Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows.

The aims of this study were to conduct a single-step genome-wide association to identify genomic regions associated with milk urea (MU) and to estimate genetic correlations between MU and milk yield (MY), milk composition (calcium content [CC], fat percentage [FP], protein percentage [PP], and casein percentage [CNP]), and cheese-making properties (CMP; coagulation time [CT], curd firmness after 30 min from rennet addition [a30], and titratable acidity [TA]). The used data have been collected from 2015 to 2020 on 78,073 first-parity (485,218 test-day records) and 48,766 second-parity (284,942 test-day records) Holstein cows distributed in 671 herds in the Walloon Region of Belgium. Data of 565,533 SNP located on 29 BTA of 6,617 animals (1,712 males) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of ∼216 kb) was calculated, and the top-3 genomic regions explaining the largest rate of the genetic variance were considered promising regions and used to identify potential candidate genes. Mean (SD) MU was 25.38 (8.02) mg/dL and 25.03 (8.06) mg/dL in the first and second lactation, respectively. Mean heritability estimates for daily MU were 0.21 and 0.23 for the first and second lactation, respectively. The genetic correlations estimated between MU and MY, milk composition, and CMP were quite low (ranged from -0.10 [CC] to 0.10 [TA] and -0.05 [CT] to 0.13 [TA] for the first and second lactations, respectively). The top-3 regions associated with MU were located from 80.61 to 80.74 Mb on BTA6, 103.26 to 103.41 Mb on BTA11, and 1.59 to 2.15 Mb on BTA14. Genes including KCNT1, MROH1, SHARPIN, TSSK5, CPSF1, HSF1, TONSL, DGAT1, SCX, and MAF1 were identified as positional candidate genes for MU. The findings of this study can be used for a better understanding of the genomic architecture underlying MU in Holstein cattle.

Single-step genome-wide association analyses for selected infrared-predicted cheese-making traits in Walloon Holstein cows.

This study aimed to perform genome-wide association study to identify genomic regions associated with milk production and cheese-making properties (CMP) in Walloon Holstein cows. The studied traits were milk yield, fat percentage, protein percentage, casein percentage (CNP), calcium content, somatic cell score (SCS), coagulation time, curd firmness after 30 min from rennet addition, and titratable acidity. The used data have been collected from 2014 to 2020 on 78,073 first-parity (485,218 test-day records), 48,766 second-parity (284,942 test-day records), and 21,948 third-parity (105,112 test-day records) Holstein cows distributed in 671 herds in the Walloon Region of Belgium. Data of 565,533 single nucleotide polymorphisms (SNP), located on 29 Bos taurus autosomes (BTA) of 6,617 animals (1,712 males), were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of ∼216 KB) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for positional candidate genes. Heritability estimates for the studied traits ranged from 0.10 (SCS) to 0.53 (CNP), 0.10 (SCS) to 0.50 (CNP), and 0.12 (SCS) to 0.49 (CNP) in the first, second, and third parity, respectively. Genome-wide association analyses identified 6 genomic regions (BTA1, BTA14 [4 regions], and BTA20) associated with the considered traits. Genes including the SLC37A1 (BTA1), SHARPIN, MROH1, DGAT1, FAM83H, TIGD5, MROH6, NAPRT, ADGRB1, GML, LYPD2, JRK (BTA14), and TRIO (BTA20) were identified as positional candidate genes for the studied CMP. The findings of this study help to unravel the genomic background of a cow's ability for cheese production and can be used for the future implementation and use of genomic evaluation to improve the cheese-making traits in Walloon Holstein cows.

Genome-wide association study and functional annotation analyses for nitrogen efficiency index and its composition traits in dairy cattle.

