Short communication: Genetic correlations between methane and milk production, conformation, and functional traits.

Livestock produce CH4, contributing to the global warming effect. One of the currently investigated solutions to reduce CH4 production is selective breeding. The goal of this study was to estimate the genetic correlations between CH4 and milk production, conformation, and functional traits used in the selection index for Polish-Holstein cows. In total, 34,429 daily CH4 production observations collected from 483 cows were available, out of which 281 cows were genotyped. The CH4 was measured using a so-called sniffer device installed in an automated milking system. Breeding values for CH4 were estimated with the use of single-step genomic BLUP, and breeding values for remaining traits were obtained from the Polish national genomic evaluation. Genetic correlations between CH4 production and remaining traits were estimated using bivariate analyses. The estimated genetic correlations were in general low. The highest values were estimated for fat yield (0.21), milk yield (0.15), chest width (0.15), size (0.15), dairy strength (0.11), and somatic cell count (0.11). These estimates, as opposed to estimates for the remaining traits, were significantly different from zero.

Technical note: Interchangeability and comparison of methane measurements in dairy cows with 2 noninvasive infrared systems.

This study aimed to compare measurements of methane (CH4) and carbon dioxide (CO2) concentrations in the breath of dairy cows kept in commercial conditions using the Fourier-transform infrared spectroscopy (FTIR) and nondispersive infrared spectroscopy (NDIR) methods. The measurement systems were installed in an automated milking system. Measurements were carried out for 5 d using both systems during milkings. The measurements were averaged per milking, giving 467 observations of CH4 and CO2 concentrations of 44 Holstein Friesian cows. The Pearson correlation between observations from the 2 systems was 0.86 for CH4, 0.84 for CO2, and 0.88 for their ratio. The repeatability of FTIR (0.53 for CH4, 0.57 for CO2, and 0.28 for their ratio) was somewhat higher than that of NDIR (0.57 for CH4, 0.47 for CO2, and 0.25 for their ratio). The coefficient of individual agreement was 0.98 for CH4, 0.89 for CO2, and 0.89 for their ratio; the concordance correlation coefficient was 0.48 for both gases and 0.24 for their ratio. We showed that FTIR and NDIR give similar results in commercial farm conditions. They can therefore be used interchangeably to generate a larger data set, which could then be further used for genetic evaluation.

Reliability of direct genomic values for animals with different relationships within and to the reference population.

Accuracy of genomic selection depends on the accuracy of prediction of single nucleotide polymorphism effects and the proportion of genetic variance explained by markers. Design of the reference population with respect to its family structure may influence the accuracy of genomic selection. The objective of this study was to investigate the effect of various relationship levels within the reference population and different level of relationship of evaluated animals to the reference population on the reliability of direct genomic breeding values (DGV). The DGV reliabilities, expressed as squared correlation between estimated and true breeding value, were calculated for evaluated animals at 3 heritability levels. To emulate a trait that is difficult or expensive to measure, such as methane emission, reference populations were kept small and consisted of females with own performance records. A population reflecting a dairy cattle population structure was simulated. Four chosen reference populations consisted of all females available in the first genotyped generation. They consisted of highly (HR), moderately (MR), or lowly (LR) related animals, by selecting paternal half-sib families of decreasing size, or consisted of randomly chosen animals (RND). Of those 4 reference populations, RND had the lowest average relationship. Three sets of evaluated animals were chosen from 3 consecutive generations of genotyped animals, starting from the same generation as the reference population. Reliabilities of DGV predictions were calculated deterministically using selection index theory. The randomly chosen reference population had the lowest average relationship within the reference population. Average reliabilities increased when average relationship within the reference population decreased and the highest average reliabilities were achieved for RND (e.g., from 0.53 in HR to 0.61 in RND for a heritability of 0.30). A higher relationship to the reference population resulted in higher reliability values. At the average squared relationship of evaluated animals to the reference population of 0.005, reliabilities were, on average, 0.49 (HR) and 0.63 (RND) for a heritability of 0.30; 0.20 (HR) and 0.27 (RND) for a heritability of 0.05; and 0.07 (HR) and 0.09 (RND) for a heritability of 0.01. Substantial decrease in the reliability was observed when the number of generations to the reference population increased [e.g., for heritability of 0.30, the decrease from evaluated set I (chosen from the same generation as the reference population) to II (one generation younger than the reference population) was 0.04 for HR, and 0.07 for RND]. In this study, the importance of the design of a reference population consisting of cows was shown and optimal designs of the reference population for genomic prediction were suggested.

