Distortion of Mendelian segregation across the Angus cattle genome uncovering regions affecting reproduction.

Nowadays, the availability of genotyped trios (sire-dam-offspring) in the livestock industry enables the implementation of the transmission ratio distortion (TRD) approach to discover deleterious alleles in the genome. Various biological mechanisms at different stages of the reproductive cycle such as gametogenesis, embryo development and postnatal viability can induce signals of TRD (i.e., deviation from Mendelian inheritance expectations). In this study, TRD was evaluated using both SNP-by-SNP and sliding windows of 2-, 4-, 7-, 10- and 20-SNP across 92,942 autosomal SNPs for 258,140 genotyped Angus cattle including 7,486 sires, 72,688 dams and 205,966 offspring. Transmission ratio distortion was characterized using allelic (specific- and unspecific-parent TRD) and genotypic parameterizations (additive- and dominance-TRD). Across the Angus autosomal chromosomes, 851 regions were clearly found with decisive evidence for TRD. Among these findings, 19 haplotypes with recessive patterns (potential lethality for homozygote individuals) and 52 regions with allelic patterns exhibiting complete or quasi-complete absence for homozygous individuals in addition to under-representation (potentially reduced viability) of the carrier (heterozygous) offspring were found. In addition, 64 (12) and 20 (4) regions showed significant influence on the trait heifer pregnancy at p-value < 0.05 (after chromosome-wise false discovery rate) and 0.01, respectively, reducing the pregnancy rate up to 15%, thus, supporting the biological importance of TRD phenomenon in reproduction.

Single-step genomic predictions for heat tolerance of production yields in US Holsteins and Jerseys.

The physiological stress caused by excessive heat affects dairy cattle health and production. This study sought to investigate the effect of heat stress on test-day yields in US Holstein and Jersey cows and develop single-step genomic predictions to identify heat tolerant animals. Data included 12.8 million and 2.1 million test-day records, respectively, for 923,026 Holstein and 153,710 Jersey cows in 27 US states. From 2015 through 2021, test-day records from the first 5 lactations included milk, fat, and protein yields (kg). Cow records were included if they had at least 5 test-day records per lactation. Heat stress was quantified by analyzing the effect of a 5-d hourly average temperature-humidity index (THI5d¯) on observed test-day yields. Using a multiple trait repeatability model, a heat threshold (THI threshold) was determined fowr each breed based on the point that the average adjusted yields started to decrease, which was 69 for Holsteins and 72 for Jerseys. An additive genetic component of general production and heat tolerance production were estimated using a multiple trait reaction norm model and single-step genomic BLUP methodology. Random effects were regressed on a function of 5-d hourly average (THI5d¯) and THI threshold. The proportion of test-day records that occurred on or above the respective heat thresholds was 15% for Holstein and 10% for Jersey. Heritability of milk, fat, and protein yields under heat stress for Holsteins increased, with a small standard error, indicating that the additive genetic component for heat tolerance of these traits was observed. This was not as evident in Jersey traits. For Jersey, the permanent environment explained the same or more of the variation in fat and protein yield under heat stress indicating that nongenetic factors may determine heat tolerance for these Jersey traits. Correlations between the general genetic merit of production (in the absence of heat stress) and heat tolerance genetic merit of production traits were moderate in strength and negative. This indicated that selecting for general genetic merit without consideration of heat tolerance genetic merit of production may result in less favorable performance in hot and humid climates. A general genomic estimated breeding value for genetic merit and a heat tolerance genomic estimated breeding value were calculated for each animal. This study contributes to the investigation of the impact of heat stress on US dairy cattle production yields and offers a basis for the implementation of genomic selection. The results indicate that genomic selection for heat tolerance of production yields is possible for US Holsteins and Jerseys, but a study to validate the genomic predictions should be explored.

Genome-wide association analysis for ß-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 ß-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.

Use of a single-step approach for integrating foreign information into national genomic evaluation in Holstein cattle.