The aims of this study were (1) to identify genomic regions associated with a N efficiency index (NEI) and its composition traits and (2) to analyze the functional annotation of identified genomic regions. The NEI included N intake (NINT1), milk true protein N (MTPN1), milk urea N yield (MUNY1) in primiparous cattle, and N intake (NINT2+), milk true protein N (MTPN2+), and milk urea N yield (MUNY2+) in multiparous cattle (2 to 5 parities). The edited data included 1,043,171 records on 342,847 cows distributed in 1,931 herds. The pedigree consisted of 505,125 animals (17,797 males). Data of 565,049 SNPs were available for 6,998 animals included in the pedigree (5,251 females and 1,747 males). The SNP effects were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of about 240 kb) was calculated. The top 3 genomic regions explaining the largest rate of the total additive genetic variance of the NEI and its composition traits were selected for candidate gene identification and quantitative trait loci (QTL) annotation. The selected genomic regions explained from 0.17% (MTPN2+) to 0.58% (NEI) of the total additive genetic variance. The largest explanatory genomic regions of NEI, NINT1, NINT2+, MTPN1, MTPN2+, MUNY1, and MUNY2+ were Bos taurus autosome 14 (1.52-2.09 Mb), 26 (9.24-9.66 Mb), 16 (75.41-75.51 Mb), 6 (8.73-88.92 Mb), 6 (8.73-88.92 Mb), 11 (103.26-103.41 Mb), 11 (103.26-103.41 Mb). Based on the literature, gene ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction, 16 key candidate genes were identified for NEI and its composition traits, which are mainly expressed in the milk cell, mammary, and liver tissues. The number of enriched QTL related to NEI, NINT1, NINT2+, MTPN1, and MTPN2+ were 41, 6, 4, 11, 36, 32, and 32, respectively, and most of them were related to the milk, health, and production classes. In conclusion, this study identified genomic regions associated with NEI and its composition traits, and identified key candidate genes describing the genetic mechanisms of N use efficiency-related traits. Furthermore, the NEI reflects not only its composition traits but also the interactions among them.

Single-step genome-wide association for selected milk fatty acids in Dual-Purpose Belgian Blue cows.

The aim of this study was to estimate genetic parameters and identify genomic regions associated with selected individual and groups of milk fatty acids (FA) predicted by milk mid-infrared spectrometry in Dual-Purpose Belgian Blue cows. The used data were 69,349 test-day records of milk yield, fat percentage, and protein percentage along with selected individual and groups FA of milk (g/dL milk) collected from 2007 to 2020 on 7,392 first-parity (40,903 test-day records), and 5,185 second-parity (28,446 test-day records) cows distributed in 104 herds in the Walloon Region of Belgium. Data of 28,466 SNPs, located on 29 Bos taurus autosomes (BTA), of 1,699 animals (639 males and 1,060 females) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic best linear unbiased prediction approach. The proportion of genetic variance explained by each 25-SNP sliding window (with an average size of ~2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Average daily heritability estimated for the included milk FA traits ranged from 0.01 (C4:0) to 0.48 (C12:0) and 0.01 (C4:0) to 0.42 (C12:0) in the first and second parities, respectively. Genetic correlations found between milk yield and the studied individual milk FA, except for C18:0, C18:1 trans, C18:1 cis-9, were positive. The results showed that fat percentage and protein percentage were positively genetically correlated with all studied individual milk FA. Genome-wide association analyses identified 11 genomic regions distributed over 8 chromosomes [BTA1, BTA4, BTA10, BTA14 (4 regions), BTA19, BTA22, BTA24, and BTA26] associated with the studied FA traits, though those found on BTA14 partly overlapped. The genomic regions identified differed between parities and lactation stages. Although these differences in genomic regions detected may be due to the power of quantitative trait locus detection, it also suggests that candidate genes underlie the phenotypic expression of the studied traits may vary between parities and lactation stages. These findings increase our understanding about the genetic background of milk FA and can be used for the future implementation of genomic evaluation to improve milk FA profile in Dual-Purpose Belgian Blue cows.

Validating genomic prediction for nitrogen efficiency index and its composition traits of Holstein cows in early lactation.

Nitrogen (N) use efficiency (NUE) is an economically important trait for dairy cows. Recently, we proposed a new N efficiency index (NEI), that simultaneously considers both NUE and N pollution. This study aimed to validate the genomic prediction for NEI and its composition traits and investigate the relationship between SNP effects estimated directly from NEI and indirectly from its composition traits. The NEI composition included genomic estimated breeding value of N intake (NINT), milk true protein N (MTPN) and milk urea N yield. The edited data were 132,899 records on 52,064 cows distributed in 773 herds. The pedigree contained 122,368 animals. Genotypic data of 566,294 SNP was available for 4514 individuals. A total of 4413 cows (including 181 genotyped) and 56 bulls (including 32 genotyped) were selected as the validation populations. The linear regression method was used to validate the genomic prediction of NEI and its composition traits using best linear unbiased prediction (BLUP) and single-step genomic BLUP (ssGBLUP). The mean theoretical accuracies of validation populations obtained from ssGBLUP were higher than those obtained from BLUP for both NEI and its composition traits, ranging from 0.57 (MTPN) to 0.72 (NINT). The highest mean prediction accuracies for NEI and its composition traits were observed for the genotyped cows estimated under ssGBLUP, ranging from 0.48 (MTPN) to 0.66 (NINT). Furthermore, the SNP effects estimated from NEI composition traits, multiplied by the relative weight were the same as those estimated directly from NEI. This study preliminary showed that genomic prediction can be used for NEI, however, we acknowledge the need for further validation of this result in a larger dataset. Moreover, the SNP effects of NEI can be indirectly calculated using the SNP effects estimated from its composition traits. This study provided a basis for adding genomic information to establish NEI as part of future routine genomic evaluation programs.

