no substantial re-ranking of the animals is expected from the different models. So, even though a threshold model is better suited for the analysis of categorical data, a linear model could be used for the analysis of embryo quality because it is less computationally demanding.

Short communication: Genetic correlations between number of embryos produced using in vivo and in vitro techniques in heifer and cow donors

Multiple embryos can be produced from a heifer or cow donors using an in vivo or an in vitro technique. Comparisons of the number of embryos produced by the same donors as heifers and cows and using different techniques are limited. The main objectives of this study were to assess the genetic correlation between the number of embryos produced by Holstein donors using an in vivo and in vitro technique as a heifer and as a cow. The data set used was recorded by Holstein Canada and included all successful superovulations or ovum pickup and in vitro fertilization procedures performed on Holstein donors for more than 20yr. The type of technique used was known for all records and the status of the donor at recovery was retrieved from calving records. Bivariate repeatability animal model analyses were performed for both the total number of embryos (NE) and the number of viable embryos (VE) recovered per procedure. Logarithmic transformation was performed on the traits to normalize the data. Heritability estimates for the donor varied between 0.14 (0.02) and 0.19 (0.03) over all analyses, indicating that the number of embryos produced by a donor is influenced by the genetic potential of the donor. Genetic correlations between records produced in vivo and in vitro were moderately high and positive (NE=0.85±0.07; VE=0.63±0.09), suggesting that donors with high genetic potential for in vivo superovulation tend also to have high potential to produce multiple embryos in vitro. Similarly, the moderately high genetic correlations (NE=0.79±0.05; VE=0.72±0.05) found between heifer and cow records indicate that a donor tends to produce a comparable number of embryos as a heifer or as a cow. The estimated repeatabilities (0.23 to 0.35) indicated that the number of embryos recovered should be somewhat repeatable in the same donor over time. On the other hand, the service sires seem not to play an important role on the total number of embryos produced by a donor no matter the technique used or the status of the donor at recovery.

Angiopoietin-2 (ANGPT2) as a candidate gene for somatic cell score in German Holstein cattle

This study evaluated the bovine angiopoietin-2 (ANGPT2) gene as a functional and positional candidate gene underlying a previously fine mapped quantitative trait locus (QTL) for somatic cell score on bovine chromosome 27. The gene product angiopoietin-2 is directly involved in the extravasation of neutrophils, making it a promising candidate to control the amount of somatic cells in milk. A total of 11 polymorphisms were identified within the gene by comparatively resequencing the entire open reading frame of the gene as well as adjacent intronic regions. Four selected variants were genotyped in the same granddaughter design used for QTL mapping and an association study was carried out applying 2 complementary approaches. A variable number of tandem repeats in intron 7 of the gene was found to be significantly associated with cell score in all approaches and explains approximately half of the QTL variance. Analysis of ANGPT2 mRNA expression in different localizations of the udder in animals putatively carrying divergent QTL alleles revealed differential expression in the udder lymph node. Together with the physiological role of angiopoietin-2, these results support a role of ANGPT2 in the genetic control of somatic cell score. Further studies are, however, needed to further underpin this hypothesis.

A two-step approach to map quantitative trait loci for meat quality in connected porcine F(2) crosses considering main and epistatic effects

The aim of this study was to map QTL for meat quality traits in three connected porcine F(2) crosses comprising around 1000 individuals. The three crosses were derived from the founder breeds Chinese Meishan, European Wild Boar and Pietrain. The animals were genotyped genomewide for approximately 250 genetic markers, mostly microsatellites. They were phenotyped for seven meat quality traits (pH at 45 min and 24 h after slaughter, conductivity at 45 min and 24 h after slaughter, meat colour, drip loss and rigour). QTL mapping was conducted using a two-step procedure. In the first step, the QTL were mapped using a multi-QTL multi-allele model that was tailored to analyse multiple connected F(2) crosses. It considered additive, dominance and imprinting effects. The major gene RYR1:g.1843C>T affecting the meat quality on SSC6 was included as a cofactor in the model. The mapped QTL were tested for pairwise epistatic effects in the second step. All possible epistatic effects between additive, dominant and imprinting effects were considered, leading to nine orthogonal forms of epistasis. Numerous QTL were found. The most interesting chromosome was SSC6. Not all genetic variance of meat quality was explained by RYR1:g.1843C>T. A small confidence interval was obtained, which facilitated the identification of candidate genes underlying the QTL. Epistasis was significant for the pairwise QTL on SSC12 and SSC14 for pH24 and for the QTL on SSC2 and SSC5 for rigour. Some evidence for additional pairwise epistatic effects was found, although not significant. Imprinting was involved in epistasis.