The impact of genotyping different groups of animals on accuracy when moving from traditional to genomic selection.

Compared with traditional selection, the use of genomic information tends to increase the accuracy of estimated breeding values (EBV). The cause of this increase is, however, unknown. To explore this phenomenon, this study investigated whether the increase in accuracy when moving from traditional (AA) to genomic selection (GG) was mainly due to genotyping the reference population (GA) or the evaluated animals (AG). In it, a combined relationship matrix for simultaneous use of genotyped and ungenotyped animals was applied. A simulated data set reflected the dairy cattle population. Four differently designed (i.e., different average relationships within the reference population) small reference populations and 3 heritability levels were considered. The animals in the reference populations had high, moderate, low, and random (RND) relationships. The evaluated animals were juveniles. The small reference populations simulated difficult or expensive to measure traits (i.e., methane emission). The accuracy of selection was expressed as the reliability of (genomic) EBV and was predicted based on selection index theory using relationships. Connectedness between the reference populations and evaluated animals was calculated using the prediction error variance. Average (genomic) EBV reliabilities increased with heritability and with a decrease in the average relationship within the reference population. Reliabilities in AA and AG were lower than those in GG and were higher than those in GA (respectively, 0.039, 0.042, 0.052, and 0.048 for RND and a heritability of 0.01). Differences between AA and GA were small. Average connectedness with all animals in the reference population for all scenarios and reference populations ranged from 0.003 to 0.024; it was lowest when the animals were not genotyped (AA; e.g., 0.004 for RND) and highest when all the animals were genotyped (GG; e.g., 0.024 for RND). Differences present across designs of the reference populations were very small. Genomic relationships among animals in the reference population might be less important than those for the evaluated animals with no phenotypic observations. Thus, the main origin of the gain in accuracy when using genomic selection is due to genotyping the evaluated animals. However, genotyping only one group of animals will always yield less accurate estimates.

Genome-wide association identifies methane production level relation to genetic control of digestive tract development in dairy cows.

The global temperatures are increasing. This increase is partly due to methane (CH4) production from ruminants, including dairy cattle. Recent studies on dairy cattle have revealed the existence of a heritable variation in CH4 production that enables mitigation strategies based on selective breeding. We have exploited the available heritable variation to study the genetic architecture of CH4 production and detected genomic regions affecting CH4 production. Although the detected regions explained only a small proportion of the heritable variance, we showed that potential QTL regions affecting CH4 production were located within QTLs related to feed efficiency, milk-related traits, body size and health status. Five candidate genes were found: CYP51A1 on BTA 4, PPP1R16B on BTA 13, and NTHL1, TSC2, and PKD1 on BTA 25. These candidate genes were involved in a number of metabolic processes that are possibly related to CH4 production. One of the most promising candidate genes (PKD1) was related to the development of the digestive tract. The results indicate that CH4 production is a highly polygenic trait.

Heritability of methane emissions from dairy cows over a lactation measured on commercial farms.