The use of multi-trait across-country evaluation (MACE) and the exchange of genomic information among countries allows national breeding programs to combine foreign and national data to increase the size of the training populations and potentially increase accuracy of genomic prediction of breeding values. By including genotyped and nongenotyped animals simultaneously in the evaluation, the single-step genomic BLUP (GBLUP) approach has the potential to deliver more accurate and less biased genomic evaluations. A single-step genomic BLUP approach, which enables integration of data from MACE evaluations, can be used to obtain genomic predictions while avoiding double-counting of information. The objectives of this study were to apply a single-step approach that simultaneously includes domestic and MACE information for genomic evaluation of workability traits in Canadian Holstein cattle, and compare the results obtained with this methodology with those obtained using a multi-step approach (msGBLUP). By including MACE bulls in the training population, msGBLUP led to an increase in reliability of genomic predictions of 4.8 and 15.4% for milking temperament and milking speed, respectively, compared with a traditional evaluation using only pedigree and phenotypic information. Integration of MACE data through a single-step approach (ssGBLUPIM) yielded the highest reliabilities compared with other considered methods. Integration of MACE data also helped reduce bias of genomic predictions. When using ssGBLUPIM, the bias of genomic predictions decreased by half compared with msGBLUP using domestic and MACE information. Therefore, the reliability and bias of genomic predictions for both traits improved substantially when a single-step approach was used for evaluation compared with a multi-step approach. The use of a single-step approach with integration of MACE information provides an alternative to the current method used in Canadian genomic evaluations.

Estimating the effect of the deleterious recessive haplotypes AH1 and AH2 on reproduction performance of Ayrshire cattle.

The effects of 2 deleterious recessive haplotypes on reproduction performance of Ayrshire cattle, Ayrshire Haplotype 1 (AH1) and Ayrshire Haplotype 2 (AH2), were investigated in Canadian Ayrshire cattle. We calculated their phenotypic effects on stillbirth (SB) rate and 56-d nonreturn rate (NRR) by estimating the interaction of service sire carrier status with maternal grandsire carrier status using the official Canadian evaluation models for those 2 traits. The interaction term included 9 subclasses for the 3 possible statuses of each bull: haplotype carrier, noncarrier, or not genotyped. For AH1, 394 carriers and 1,433 noncarriers were available, whereas 313 carriers and 1,543 noncarriers were available for the AH2 haplotype. The number of matings considered for SB was 34,312 for heifers (first parity) and 115,935 for cows (later parities). For NRR, 49,479 matings for heifers and 160,528 for cows were used to estimate the haplotype effects. We observed a negative effect of AH1 on SB rates, which was 2.0% higher for matings of AH1-carrier sires to dams that had an AH1-carrier sire; this effect was found for both heifers and cows. However, AH1 had small, generally nonsignificant effects on NRR. The AH2 haplotype had a substantial negative effect on NRR, with 5.1% more heifers and 4.0% more cows returning to service, but the effects on SB rates were inconsistent and mostly small effects. Our results validate the harmful effects of AH1 and AH2 on reproduction traits in the Canadian Ayrshire population. This information will be of great interest for the dairy industry, allowing producers to make mating decisions that would reduce reproductive losses.

Implementation of Bayesian methods to identify SNP and haplotype regions with transmission ratio distortion across the whole genome: TRDscan v.1.0.

Realized deviations from the expected Mendelian inheritance of alleles from heterozygous parents have been previously reported in a broad range of organisms (i.e., transmission ratio distortion; TRD). Various biological mechanisms affecting gametes, embryos, fetuses, or even postnatal offspring can produce patterns of TRD. However, knowledge about its prevalence and potential causes in livestock species is still scarce. Specific Bayesian models have been recently developed for the analyses of TRD for biallelic loci, which accommodated a wide range of population structures, enabling TRD investigation in livestock populations. The parameterization of these models is flexible and allows the study of overall (parent-unspecific) TRD and sire- and dam-specific TRD. This research aimed at deriving Bayesian models for fitting TRD on the basis of haplotypes, testing the models for both haplotype- and SNP-based methods in simulated data and actual Holstein genotypes, and developing a specific software for TRD analyses. Results obtained on simulated data sets showed that the statistical power of the analysis increased with sample size of trios (n), proportion of heterozygous parents, and the magnitude of the TRD. On the other hand, the statistical power to detect TRD decreased with the number of alleles at each loci. Bayesian analyses showed a strong Pearson correlation coefficient (≥0.97) between simulated and estimated TRD that reached the significance level of Bayes factor ≥10 for both single-marker and haplotype analyses when n ≥ 25. Moreover, the accuracy in terms of the mean absolute error decreased with the increase of the sample size and increased with the number of alleles at each loci. Using real data (55,732 genotypes of Holstein trios), SNP- and haplotype-based distortions were detected with overall TRD, sire-TRD, or dam-TRD, showing different magnitudes of TRD and statistical relevance. Additionally, the haplotype-based method showed more ability to capture TRD compared with individual SNP. To discard possible random TRD in real data, an approximate empirical null distribution of TRD was developed. The program TRDscan v.1.0 was written in Fortran 2008 language and provides a powerful statistical tool to scan for TRD regions across the whole genome. This developed program is freely available at http://www.casellas.info/files/TRDscan.zip.