Defining a nitrogen efficiency index in Holstein cows and assessing its potential effect on the breeding program of bulls.

The purposes of this study were (1) to explore the relationship between 3 milk mid-infrared predicted features including nitrogen intake (NINT), milk true protein N (MTPN), and milk urea-N yield (MUNY); (2) to integrate these 3 features into an N efficiency index (NEI) and analyses approximate genetic correlations between the NEI and 37 traits (indices) of interest; and (3) to assess the potential effect of including the NEI into breeding programs of bulls. The edited data were 1,043,171 test-day records on 342,847 cows in 1,931 herds and 143,595 test-day records on 53,660 cows in 766 herds used for estimating breeding values (EBV) and variance components, respectively. The used records were within 5 to 50 d in milk. The records were grouped into primiparous and multiparous. The genetic parameters for the included mid-infrared features and EBV of the animals included in the pedigree were estimated using a multiple-trait repeatability animal model. Then, the EBV of the NINT, MTPN, MUNY were integrated into the NEI using a selection index assuming weights based on the N partitioning. The approximate genetic correlations between the NEI and 37 traits of interest were estimated using the EBV of the selected bulls. The bulls born from 2011 to 2014 with NEI were selected and the NEI distribution of these bulls having EBV for the 8 selected traits (indices) was checked. The heritability and repeatability estimates for NINT, MTPN, and MUNY ranged from 0.09 to 0.13, and 0.37 to 0.65, respectively. The genetic and phenotypic correlations between NINT, MTPN, and MUNY ranged from -0.31 to 0.87, and -0.02 to 0.42, respectively. The NEI ranged from -13.13 to 12.55 kg/d. In total, 736 bulls with reliability ≥0.50 for all included traits (NEI and 37 traits) and at least 10 daughters distributed in at least 10 herds were selected to investigate genetic aspects of the NEI. The NEI had positive genetic correlations with production yield traits (0.08-0.46), and negative genetic correlations with the investigated functional traits and indices (-0.71 to -0.07), except for the production economic index and functional type economic index. The daughters of bulls with higher NEI had lower NINT and MUNY, and higher MTPN. Furthermore, 26% of the bulls (n = 50) with NEI born between 2011 to 2014 had higher NEI and global economic index than the average in the selected bulls. Finally, the developed NEI has the advantage of large-scale prediction and therefore has the potential for routine application in dairy cattle breeding in the future.

Genome-wide association study for selected cheese-making properties in Dual-Purpose Belgian Blue cows.

This study aimed to estimate genetic parameters and identify genomic region(s) associated with selected cheese-making properties (CMP) in Dual-Purpose Belgian Blue (DPBB) cows. Edited data were 46,301 test-day records of milk yield, fat percentage, protein percentage, casein percentage, milk calcium content (CC), coagulation time (CT), curd firmness after 30 min from rennet addition (a30), and milk titratable acidity (MTA) collected from 2014 to 2020 on 4,077 first-parity (26,027 test-day records), and 3,258 second-parity DPBB cows (20,274 test-day records) distributed in 124 herds in the Walloon Region of Belgium. Data of 28,266 SNP, located on 29 Bos taurus autosomes (BTA) of 1,699 animals were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 25 consecutive SNPs (with an average size of ∼2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Heritability estimates for the included CMP ranged from 0.19 (CC) to 0.50 (MTA), and 0.24 (CC) to 0.41 (MTA) in the first and second parity, respectively. The genetic correlation estimated between CT and a30 varied from -0.61 to -0.41 and from -0.55 to -0.38 in the first and second lactations, respectively. Negative genetic correlations were found between CT and milk yield and composition, while those estimated between curd firmness and milk composition were positive. Genome-wide association analyses results identified 4 genomic regions (BTA1, BTA3, BTA7, and BTA11) associated with the considered CMP. The identified genomic regions showed contrasting results between parities and among the different stages of each parity. It suggests that different sets of candidate genes underlie the phenotypic expression of the considered CMP between parities and lactation stages of each parity. The findings of this study can be used for future implementation and use of genomic evaluation to improve the cheese-making traits in DPBB cows.

