The effect of progesterone concentrations during superovulation of Holstein heifers in a randomized trial.

The aim of this study was to evaluate the effect of different progesterone (P4) concentrations during the follicular growth on the intensity of estrous expression, ovarian response to the superovulatory treatment, and embryo production and quality in superovulated heifers. A total of 63 Holstein heifers were randomly assigned into 2 experimental groups: Low P4 (n = 31) and High P4 (n = 32). Animals received a pre-synchronization protocol followed by a protocol of superovulation that included the allocated P4 treatment. Activity was monitored continuously by an automated activity monitor, and estrus characteristics (maximum intensity and duration) were recorded. Embryo collection was performed 7 d post artificial insemination (AI). Embryos were counted and graded from good or excellent (1) to degenerated (4). The outcomes of interest were: number and diameter of follicles at the time of AI, ovulation success (confirmed 7 d post-AI), time to estrus event, maximum intensity and duration of estrus, number and quality of embryos. Data were analyzed according to the type of outcome variable using logistic, linear, or Poisson regression models. A total of 105 embryos (High P4: n = 42; Low P4: n = 63) were graded for quality. Different P4 levels did not affect the maximum intensity (High P4 = 497.8 ± 23.9%; Low P4 = 542.2 ± 23.5%) or the duration (High P4 = 13.5 ± 1.5 h; Low P4 = 14.3 ± 1.4 h) of estrus. Heifers in the High P4 treatment had greater number of follicles at time of AI (High P4 = 16.6 ± 1.6 follicles; Low P4 = 13.9 ± 1.2 follicles), but with smaller diameter (High P4 = 11.3 ± 0.1 mm; Low P4 = 12.0 ± 0.1 mm) compared with Low P4. High P4 heifers tended to have better embryo quality compared with Low P4 heifers (odds ratio = 1.98; 95% CI = 0.90-4.35). High P4 heifers had less embryos than Low P4 heifers, but this was modified by the CIDR (intravaginal implant of P4) removal to estrus interval (interval 0-21 h: mean ratio = 1.15, 95% CI = 0.42-1.87; interval 22-46 h: mean ratio = 0.58, 95% CI = 0.27-0.96). Although estrous expression was not associated with embryo quality, as the duration and the maximum intensity of estrous expression increased, the number of embryos recovered 7 d post-AI increased (duration: mean ratio = 1.04; 95% CI = 1.03-1.05; maximum intensity: mean ratio = 1.50; 95% CI = 1.42-1.58). In conclusion, P4 during the follicular growth, and intensity of estrus, are playing a role in regulating the quality and the number of embryos produced by superovulated heifers. This study was supported by contributions from Resilient Dairy Genome Project and the Natural Sciences and Engineering Research Council.

Machine learning classification of breeding protocol descriptions from Canadian Holsteins.

Dairy farmers are motivated to ensure cows become pregnant in an optimal and timely manner. Although timed artificial insemination (TAI) is a successful management tool in dairy cattle, it masks an animal's innate fertility performance, likely reducing the accuracy of genetic evaluations for fertility traits. Therefore, separating fertility traits based on the recorded management technique involved in the breeding process or adding the breeding protocol as an effect to the model can be viable approaches to address the potential bias caused by such management decisions. Nevertheless, there is a lack of specificity and uniformity in the recording of breeding protocol descriptions by dairy farmers. Therefore, this study investigated the use of 8 supervised machine learning algorithms to classify 1,835 unique breeding protocol descriptions from 981 herds into the following 2 classes: TAI or other than TAI. Our results showed that models that used a stacking classifier algorithm had the highest Matthews correlation coefficient (0.94 ± 0.04, mean ± SD) and maximized precision and recall (F1-score = 0.96 ± 0.03) on test data. Nonetheless, their F1-scores on test data were not different from 5 out of the other 7 algorithms considered. Altogether, results presented herein suggest machine learning algorithms can be used to produce robust models that correctly identify TAI protocols from dairy cattle breeding records, thus opening the opportunity for unbiased genetic evaluation of animals based on their natural fertility.

Occurrence and greater intensity of estrus in recipient lactating dairy cows improve pregnancy per embryo transfer.