Methane emission is currently an important trait in studies on ruminants due to its environmental and economic impact. Recent studies were based on short-time measurements on individual cows. As methane emission is a longitudinal trait, it is important to investigate its changes over a full lactation. In this study, we aimed to estimate the heritability of the estimated methane emissions from dairy cows using Fourier-transform infrared spectroscopy during milking in an automated milking system by implementing the random regression method. The methane measurements were taken on 485 Polish Holstein-Friesian cows at 2 commercial farms located in western Poland. The overall daily estimated methane emission was 279 g/d. Genetic variance fluctuated over the course of lactation around the average level of 1,509 (g/d), with the highest level, 1,866 (g/d), at the end of the lactation. The permanent environment variance values started at 2,865 (g/d) and then dropped to around 846 (g/d) at 100 d in milk (DIM) to reach the level of 2,444 (g/d) at the end of lactation. The residual variance was estimated at 2,620 (g/d). The average repeatability was 0.25. The heritability level fluctuated over the course of lactation, starting at 0.23 (SE 0.12) and then increasing to its maximum value of 0.3 (SE 0.08) at 212 DIM and ending at the level of 0.27 (SE 0.12). Average heritability was 0.27 (average SE 0.09). We have shown that estimated methane emission is a heritable trait and that the heritability level changes over the course of lactation. The observed changes and low genetic correlations between distant DIM suggest that it may be important to consider the period in which methane phenotypes are collected.

Genetic analysis of milk production traits of polish black and white cattle using large-scale random regression test-day models.

Genetic parameters for milk, fat, and protein yield and persistency in the first 3 lactations of Polish Black and White cattle were estimated. A multiple-lactation model was applied with random herd-test-day effect, fixed regressions for herd-year and age-season of calving, and random regressions for the additive genetic and permanent environmental effects. Three data sets with slightly different edits on minimal number of days in milk and the size of herd-year class were used. Each subset included more than 0.5 million test-day records and more than 58,000 cows. Estimates of covariance components and genetic parameters for each trait were obtained by Bayesian methods using the Gibbs sampler. Due to the large size and a good structure of the data, no differences in estimates were found when additional criteria for record selection were applied. More than 95% of the genetic variance for all traits and lactations was explained by the first 2 principal components, which were associated with the mean yield and lactation persistency. Heritabilities of 305-d milk yield in the first 3 lactations (0.18, 0.16, 0.17) were lower than those for fat (0.12, 0.11, 0.12) and protein (0.13, 0.14, 0.15). Estimates of daily heritabilities increased in general with days in milk for all traits and lactations, with no apparent abnormalities at the beginning or end of lactation. Genetic correlations between yields in different lactations ranged from 0.74 (fat yield in lactations 1 and 3) to 0.89 (milk yield in lactations 2 and 3). Persistency of lactation was defined as the linear regression coefficient of the lactation curve. Heritability of persistency increased with lactation number for all traits and genetic correlations between persistency in different lactations were smaller than those for 305d yield. Persistency was not genetically correlated with the total yield in lactation.

Comparison of random regression test-day models for Polish Black and White cattle.

Test-day milk yields of first-lactation Black and White cows were used to select the model for routine genetic evaluation of dairy cattle in Poland. The population of Polish Black and White cows is characterized by small herd size, low level of production, and relatively early peak of lactation. Several random regression models for first-lactation milk yield were initially compared using the "percentage of squared bias" criterion and the correlations between true and predicted breeding values. Models with random herd-test-date effects, fixed age-season and herd-year curves, and random additive genetic and permanent environmental curves (Legendre polynomials of different orders were used for all regressions) were chosen for further studies. Additional comparisons included analyses of the residuals and shapes of variance curves in days in milk. The low production level and early peak of lactation of the breed required the use of Legendre polynomials of order 5 to describe age-season lactation curves. For the other curves, Legendre polynomials of order 3 satisfactorily described daily milk yield variation. Fitting third-order polynomials for the permanent environmental effect made it possible to adequately account for heterogeneous residual variance at different stages of lactation.

Approximation of reliabilities for multiple-trait model with maternal effects.