Estimation of genetic parameters for predicted nitrogen use efficiency and losses in early lactation of Holstein cows.

The objective of this study was to estimate genetic parameters of predicted N use efficiency (PNUE) and N losses (PNL) as proxies of N use and loss for Holstein cows. Furthermore, we have assessed approximate genetic correlations between PNUE, PNL, and dairy production, health, longevity, and conformation traits. These traits are considered important in many countries and are currently evaluated by the International Bull Evaluation Service (Interbull). The values of PNUE and PNL were obtained by using the combined milk mid-infrared (MIR) spectrum, parity, and milk yield-based prediction equations on test-day MIR records with days in milk (DIM) between 5 and 50 d. After editing, the final data set comprised 46,163 records of 21,462 cows from 154 farms in 5 countries. Each trait was divided into primiparous and multiparous (including second to fifth parity) groups. Genetic parameters and breeding values were estimated by using a multitrait (2-trait, 2-parity classes) repeatability model. Herd-year-season of calving, DIM, age of calving, and parity were used as fixed effects. Random effects were defined as parity (within-parity permanent environment), nongenetic cow (across-parity permanent environment), additive genetic animal, and residual effects. The estimated heritability of PNUE and PNL in the first and later parity were 0.13, 0.12, 0.14, and 0.13, and the repeatability values were 0.49, 0.40, 0.55, and 0.43, respectively. The estimated approximate genetic correlations between PNUE and PNL were negative and high (from -0.89 to -0.53), whereas the phenotypic correlations were also negative but relatively low (from -0.45 to -0.11). At a level of reliability of more than 0.30 for all novel traits, a total of 504 bulls born after 1995 had also publishable Interbull multiple-trait across-country estimated breeding values (EBV). The approximate genetic correlations between PNUE and the other 30 traits of interest, estimated as corrected correlations between EBV of bulls, ranged from -0.46 (udder depth) to 0.47 (milk yield). Obtained results showed the complex genetic relationship between efficiency, production, and other traits: for instance, more efficient cows seem to give more milk, which is linked to deeper udders, but seem to have lower health, fertility, and longevity. Additionally, the approximate genetic correlations between PNL, lower values representing less loss of N, and the 30 other traits, were from -0.32 (angularity) to 0.57 (direct calving ease). Even if further research is needed, our results provided preliminary evidence that the PNUE and PNL traits used as proxies could be included in genetic improvement programs in Holstein cows and could help their management.

Genetic analysis of milk urea concentration and its genetic relationship with selected traits of interest in dairy cows.

The aim of this study was to estimate genetic parameters of milk urea concentration (MU) and its genetic correlations with milk production traits, longevity, and functional traits in the first 3 parities in dairy cows. The edited data set consisted in 9,107,349 MU test-day records from the first 3 parities of 560,739 cows in 2,356 herds collected during the years 1994 to 2020. To estimate the genetic parameters of MU, data of 109 randomly selected herds, with a total of 770,016 MU test-day records, were used. Genetic parameters and estimated breeding values were estimated using a multiple-trait (parity) random regression model. Herd-test-day, age-year-season of calving, and days in milk classes (every 5 d as a class) were used as fixed effects, whereas effects of herd-year of calving, permanent environment, and animal were modeled using random regressions and Legendre polynomials of order 2. The average daily heritability and repeatability of MU during days in milk 5 to 365 in the first 3 parities were 0.19, 0.22, 0.20, and 0.48, 0.48, 0.47, respectively. The mean genetic correlation estimated among MU in the first 3 parities ranged from 0.96 to 0.97. The average daily estimated breeding values for MU of the selected bulls (n = 1,900) ranged from -9.09 to 7.37 mg/dL. In the last 10 yr, the genetic trend of MU has gradually increased. The genetic correlation between MU and 11 traits of interest ranged from -0.28 (milk yield) to 0.28 (somatic cell score). The findings of this study can be used as the first step for development of a routine genetic evaluation for MU and its inclusion into the genetic selection program in the Walloon Region of Belgium.