The aim of this study was to determine the association between occurrence and intensity of estrous expression with pregnancy success in recipient lactating dairy cows subjected to embryo transfer (ET). Two observational studies were conducted. Holstein cows were synchronized using the same timed ET protocol, based on estradiol and progesterone in both experiments. At 9 d after the end of the timed ET protocol only animals that had ovulated were implanted with a 7-d embryo [experiment 1 (Exp. 1); n = 1,401 ET events from 1,045 cows, and experiment 2 (Exp. 2); n = 1,147 ET events from 657 cows]. Embryos were produced in vivo (Exp. 1 and Exp. 2) and in vitro (only Exp. 2), then transferred to recipient cows as fresh or frozen-thawed. Pregnancy was confirmed at 29 and 58 d after the end of timed ET protocol. In Exp. 1, animals had their estrous expression monitored through a tail chalk applied on the tail head of the cows and evaluated daily for chalk removal (no estrus: 100% of chalk remaining; estrus: <50% of chalk remaining). In Exp. 2, cows were continuously monitored by a leg-mounted automated activity monitor. Estrous expression was quantified using the relative increase in physical activity at estrus in relation to the days before estrus. Estrous expression was classified as no estrus [<100% relative increase in activity (RI)], weak intensity (100-299% RI), and strong intensity (≥300% RI). Data were analyzed by analysis of variance using mixed linear regression models (GLIMMIX) in SAS (SAS Institute Inc.). A total of 65.2% (914/1,401) and 89.2% (1,019/1,142) of cows from Exp. 1 and Exp. 2, respectively, displayed estrus at the end of the ovulation synchronization protocol. In Exp. 1, cows expressing estrus before to ET had greater pregnancy per ET than those that did not [41.0 ± 2.3% (381/914) vs. 31.5 ± 2.9% (151/487), respectively]. Similarly, in Exp. 2, cows classified in the strong intensity group had greater pregnancy per ET compared with cows in the weak intensity and no estrus groups [41.3 ± 2.2% (213/571) vs. 32.7 ± 2.7% (115/353) vs. 11.3 ± 3.5% (26/218), respectively]. There was no effect of ET type on pregnancy per ET in Exp. 1. However, in Exp. 2, cows that received an in vivo-produced embryo, either fresh or frozen, had greater pregnancy per ET compared with cows that received in vitro-produced embryo. Cows receiving embryos in the early blastocyst and blastocyst stage had greater fertility compared with cows receiving embryos in the morula stage. There was an interaction between the occurrence of estrus and the stage of embryo development on pregnancy per ET, cows which displayed estrus and received a morula or early blastocyst had greater pregnancy per ET than cows that did not display estrus. In conclusion, the occurrence and the intensity of estrous expression improved pregnancy per ET in recipient lactating dairy cows and thus could be used as a tool to assist in the decision making of reproduction strategies in dairy farms.

Estimated genetic parameters for all genetically evaluated traits in Canadian Holsteins.

Genetic improvement is a crucial tool to deal with the increasing demand for high quality, sustainably produced dairy. Breeding programs are based on genetic parameters, such as heritability and genetic correlations, for economically important traits in a population. In this study, we estimated population genetic parameters and genetic trends for 67 traits evaluated on heifers and first-lactation Canadian Holstein cows. The data consisted of approximately 500,000 records with pedigree information collected from 1980 to 2019. Genetic parameters were estimated using bivariate linear animal models under a Bayesian approach. Analyses for the 67 traits resulted in 2,211 bivariate combinations, from which the estimated genetic parameters are reported here. The most highly heritable traits were fat percent (0.66) and protein percent (0.69), followed by stature (0.47). Lowest heritabilities (0.01) were observed for disease-related traits, such as lameness and toe ulcer, and calf survival. The genetic correlations between gestation length, calf size, and calving ease measured on both heifer and cows were close to unity. On the other hand, traits such as body condition score and pin width, cystic ovaries and sole ulcer, rear teat placement, and toe ulcer were genetically unrelated. This study reports genetic parameters that have not been previously published for Canadian Holstein cows, and provides updates of those previously estimated. These estimates are useful for building new indexes, updating existing selection indexes, and for predicting correlated responses due to inclusion of novel traits in the breeding programs.

Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach.