Refined mapping of quantitative trait loci for somatic cell score on BTA02 in the German Holstein

The aim of this study was to more precisely map a previously reported quantitative trait locus (QTL) affecting somatic cell score on Bos taurus autosome 2 by increasing the number of markers fourfold, analysing more families and exploiting within-population linkage disequilibrium (LD). A granddaughter design of 10 German Holstein grandsire families with 1121 progeny tested sons was used. Twenty-six markers with an average marker spacing of 3.14 cM were genotyped along 81.6 cM. Linkage analysis (LA) was performed using variance-component methodology. The incorporation of LD was first done using variance-component methods followed by regression on marker alleles. LA revealed genome-wide significance (LOD > 3) at 15 contiguous marker-intervals, with the maximum test-statistic between DIK2862 and BMS778 and a 1-lod drop-off interval of 38 cM. While the variance-component methods could not detect any LD, two individual markers with a significant effect (ILSTS098, p < 0.05; BMS778, p < 0.01) were found by regression analysis. Compared with previous results QTL-localisation was substantially narrowed; further fine-mapping should focus on the close vicinity of BMS778.

Refined mapping of a QTL for somatic cell score on BTA27 in the German Holstein using combined linkage and linkage disequilibrium analysis

Genetic selection for udder health is often based on the indicator trait somatic cell score (SCS), which is correlated with clinical mastitis and has a moderate heritability. We used combined linkage and linkage disequilibrium analysis to refine mapping of a previously reported quantitative trait locus (QTL) affecting SCS on Bos taurus autosome 27 (BTA27) in the German Holstein population. A granddaughter design of six grandsire families with 492 sons progeny tested for an average of 190 daughters per son was investigated. Nineteen microsatellite markers were genotyped along a segment of 26.2 cM proximally on BTA27. A chromosome-wide significant QTL was identified between DIK2879 and KIBS272 using combined analysis. The region of interest for future fine mapping experiments was narrowed to the marker interval KIBS272-DIK2191 with a confidence interval of 3.27 cM. The QTL was estimated to be responsible for 18% of the genetic variation in SCS. Application of a 2-QTL model did not result in higher test statistics. Animals likely to be heterozygous or homozygous at the QTL were identified. This study provides a basis for the selection of further markers in linkage disequilibrium with the QTL affecting SCS on BTA27. Key words: Fine-mapping, mastitis, BTA27, somatic cell score, Holstein

Refined positioning of a quantitative trait locus affecting somatic cell score on chromosome 18 in the German Holstein using linkage disequilibrium

Combined linkage and linkage disequilibrium analysis (LALD) was conducted to more accurately map a previously reported quantitative trait locus (QTL) affecting somatic cell score on bovine chromosome 18. A grand-daughter design consisting of 6 German Holstein grandsire families with 1,054 progeny-tested genotyped sons was used in this study. Twenty microsatellite markers, 5 single nucleotide polymorphisms, and an erythrocyte antigen marker with an average marker spacing of 1.95 cM were analyzed along a chromosomal segment of 50.80 cM. Variance components were estimated and restricted maximum likelihood test statistics were calculated at the midpoint of each marker interval. The test statistics calculated in single-QTL linkage analysis exceeded the genome-wide significance threshold at several putative QTL positions. Using LALD, we were successful in assigning a genome-wide significant QTL to a confidence interval of 10.8 cM between the markers ILSTS002 and BMS833. The QTL in this marker interval was estimated to be responsible for between 5.89 and 13.86% of the genetic variation in somatic cell score. In contrast to the single-QTL linkage analysis model, LALD analyses with a 2-QTL model confirmed the position of one QTL, but gave no conclusive evidence for the existence or position of a second QTL. Ultimately, the QTL position was narrowed down considerably compared with previous results with a refined confidence interval of less than 11 cM.

TIGER: A software system for fine-mapping quantitative trait loci

Abstract. The localisation of quantitative trait loci which contribute significantly to phenotype variation of economically important traits in domestic species has become an important goal in animal genomics. Several such loci have been roughly identified using linkage analyses; however the focus has now shifted towards fine mapping and pinpointing causal mutations. In the context of a cooperative national research project, the software system TIGER was developed. TIGER is a UNIX script linking several individual Fortran programmes and is used for comprehensive variance component analysis of fine mapping data. Starting with raw genotype data, pedigree and marker map information and ending with a residual maximum likelihood-based test for each putative quantitative trait locus position, the software provides the user with an "all in one" package capable of linkage analysis, linkage disequilibrium analysis and combined linkage/linkage disequilibrium analysis. The software system has been employed in 4 fine mapping projects on 4 distinct cattle chromosomes.

Computing the condensed conditional gametic QTL relationship matrix and its inverse

Abstract. The inverse of the conditional gametic relationship matrix (G-1) for a marked quantitative trait locus (MQTL) is required for estimation of gametic effects in best linear unbiased prediction (BLUP) of breeding values if marker data are available. Calculation of the "condensed" gametic relationship matrix G* – a version of G where linear dependencies have been removed – and its inverse G*-1 is described using a series of simplified equations following a known algorithm. The software program COBRA (covariance between relatives for a marked QTL) is introduced, and techniques for storing and computing the condensed gametic relationship matrix G* and the non-zero elements of its inverse are discussed. The program operates with both simple pedigrees and those augmented by transmission probabilities derived from marker data. Using sparse matrix storage techniques, G* and its inverse can be efficiently stored in computer memory. COBRA is written in FORTRAN 90/95 and runs on a variety of computers. Pedigree data and information for a single MQTL in the German Holstein population are used to test the efficiency of the program.