Predicting milk mid-infrared spectra from first-parity Holstein cows using a test-day mixed model with the perspective of herd management.

The use of test-day models to model milk mid-infrared (MIR) spectra for genetic purposes has already been explored; however, little attention has been given to their use to predict milk MIR spectra for management purposes. The aim of this paper was to study the ability of a test-day mixed model to predict milk MIR spectra for management purposes. A data set containing 467,496 test-day observations from 53,781 Holstein dairy cows in first lactation was used for model building. Principal component analysis was implemented on the selected 311 MIR spectral wavenumbers to reduce the number of traits for modeling; 12 principal components (PC) were retained, explaining approximately 96% of the total spectral variation. Each of the retained PC was modeled using a single trait test-day mixed model. The model solutions were used to compute the predicted scores of each PC, followed by a back-transformation to obtain the 311 predicted MIR spectral wavenumbers. Four new data sets, containing altogether 122,032 records, were used to test the ability of the model to predict milk MIR spectra in 4 distinct scenarios with different levels of information about the cows. The average correlation between observed and predicted values of each spectral wavenumber was 0.85 for the modeling data set and ranged from 0.36 to 0.62 for the scenarios. Correlations between milk fat, protein, and lactose contents predicted from the observed spectra and from the modeled spectra ranged from 0.83 to 0.89 for the modeling set and from 0.32 to 0.73 for the scenarios. Our results demonstrated a moderate but promising ability to predict milk MIR spectra using a test-day mixed model. Current and future MIR traits prediction equations could be applied on the modeled spectra to predict all MIR traits in different situations instead of developing one test-day model separately for each trait. Modeling MIR spectra would benefit farmers for cow and herd management, for instance through prediction of future records or comparison between observed and expected wavenumbers or MIR traits for the detection of health and management problems. Potential resulting tools could be incorporated into milk recording systems.

Capitalizing on fine milk composition for breeding and management of dairy cows.

The challenge of managing and breeding dairy cows is permanently adapting to changing production circumstances under socio-economic constraints. If managing and breeding address different timeframes of action, both need relevant phenotypes that allow for precise monitoring of the status of the cows, and their health, behavior, and well-being as well as their environmental impact and the quality of their products (i.e., milk and subsequently dairy products). Milk composition has been identified as an important source of information because it could reflect, at least partially, all these elements. Major conventional milk components such as fat, protein, urea, and lactose contents are routinely predicted by mid-infrared (MIR) spectrometry and have been widely used for these purposes. But, milk composition is much more complex and other nonconventional milk components, potentially predicted by MIR, might be informative. Such new milk-based phenotypes should be considered given that they are cheap, rapidly obtained, usable on a large scale, robust, and reliable. In a first approach, new phenotypes can be predicted from MIR spectra using techniques based on classical prediction equations. This method was used successfully for many novel traits (e.g., fatty acids, lactoferrin, minerals, milk technological properties, citrate) that can be then useful for management and breeding purposes. An innovation was to consider the longitudinal nature of the relationship between the trait of interest and the MIR spectra (e.g., to predict methane from MIR). By avoiding intermediate steps, prediction errors can be minimized when traits of interest (e.g., methane, energy balance, ketosis) are predicted directly from MIR spectra. In a second approach, research is ongoing to detect and exploit patterns in an innovative manner, by comparing observed with expected MIR spectra directly (e.g., pregnancy). All of these traits can then be used to define best practices, adjust feeding and health management, improve animal welfare, improve milk quality, and mitigate environmental impact. Under the condition that MIR data are available on a large scale, phenotypes for these traits will allow genetic and genomic evaluations. Introduction of novel traits into the breeding objectives will need additional research to clarify socio-economic weights and genetic correlations with other traits of interest.

Genetic parameters for direct and maternal calving ease in Walloon dairy cattle based on linear and threshold models.