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.

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.

Relationships of nutritional plane and feed efficiency with sexual development and fertility related measures in young beef bulls.

Sexual development in beef bulls appears to be influenced by nutritional plane and feed efficiency. Yearling bulls fed high (GRAIN = 49) and moderate (ROUGHAGE = 109) nutritional planes, were submitted to a performance test where scrotal circumference (SC), scrotum and testis ultrasonograms and hormones were monitored throughout. Scrotal thermographs, blood cell counts and semen were evaluated at the end of the test. Residual feed intake (RFI) was the measure of feed efficiency, and bulls within each population were characterized as efficient and inefficient. During the test period, the GRAIN group had greater triiodothyronine (T3), leptin and scrotal skin thickness (SST) while having greater T3, leptin, % motile sperm, % normal sperm, scrotal temperature and values for red blood cell variables at the end of the test when compared to the ROUGHAGE group. During the test, the efficient GRAIN group had lesser testis pixel intensity while at the end of the performance test the bulls of this group had greater % normal sperm and lower testis pixel intensity compared to bulls in inefficient GRAIN group. In comparison, the efficient ROUGHAGE group had less T3, SC and SST while at the end of the test these bulls had less T3, leptin, SC, SST and scrotal temperature compared to bulls in the inefficient ROUGHAGE group. Complete blood cell variables, semen quality, scrotal biometry and thermography explained most of the variation in RFI. Results of the present study support the hypothesis that there is an antagonistic relationship between feed efficiency and sexual development in young bulls, which seems partially offset when there is a greater plane of nutrition. Thus, feed efficiency should be factored in the reproductive evaluation of sires.

The genetic architecture of milk ELISA scores as an indicator of Johne's disease (paratuberculosis) in dairy cattle.

Johne's disease (or paratuberculosis), caused by Mycobacterium avium ssp. paratuberculosis (MAP) infection, is a globally prevalent disease with severe economic and welfare implications. With no effective treatment available, understanding the role of genetics influencing host infection status is essential to develop selection strategies to breed for increased resistance to MAP infection. The main objectives of this study were to estimate genetic parameters for the MAP-specific antibody response using milk ELISA scores in Canadian Holstein cattle as an indicator of resistance to Johne's disease, and to unravel genomic regions and candidate genes significantly associated with MAP infection. After data editing, 168,987 milk ELISA records from 2,306 herds, obtained from CanWest Dairy Herd Improvement, were used for further analyses. Variance and heritability estimates for MAP infection status were determined using univariate linear animal models under 3 scenarios: (a) SCEN1: the complete data set (all herds); (b) SCEN2: herds with at least one suspect or test-positive animal (ELISA optical density ≥0.07); and (c) SCEN3: herds with at least one test-positive animal (ELISA optical density ≥0.11). Heritability estimates were calculated as 0.066, 0.064, and 0.063 for SCEN1, SCEN2, and SCEN3, respectively. The correlations between estimated breeding values for resistance to MAP infection and other economically important traits, when significant, were favorable and of low magnitude. Genome-wide association analyses identified important genomic regions on Bos taurus autosome (BTA)1, BTA7, BTA9, BTA14, BTA15, BTA17, BTA19, and BTA25 showing significant association with MAP infection status. These regions included 2 single nucleotide polymorphisms located 2 kb upstream of positional candidate genes CD86 and WNT9B, which play key roles in host immune response and tissue homeostasis. This study revealed the genetic architecture of MAP infection in Canadian Holstein cattle as measured by milk ELISA scores by estimating genetic parameters along with the identification of genomic regions potentially influencing MAP infection status. These findings will be of significant value toward implementing genetic and genomic evaluations for resistance to MAP infection in Holstein cattle.