Deviation from Mendelian inheritance expectations (transmission ratio distortion, TRD) has been observed in several species, including the mouse and humans. In this study, TRD was characterized in the turkey genome using both allelic (specific- and unspecific-parent TRD) and genotypic (additive- and dominance-TRD) parameterizations within a Bayesian framework. In this study, we evaluated TRD for 23 243 genotyped Turkeys across 56 393 autosomal SNPs. The analyses included 500 sires, 2013 dams and 11 047 offspring (trios). Three different haplotype sliding windows of 4, 10 and 20 SNPs were used across the autosomal chromosomes. Based on the genotypic parameterizations, 14 haplotypes showed additive and dominance TRD effects highlighting regions with a recessive TRD pattern. In contrast, the allelic model uncovered 12 haplotype alleles with the allelic TRD pattern which showed an underrepresentation of heterozygous offspring in addition to the absence of homozygous animals. For regions with the allelic pattern, only one particular region showed a parent-specific TRD where the penetrance was high via the dam, but low via the sire. The gene set analysis uncovered several gene ontology functional terms, Reactome pathways and several Medical Subject Headings that showed significant enrichment of genes associated with TRD. Many of these gene ontology functional terms (e.g. mitotic spindle assembly checkpoint, DRM complex and Aneuploidy), Reactome pathways (e.g. Mismatch repair) and Medical Subject Headings (e.g. Adenosine monophosphate) are known to be related to fertility, embryo development and lethality. The results of this study revealed potential novel candidate lethal haplotypes, functional terms and pathways that may enhance breeding programs in Turkeys through reducing mortality and improving reproduction rate.

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-1ß, 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.

Symposium review: The choice and collection of new relevant phenotypes for fertility selection.

In dairy production, high fertility contributes to herd profitability by achieving greater production and maintaining short calving intervals. Improved management practices and genetic selection have contributed to reversing negative trends in dairy cow fertility, but further progress is still required. Phenotypes included in current genetic evaluations are largely interval and binary traits calculated from insemination and calving date records. Several indicator traits such as calving, health, variation in body condition score, and longevity traits also apply to genetic improvement of fertility. Several fertility traits are included in the selection indices of many countries, but for improved selection, the development of novel phenotypes that more closely describe the physiology of reproduction and limit management bias could be more effective. Progesterone-based phenotypes can be determined from milk samples to describe the heritable interval from calving to corpus luteum activity, as well as additional measures of cow cyclicity. A fundamental component of artificial insemination practices is the observation of estrus. Novel phenotypes collected on estrous activity could be used to select for cows clearly displaying heat, as those cows are more likely to be inseminated at the right time and therefore have greater fertility performance. On-farm technologies, including in-line milk testing and activity monitors, may allow for phenotyping novel traits on large numbers of animals. Additionally, selection for improved fertility using traditional traits could benefit from refined and accurate recording and implementation of parameters such as pregnancy confirmation and reproductive management strategy, to differentiate embryonic or fetal loss, and to ensure selection for reproductive capability without producer intervention. Opportunities exist to achieve genetic improvement of reproductive efficiency in cattle using novel phenotypes, which is required for long-term sustainability of the dairy cattle population and industry.

Genetics and genomics of reproductive disorders in Canadian Holstein cattle.

In Canada, reproductive disorders known to affect the profitability of dairy cattle herds have been recorded by producers on a voluntary basis since 2007. Previous studies have shown the feasibility of using producer-recorded health data for genetic evaluations. Despite low heritability estimates and limited availability of phenotypic information, sufficient genetic variation has been observed for those traits to indicate that genetic progress, although slow, can be achieved. Pedigree- and genomic-based analyses were performed on producer-recorded health data of reproductive disorders, including retained placenta (RETP), metritis (METR), and cystic ovaries (CYST) using traditional BLUP and single-step genomic BLUP. Genome-wide association studies and functional analyses were carried out to unravel significant genomic regions and biological pathways, and to better understand the genetic mechanisms underlying RETP, METR, and CYST. Heritability estimates (posterior standard deviation in parentheses) were 0.02 (0.003), 0.01 (0.004), and 0.02 (0.003) for CYST, METR, and RETP, respectively. A moderate to strong genetic correlation of 0.69 (0.102) was found between METR and RETP. Averaged over all traits, sire proof reliabilities increased by approximately 11 percentage points with the incorporation of genomic data using a multiple-trait linear model. Biological pathways and associated genes underlying the studied traits were identified and will contribute to a better understanding of the biology of these 3 health disorders in dairy cattle.