Calving ease scores from Holstein dairy cattle in the Walloon Region of Belgium were analysed using univariate linear and threshold animal models. Variance components and derived genetic parameters were estimated from a data set including 33,155 calving records. Included in the models were season, herd and sex of calf × age of dam classes × group of calvings interaction as fixed effects, herd × year of calving, maternal permanent environment and animal direct and maternal additive genetic as random effects. Models were fitted with the genetic correlation between direct and maternal additive genetic effects either estimated or constrained to zero. Direct heritability for calving ease was approximately 8% with linear models and approximately 12% with threshold models. Maternal heritabilities were approximately 2 and 4%, respectively. Genetic correlation between direct and maternal additive effects was found to be not significantly different from zero. Models were compared in terms of goodness of fit and predictive ability. Criteria of comparison such as mean squared error, correlation between observed and predicted calving ease scores as well as between estimated breeding values were estimated from 85,118 calving records. The results provided few differences between linear and threshold models even though correlations between estimated breeding values from subsets of data for sires with progeny from linear model were 17 and 23% greater for direct and maternal genetic effects, respectively, than from threshold model. For the purpose of genetic evaluation for calving ease in Walloon Holstein dairy cattle, the linear animal model without covariance between direct and maternal additive effects was found to be the best choice.

Genomic location of the bovine growth hormone secretagogue receptor (GHSR) gene and investigation of genetic polymorphism.

The growth hormone secretagogue receptor (GHSR) is involved in the regulation of energetic homeostasis and GH secretion. In this study, the bovine GHSR gene was mapped to BTA1 between BL26 and BMS4004. Two different bovine GHSR CDS (GHSR1a and GHSR1b) were sequenced. Six polymorphisms (five SNPs and one 3-bp indel) were also identified, three of them leading to amino acid variations L24V, D194N, and Del R242. These variations are located in the extracellular N-terminal end, the exoloop 2, and the cytoloop 3 of the receptor, respectively.

Estimation of test-day model (co)variance components across breeds using New Zealand dairy cattle data.

In New Zealand, a large proportion of cows are currently crossbreds, mostly Holstein-Friesians (HF) x Jersey (JE). The genetic evaluation system for milk yields is considering the same additive genetic effects for all breeds. The objective was to model different additive effects according to parental breeds to obtain first estimates of correlations among breed-specific effects and to study the usefulness of this type of random regression test-day model. Estimates of (co)variance components for purebred HF and JE cattle in purebred herds were computed by using a single-breed model. This analysis showed differences between the 2 breeds, with a greater variability in the HF breed. (Co)variance components for purebred HF and JE and crossbred HF x JE cattle were then estimated by using a complete multibreed model in which computations of complete across-breed (co)variances were simplified by correlating only eigenvectors for HF and JE random regressions of the same order as obtained from the single-breed analysis. Parameter estimates differed more strongly than expected between the single-breed and multibreed analyses, especially for JE. This could be due to differences between animals and management in purebred and non-purebred herds. In addition, the model used only partially accounted for heterosis. The multibreed analysis showed additive genetic differences between the HF and JE breeds, expressed as genetic correlations of additive effects in both breeds, especially in linear and quadratic Legendre polynomials (respectively, 0.807 and 0.604). The differences were small for overall milk production (0.926). Results showed that permanent environmental lactation curves were highly correlated across breeds; however, intraherd lactation curves were also affected by the breed-environment interaction. This result may indicate the existence of breed-specific competition effects that vary through the different lactation stages. In conclusion, a multibreed model similar to the one presented could optimally use the environmental and genetic parameters and provide breed-dependent additive breeding values. This model could also be a useful tool to evaluate crossbred dairy cattle populations like those in New Zealand. However, a routine evaluation would still require the development of an improved methodology. It would also be computationally very challenging because of the simultaneous presence of a large number of breeds.

Accuracy of prediction of gene content in large animal populations and its use for candidate gene detection and genetic evaluation.

To estimate and to use the effects of single genes on quantitative traits, genotypes need to be known. However, in large animal populations, the majority of animals are not genotyped. These missing genotypes have to be estimated. However, currently used methods are impractical for large pedigrees. An alternative method to estimate missing gene content, defined as the number of copies of a particular allele, was recently developed. In this study, the proposed method was tested by assessing its accuracy in estimation and use of gene content in large animal populations. This was done for the bovine transmembrane growth hormone receptor and its effects on first-lactation milk, fat, and protein test-day yields and somatic cell score in Holstein cows. Estimated gene substitution effects of replacing a copy of the phenylalanine-coding allele with a copy of the tyrosine-coding allele were 295 g/d for milk, -8.14 g/d for fat, -1.83 g/d for protein, and -0.022/d for somatic cell score. However, only the gene substitution effect for milk was found to be significant. The accuracy of the estimated effects was evaluated by simulations and permutations. To validate the use of predicted gene content in a mixed inheritance model, a cross-validation study was done. The model with an additional regression of milk, fat, and protein yields and SCS on predicted gene content showed a better capacity to predict breeding values for milk, fat, and protein. Given these results, the estimation and use of allelic effects using this method proved functional and accurate.