Comparison of genomic predictions for lowly heritable traits using multi-step and single-step genomic best linear unbiased predictor in Holstein cattle.

The success and sustainability of a breeding program incorporating genomic information is largely dependent on the accuracy of predictions. For low heritability traits, large training populations are required to achieve high accuracies of genomic estimated breeding values (GEBV). By including genotyped and nongenotyped animals simultaneously in the evaluation, the single-step genomic BLUP (ssGBLUP) approach has the potential to deliver more accurate and less biased genomic evaluations. The aim of this study was to compare the accuracy and bias of genomic predictions for various traits in Canadian Holstein cattle using ssGBLUP and multi-step genomic BLUP (msGBLUP) under different strategies, such as (1) adding genomic information of cows in the analysis, (2) testing different adjustments of the genomic relationship matrix, and (3) using a blending approach to obtain GEBV from msGBLUP. The following genomic predictions were evaluated regarding accuracy and bias: (1) GEBV estimated by ssGBLUP; (2) direct genomic value estimated by msGBLUP with polygenic effects of 5 and 20%; and (3) GEBV calculated by a blending approach of direct genomic value with estimated breeding values using polygenic effects of 5 and 20%. The effect of adding genomic information of cows in the evaluation was also assessed for each approach. When genomic information was included in the analyses, the average improvement in observed reliability of predictions was observed to be 7 and 13 percentage points for reproductive and workability traits, respectively, compared with traditional BLUP. Absolute deviation from 1 of the regression coefficient of the linear regression of de-regressed estimated breeding values on genomic predictions went from 0.19 when using traditional BLUP to 0.22 when using the msGBLUP method, and to 0.14 when using the ssGBLUP method. The use of polygenic weight of 20% in the msGBLUP slightly improved the reliability of predictions, while reducing the bias. A similar trend was observed when a blending approach was used. Adding genomic information of cows increased reliabilities, while decreasing bias of genomic predictions when using the ssGBLUP method. Differences between using a training population with cows and bulls or with only bulls for the msGBLUP method were small, likely due to the small number of cows included in the analysis. Predictions for lowly heritable traits benefit greatly from genomic information, especially when all phenotypes, pedigrees, and genotypes are used in a single-step approach.

Short communication: Uncovering quantitative trait loci associated with resistance to Mycobacterium avium ssp. paratuberculosis infection in Holstein cattle using a high-density single nucleotide polymorphism panel.

Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of Johne's disease in cattle. Johne's disease is a disease of significant economic, animal welfare, and public health concern around the globe. Therefore, understanding the genetic architecture of resistance to MAP infection has great relevance to advance genetic selection methods to breed more resistant animals. The objectives of this study were to perform a genome-wide association study of previously analyzed 50K genotypes now imputed to a high-density single nucleotide polymorphism panel (777K), aiming to validate previously reported associations and potentially identify additional single nucleotide polymorphisms associated with antibody response to MAP infection. A principal component regression-based genome-wide association study revealed 15 putative quantitative trait loci (QTL) associated with the MAP infection phenotype (serum or milk ELISA tests) on 9 different chromosomes (Bos taurus autosomes 5, 6, 7, 10, 14, 15, 16, 20, and 21). These results validated previous findings and identified new QTL on Bos taurus autosomes 15, 16, 20, and 21. The positional candidate genes NLRP3, IFi47, TRIM41, TNFRSF18, and TNFRSF4 lying within these QTL were identified. Further functional validation of these genes is now warranted to investigate their roles in regulating the immune response and, consequently, cattle resistance to MAP infection.

Genome-wide association study and in silico functional analysis of the number of embryos produced by Holstein donors.