Efficiency of different selection strategies against boar taint in pigs.

The breeding scheme of a Swiss sire line was modeled to compare different target traits and information sources for selection against boar taint. The impact of selection against boar taint on production traits was assessed for different economic weights of boar taint compounds. Genetic gain and breeding costs were evaluated using ZPlan+, a software based on selection index theory, gene flow method and economic modeling. Scenario I reflected the currently practiced breeding strategy as a reference scenario without selection against boar taint. Scenario II incorporated selection against the chemical compounds of boar taint, androstenone (AND), skatole (SKA) and indole (IND) with economic weights of -2.74, -1.69 and -0.99 Euro per unit of the log transformed trait, respectively. As information sources, biopsy-based performance testing of live boars (BPT) was compared with genomic selection (GS) and a combination of both. Scenario III included selection against the subjectively assessed human nose score (HNS) of boar taint. Information sources were either station testing of full and half sibs of the selection candidate or GS against HNS of boar taint compounds. In scenario I, annual genetic gain of log-transformed AND (SKA; IND) was 0.06 (0.09; 0.02) Euro, which was because of favorable genetic correlations with lean meat percentage and meat surface. In scenario II, genetic gain increased to 0.28 (0.20; 0.09) Euro per year when conducting BPT. Compared with BPT, genetic gain was smaller with GS. A combination of BPT and GS only marginally increased annual genetic gain, whereas variable costs per selection candidate augmented from 230 Euro (BPT) to 330 Euro (GS) or 380 Euro (both). The potential of GS was found to be higher when selecting against HNS, which has a low heritability. Annual genetic gain from GS was higher than from station testing of 4 full sibs and 76 half sibs with one or two measurements. The most effective strategy to reduce HNS was selecting against chemical compounds by conducting BPT. Because of heritabilities higher than 0.45 for AND, SKA and IND and high genetic correlations to HNS, the (correlated) response in units of the trait could be increased by 62% compared with scenario III with GS and even by 79% compared with scenario III, with station testing of siblings with two measurements. Increasing the economic weights of boar taint compounds amplified negative effects on average daily gain, drip loss and intramuscular fat percentage.

A performance test for boar taint compounds in live boars.

Genetically reducing boar taint using low-taint lines is considered the most sustainable and economic long-term alternative to surgical castration of male pigs. Owing to the high heritability of the main boar taint components (androstenone, skatole and indole), breeding is an excellent tool for reducing the number of tainted carcasses. To incorporate boar taint into breeding programmes, standardized performance testing is required. The objective of this study was to develop and formally present a performance test for the main boar taint compounds on live breeding candidates. First, a standardized performance test for boar taint was established. A biopsy device was developed to extract small tissue samples (200 to 300 mg) from breeding candidates. Quantification of boar taint components from these small samples using specialized chemical extraction methods proved accurate and repeatable (r = 0.938). Following establishment of the method, biopsy samples of 516 live boars (100 to 130 kg live weight) were collected in the second step. Various mixed linear models were tested for each boar taint compound; models were ranked in terms of their information content. Pedigree information of 2245 ancestors of biopsied animals was included, and genetic parameters were estimated using univariate and multivariate models. Androstenone (in µg/g liquid fat (LF): mean = 0.578, σ = 0.527), skatole (in µg/g LF: mean = 0.033, σ = 0.002) and indole (in µg/g LF: mean = 0.032, σ = 0.002) levels obtained by biopsy were plausible. Heritability estimates for androstenone calculated with univariate (0.453) and multivariate (0.452) analyses were comparable to those in the literature. Heritabilities for skatole (0.495) and indole (0.550) were higher than that for androstenone. Genetic and phenotypic correlations were similar to those published previously. Our results show that data on boar taint compounds from small adipose samples obtained by biopsy provide similar genetic parameters as that described in the literature for larger samples and are therefore a reliable performance test for boar taint in live breeding candidates.