Bayesian single-step genomic evaluations combining local and foreign information in Walloon Holsteins.

Most dairy cattle populations found in different countries around the world are small to medium sized and use many artificial insemination bulls imported from different foreign countries. The Walloon population in the southern part of Belgium is a good example for such a small-scale population. Wallonia has also a very active community of Holstein breeders requesting high level genetic evaluation services. Single-step Genomic BLUP (ssGBLUP) methods allow the simultaneous use of genomic, pedigree and phenotypic information and could reduce potential biases in the estimation of genomically enhanced breeding values (GEBV). Therefore, in the context of implementing a Walloon genomic evaluation system for Holsteins, it was considered as the best option. However, in contrast to multi-step genomic predictions, natively ssGBLUP will only use local phenotypic information and is unable to use directly important other sources of information coming from abroad, for example Multiple Across Country Evaluation (MACE) results as provided by the Interbull Center (Uppsala, Sweden). Therefore, we developed and implemented single-step Genomic Bayesian Prediction (ssGBayes), as an alternative method for the Walloon genomic evaluations. The ssGBayes method approximated the correct system of equations directly using estimated breeding values (EBV) and associated reliabilities (REL) without any explicit deregression step. In the Walloon genomic evaluation, local information refers to Walloon EBV and REL and foreign information refers to MACE EBV and associated REL. Combining simultaneously all available genotypes, pedigree, local and foreign information in an evaluation can be achieved but adding contributions to left-hand and right-hand sides subtracting double-counted contributions. Correct propagation of external information avoiding double counting of contributions due to relationships and due to records can be achieved. This ssGBayes method computed more accurate predictions for all types of animals. For example, for genotyped animals with low Walloon REL (<0.25) without MACE results but sired by genotyped bulls with MACE results, the average increase of REL for the studied traits was 0.38 points of which 0.08 points could be traced to the inclusion of MACE information. For other categories of genotyped animals, the contribution by MACE information was also high. The Walloon genomic evaluation system passed for the first time the Interbull GEBV tests for several traits in July 2013. Recent experiences reported here refer to its use in April 2016 for the routine genomic evaluations of milk production, udder health and type traits. Results showed that the proposed methodology should also be of interest for other, similar, populations.

Estimation of heritability and genetic correlations for the major fatty acids in bovine milk.

The current cattle selection program for dairy cattle in the Walloon region of Belgium does not consider the relative content of the different fatty acids (FA) in milk. However, interest by the local dairy industry in differentiated milk products is increasing. Therefore, farmers may be interested in selecting their animals based on the fat composition. The aim of this study was to evaluate the feasibility of genetic selection to improve the nutritional quality of bovine milk fat. The heritabilities and correlations among milk yield, fat, protein, and major FA contents in milk were estimated. Heritabilities for FA in milk and fat ranged from 5 to 38%. The genetic correlations estimated among FA reflected the common origin of several groups of FA. Given these results, an index including FA contents with the similar metabolic process of production in the mammary gland could be used, for example, to increase the monounsaturated and conjugated fatty acids in milk. Moreover, the genetic correlations between the percentage of fat and the content of C14:0, C12:0, C16:0, and C18:0 in fat were -0.06, 0.55, 0.60, and 0.84, respectively. This result demonstrates that an increase in fat content is not directly correlated with undesirable changes in FA profile in milk for human health. Based on the obtained genetic parameters, a future selection program to improve the FA composition of milk fat could be initiated.

Linear and curvilinear effects of inbreeding on production traits for walloon Holstein cows.