Superovulation or ovum pick-up and in vitro fertilization are technologies used to produce an increased number of embryos from elite females. Embryo production traits have been shown to be heritable, but the genes that cause this variability have not yet been assessed. The main objectives of this study were to perform a genome-wide association study (GWAS) to find single nucleotide polymorphisms (SNP) associated with embryo production traits and to identify candidate genes affecting the number of embryos produced by Holstein donors in Canada that may provide insight into the regulation of embryo production. Breeding values were estimated and de-regressed for all donors and sires using a data set of 150,971 records of superovulation or ovum pick-up and in vitro fertilization. A total of 11,607 animals were genotyped, but of that number only 5,118 were genotyped with at least a 50K SNP panel and had a de-regressed estimated breeding value reliability of at least 10%. For the GWAS, 606,406 imputed SNP on 29 autosomal chromosomes were considered after applying quality control measures. A single-SNP univariate mixed linear animal model was used to perform the GWAS, and a 5% false discovery rate was applied to adjust for multiple testing. We found 36 and 14 significant SNP associated with the total number of embryos and the number of viable embryos, respectively, with most of them located on chromosome 11. Using these significant SNP, positional genes located within 10,000 bp upstream and downstream of the SNP were retrieved. Thirteen genes were harboring or near the significant SNP for the total number of embryos, 4 of them also being near the significant SNP for viable embryos. Some of these genes (CRB2, DENND1A, MAD1L1, NDUFA8, PTGS1) could be considered as potential positional candidate genes related to the number of embryos produced by a donor. This list will need to be validated in an independent population to confirm the role of the genes for embryo production.

The effect of using cow genomic information on accuracy and bias of genomic breeding values in a simulated Holstein dairy cattle population.

Using cow data in the training population is attractive as a way to mitigate bias due to highly selected training bulls and to implement genomic selection for countries with no or limited proven bull data. However, one potential issue with cow data is a bias due to the preferential treatment. The objectives of this study were to (1) investigate the effect of including cow genotype and phenotype data into the training population on accuracy and bias of genomic predictions and (2) assess the effect of preferential treatment for different proportions of elite cows. First, a 4-pathway Holstein dairy cattle population was simulated for 2 traits with low (0.05) and moderate (0.3) heritability. Then different numbers of cows (0, 2,500, 5,000, 10,000, 15,000, or 20,000) were randomly selected and added to the training group composed of different numbers of top bulls (0, 2,500, 5,000, 10,000, or 15,000). Reliability levels of de-regressed estimated breeding values for training cows and bulls were 30 and 75% for traits with low heritability and were 60 and 90% for traits with moderate heritability, respectively. Preferential treatment was simulated by introducing upward bias equal to 35% of phenotypic variance to 5, 10, and 20% of elite bull dams in each scenario. Two different validation data sets were considered: (1) all animals in the last generation of both elite and commercial tiers (n = 42,000) and (2) only animals in the last generation of the elite tier (n = 12,000). Adding cow data into the training population led to an increase in accuracy (r) and decrease in bias of genomic predictions in all considered scenarios without preferential treatment. The gain in r was higher for the low heritable trait (from 0.004 to 0.166 r points) compared with the moderate heritable trait (from 0.004 to 0.116 r points). The gain in accuracy in scenarios with a lower number of training bulls was relatively higher (from 0.093 to 0.166 r points) than with a higher number of training bulls (from 0.004 to 0.09 r points). In this study, as expected, the bull-only reference population resulted in higher accuracy compared with the cow-only reference population of the same size. However, the cow reference population might be an option for countries with a small-scale progeny testing scheme or for minor breeds in large counties, and for traits measured only on a small fraction of the population. The inclusion of preferential treatment to 5 to 20% of the elite cows led to an adverse effect on both accuracy and bias of predictions. When preferential treatment was present, random selection of cows did not reduce the effect of preferential treatment.

Genetic correlations of mid-infrared-predicted milk fatty acid groups with milk production traits.