The nonlinear effects of inbreeding were studied by comparing linear and curvilinear regression models of phenotypic performances on inbreeding coefficients for production traits (milk, fat, and protein yields) of Holstein cows in their first lactation. Three different regression models (linear, quadratic, and cubic) were introduced separately into a single-trait, single-lactation, random regression test-day model. The significance of the different regression coefficients was studied based on a t-test after estimation of error variances and covariances associated with the different regression coefficients. All of the tested regression coefficients were significantly different from 0. The traditional regression coefficients of milk, fat, and protein yields on inbreeding were, respectively, -22.10, -1.10, and -0.72 kg for Holstein cows in their first lactation. However, the estimates of 305-d production losses for various classes of animals based on inbreeding coefficients showed that the effect of inbreeding was not a linear function of the percentage of inbreeding. The 305-d milk yield loss profiles attributable to inbreeding, obtained by the various regression models, were different. However, for inbreeding coefficients between 0 and 10%, these differences were small.

Genetic evaluation for birth and conformation traits in dual-purpose Belgian Blue cattle using a mixed inheritance model.

The segregation of the causal mutation () in the muscular hypertrophy gene in dual-purpose Belgian Blue (dpBB) cattle is considered to result in greater calving difficulty (dystocia). Establishing adapted genetic evaluations might overcome this situation through efficient selection. However, the heterogeneity of dpBB populations at the locus implies separating the major gene and other polygenic effects in complex modeling. The use of mixed inheritance models may be an interesting option because they simultaneously assume both influences. A genetic evaluation in dpBB based on a mixed inheritance model was developed for birth and conformation traits: gestation length (GL), calving difficulty (CD), birth weight (BiW), and body conformation score (BC). A total of 27,362 animals having records were used for analyses. The total number of animals in the pedigree used to build the numerator relationship matrix was 62,617. Genotypes at the locus were available for 2,671 animals. Missing records at this locus were replaced with genotype probabilities. A total of 13,221 (48.3%) were registered as dpBB, 1,287 (4.7%) as beef Belgian Blue, and 12,854 (47.0%) were unknown. From those 13,221 dpBB animals, 650, 849, and 534 had double or single copies or no copy, respectively, of the causal mutation () in the muscular hypertrophy gene, whereas 11,188 had missing genotypes. This heterogeneity at the locus may be the reason for high variability in the studied traits, that is, high heritability estimates of 0.33, 0.30, 0.38, and 0.43 for GL, CD, BiW, and BC, respectively. In general, additive ( < 0.05) and dominance ( < 0.001) allele substitution for calves and dams had significant impact for all traits. The moderate coefficient of genetic variation (27.80%) and high direct heritability (0.28) for CD suggested genetic variability in dpBB and possible genetic improvement through selection. This variability has allowed dpBB breeders to successfully apply mass selection in the past. Genetic trend means from 1988 to 2016 showed that sire selection for CD within genotype was progressively applied by breeders. The selection intensity was more important for CD in double-muscled lines than in segregated lines. Our study illustrated the possible confusion caused by the use of major genes in selection and the importance of fitting appropriate models such as mixed inheritance models that combine polygenic and gene content information.

Inbreeding depression for global and partial economic indexes, production, type, and functional traits.

The objective of this research was to examine the effects of inbreeding in the population of Holstein cattle in the Walloon region of Belgium. The effects of inbreeding on the global economic index and its components were studied by using data from the genetic evaluations of February 2004 for production, somatic cell score (SCS), computed from somatic cell counts and type. Inbreeding coefficients for 956,516 animals were computed using a method that allows assigning an inbreeding coefficient to individuals without known parents. These coefficients were equal to the mean inbreeding coefficient of contemporary individuals with known parents. The significance of inbreeding effects on the different evaluated traits and on the different indexes were tested using a t-test comparing estimated standard errors and effects. The inbreeding effect was significantly different from zero for the vast majority of evaluated traits and for all of the indexes. Inbreeding had the greatest deleterious effects on production traits. Inbreeding decreased yield of milk, fat, and protein during a lactation by 19.68, 0.96, and 0.69 kg, respectively, per each 1% increase in inbreeding. The regression coefficient of SCS per 1% increase in inbreeding was +0.005 SCS units. The inbreeding depression was thus relatively low for SCS, but inbred animals had higher SCS than non-inbred animals, indicating that inbred animals would be slightly more sensitive to mastitis than non-inbred animals. Estimates of inbreeding effects on evaluated type traits per 1% increase were small. The most strongly affected type traits were chest width, rear leg, and overall development on a standardized scale. For several type traits, particularly traits linked to the udder, the estimates suggested a favorable effect of inbreeding. The global economic index was depressed by around 6.13 euro of lifetime profit per 1% increase in inbreeding for the Holstein animals in the Walloon region of Belgium.