The objective of this research was to estimate the genetic correlations between milk mid-infrared-predicted fatty acid groups and production traits in first-parity Canadian Holsteins. Contents of short-chain, medium-chain, long-chain, saturated, and unsaturated fatty acid groupings in milk samples can be predicted using mid-infrared spectral data for cows enrolled in milk recording programs. Predicted fatty acid group contents were obtained for 49,127 test-day milk samples from 10,029 first-parity Holstein cows in 810 herds. Milk yield, fat and protein yield, fat and protein percentage, fat-to-protein ratio, and somatic cell score were also available for these test days. Genetic parameters were estimated for the fatty acid groups and production traits using multiple-trait random regression test day models by Bayesian methods via Gibbs sampling. Three separate 8- or 9-trait analyses were performed, including the 5 fatty acid groups with different combinations of the production traits. Posterior standard deviations ranged from <0.001 to 0.01. Average daily genetic correlations were negative and similar to each other for the fatty acid groups with milk yield (-0.62 to -0.59) and with protein yield (-0.32 to -0.25). Weak and positive average daily genetic correlations were found between somatic cell score and the fatty acid groups (from 0.25 to 0.36). Stronger genetic correlations with fat yield, fat and protein percentage, and fat-to-protein ratio were found with medium-chain and saturated fatty acid groups compared with those with long-chain and unsaturated fatty acid groups. Genetic correlations were very strong between the fatty acid groups and fat percentage, ranging between 0.88 for unsaturated and 0.99 for saturated fatty acids. Daily genetic correlations from 5 to 305 d in milk with milk, protein yield and percentage, and somatic cell score traits showed similar patterns for all fatty acid groups. The daily genetic correlations with fat yield at the beginning of lactation were decreasing for long-chain and unsaturated fatty acid groups and increasing for short-chain fatty acids. Genetic correlations between fat percentage and fatty acids were increasing at the beginning of lactation for short- and medium-chain and saturated fatty acids, but slightly decreasing for long-chain and unsaturated fatty acid groups. These results can be used in defining fatty acid traits and breeding objectives.

Imputation of non-genotyped sheep from the genotypes of their mates and resulting progeny.

Accurate genomic analyses are predicated on access to a large quantity of accurately genotyped and phenotyped animals. Because the cost of genotyping is often less than the cost of phenotyping, interest is increasing in generating genotypes for phenotyped animals. In some instances this may imply the requirement to genotype older animals with greater phenotypic information content. Biological material for these older informative animals may, however, no longer exist. The objective of the present study was to quantify the ability to impute 11 129 single nucleotide polymorphism (SNP) genotypes of non-genotyped animals (in this instance sires) from the genotypes of their progeny with or without including the genotypes of the progenys' dams (i.e. mates of the sire to be imputed). The impact on the accuracy of genotype imputation by including more progeny (and their dams') genotypes in the imputation reference population was also quantified. When genotypes of the dams were not available, genotypes of 41 sires with at least 15 genotyped progeny were used for the imputation; when genotypes of the dams were available, genotypes of 21 sires with at least 10 genotyped progeny were used for the imputation. Imputation was undertaken exploiting family and population level information. The mean and variability in the proportion of genotypes per individual that could not be imputed reduced as the number of progeny genotypes used per individual increased. Little improvement in the proportion of genotypes that could not be imputed was achieved once genotypes of seven progeny and their dams were used or genotypes of 11 progeny without their respective dam's genotypes were used. Mean imputation accuracy per individual (depicted by both concordance rates and correlation between true and imputed) increased with increasing progeny group size. Moreover, the range in mean imputation accuracy per individual reduced as more progeny genotypes were used in the imputation. If the genotype of the mate of the sire was also used, high accuracy of imputation (mean genotype concordance rate per individual of 0.988), with little additional benefit thereafter, was achieved with seven genotyped progeny. In the absence of genotypes on the dam, similar imputation accuracy could not be achieved even using genotypes on up to 15 progeny. Results therefore suggest, at least for the SNP density used in the present study, that it is possible to accurately impute the genotypes of a non-genotyped parent from the genotypes of its progeny and there is a benefit of also including the genotype of the sire's mate (i.e. dam of the progeny).

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.

Genome-wide association study of cell-mediated immune response in chicken.

Cell-mediated immunity (CMI) causes the intracellular destruction of the antigen or elimination of the host cell to make animals resistant against exogenous antigens and cancers. In this study, a genome-wide association study (GWAS) was carried out to identify genomic regions associated with CMI in chicken using chicken 60k high-density single nucleotide polymorphism (SNP) array. Genomic relationships were taken into account to adjust for population structure. In order to account for multiple testing, chromosome-wise false discovery rate was controlled at 5% and 10% levels. Moreover, a comparison of the power of fixed and mixed linear models based on genomic inflation factor was carried out. Mixed linear model (MLM) had better inflation rate, and therefore the results from MLM were used for subsequent analysis. Three significantly associated SNPs (FDR < 0.05) on chromosome 24 and linkage group E22C19W28_E50C23, and three suggestively associated SNPs (FDR < 0.1) on chromosome 1, 5 and 16 were identified. Pathway analysis showed that two biological pathways, which are related to immune response, were strongly associated with the candidate genes surrounding identified SNPs, and their influences were mostly on antigen processing and presentation, and cellular structure.

Heritabilities of measured and mid-infrared predicted milk fat globule size, milk fat and protein percentages, and their genetic correlations.

The objective of this study was to estimate the heritability of milk fat globule (MFG) size and mid-infrared (MIR) predicted MFG size in Holstein cattle. The genetic correlations between measured and predicted MFG size with milk fat and protein percentage were also investigated. Average MFG size was measured in 1,583 milk samples taken from 254 Holstein cows from 29 herds across Canada. Size was expressed as volume moment mean (D[4,3]) and surface moment mean (D[3,2]). Analyzed milk samples also had average MFG size predicted from their MIR spectral records. Fat and protein percentages were obtained for all test-day milk samples in the cow's lactation. Univariate and bivariate repeatability animal models were used to estimate heritability and genetic correlations. Moderate heritabilities of 0.364 and 0.466 were found for D[4,3] and D[3,2], respectively, and a strong genetic correlation was found between the 2 traits (0.98). The heritabilities for the MIR-predicted MFG size were lower than those estimated for the measured MFG size at 0.300 for predicted D[4,3] and 0.239 for predicted D[3,2]. The genetic correlation between measured and predicted D[4,3] was 0.685; the correlation was slightly higher between measured and predicted D[3,2] at 0.764, likely due to the better prediction accuracy of D[3,2]. Milk fat percentage had moderate genetic correlations with both D[4,3] and D[3,2] (0.538 and 0.681, respectively). The genetic correlation between predicted MFG size and fat percentage was much stronger (greater than 0.97 for both predicted D[4,3] and D[3,2]). The stronger correlation suggests a limitation for the use of the predicted values of MFG size as indicator traits for true average MFG size in milk in selection programs. Larger samples sizes are required to provide better evidence of the estimated genetic parameters. A genetic component appears to exist for the average MFG size in bovine milk, and the variation could be exploited in selection programs.

Genetic analysis of groups of mid-infrared predicted fatty acids in milk.

The objective of this study was to investigate genetic variability of mid-infrared predicted fatty acid groups in Canadian Holstein cattle. Genetic parameters were estimated for 5 groups of fatty acids: short-chain (4 to 10 carbons), medium-chain (11 to 16 carbons), long-chain (17 to 22 carbons), saturated, and unsaturated fatty acids. The data set included 49,127 test-day records from 10,029 first-lactation Holstein cows in 810 herds. The random regression animal test-day model included days in milk, herd-test date, and age-season of calving (polynomial regression) as fixed effects, herd-year of calving, animal additive genetic effect, and permanent environment effects as random polynomial regressions, and random residual effect. Legendre polynomials of the third degree were selected for the fixed regression for age-season of calving effect and Legendre polynomials of the fourth degree were selected for the random regression for animal additive genetic, permanent environment, and herd-year effect. The average daily heritability over the lactation for the medium-chain fatty acid group (0.32) was higher than for the short-chain (0.24) and long-chain (0.23) fatty acid groups. The average daily heritability for the saturated fatty acid group (0.33) was greater than for the unsaturated fatty acid group (0.21). Estimated average daily genetic correlations were positive among all fatty acid groups and ranged from moderate to high (0.63-0.96). The genetic correlations illustrated similarities and differences in their origin and the makeup of the groupings based on chain length and saturation. These results provide evidence for the existence of genetic variation in mid-infrared predicted fatty acid groups, and the possibility of improving milk fatty acid profile through genetic selection in Canadian dairy cattle.