Reliabilities for a multiple-trait maternal model were obtained by combining reliabilities obtained from single-trait models. Single-trait reliabilities were obtained using an approximation that supported models with additive and permanent environmental effects. For the direct effect, the maternal and permanent environmental variances were assigned to the residual. For the maternal effect, variance of the direct effect was assigned to the residual. Data included 10,550 birth weight, 11,819 weaning weight, and 3,617 postweaning gain records of Senepol cattle. Reliabilities were obtained by generalized inversion and by using single-trait and multiple-trait approximation methods. Some reliabilities obtained by inversion were negative because inbreeding was ignored in calculating the inverse of the relationship matrix. The multiple-trait approximation method reduced the bias of approximation when compared with the single-trait method. The correlations between reliabilities obtained by inversion and by multiple-trait procedures for the direct effect were 0.85 for birth weight, 0.94 for weaning weight, and 0.96 for postweaning gain. Correlations for maternal effects for birth weight and weaning weight were 0.96 to 0.98 for both approximations. Further improvements can be achieved by refining the single-trait procedures.

Effect of predictor traits on accuracy of genomic breeding values for feed intake based on a limited cow reference population.

The genomic breeding value accuracy of scarcely recorded traits is low because of the limited number of phenotypic observations. One solution to increase the breeding value accuracy is to use predictor traits. This study investigated the impact of recording additional phenotypic observations for predictor traits on reference and evaluated animals on the genomic breeding value accuracy for a scarcely recorded trait. The scarcely recorded trait was dry matter intake (DMI, n = 869) and the predictor traits were fat-protein-corrected milk (FPCM, n = 1520) and live weight (LW, n = 1309). All phenotyped animals were genotyped and originated from research farms in Ireland, the United Kingdom and the Netherlands. Multi-trait REML was used to simultaneously estimate variance components and breeding values for DMI using available predictors. In addition, analyses using only pedigree relationships were performed. Breeding value accuracy was assessed through cross-validation (CV) and prediction error variance (PEV). CV groups (n = 7) were defined by splitting animals across genetic lines and management groups within country. With no additional traits recorded for the evaluated animals, both CV- and PEV-based accuracies for DMI were substantially higher for genomic than for pedigree analyses (CV: max. 0.26 for pedigree and 0.33 for genomic analyses; PEV: max. 0.45 and 0.52, respectively). With additional traits available, the differences between pedigree and genomic accuracies diminished. With additional recording for FPCM, pedigree accuracies increased from 0.26 to 0.47 for CV and from 0.45 to 0.48 for PEV. Genomic accuracies increased from 0.33 to 0.50 for CV and from 0.52 to 0.53 for PEV. With additional recording for LW instead of FPCM, pedigree accuracies increased to 0.54 for CV and to 0.61 for PEV. Genomic accuracies increased to 0.57 for CV and to 0.60 for PEV. With both FPCM and LW available for evaluated animals, accuracy was highest (0.62 for CV and 0.61 for PEV in pedigree, and 0.63 for CV and 0.61 for PEV in genomic analyses). Recording predictor traits for only the reference population did not increase DMI breeding value accuracy. Recording predictor traits for both reference and evaluated animals significantly increased DMI breeding value accuracy and removed the bias observed when only reference animals had records. The benefit of using genomic instead of pedigree relationships was reduced when more predictor traits were used. Using predictor traits may be an inexpensive way to significantly increase the accuracy and remove the bias of (genomic) breeding values of scarcely recorded traits such as feed intake.

Multi-breed genetic evaluation in a Gelbvieh population.

A multi-breed model was presented for the genetic evaluation of growth traits in beef cattle. In addition to the fixed effects, random direct and maternal genetic effects, and random maternal permanent environmental effects are considered; the model also fits direct and maternal heterosis and direct and maternal breed-of-founder (BOF) x generation group effects using a Bayesian approach that weights prior literature estimates relative to information supplied by the dataset to which the model will be applied. The multi-breed evaluation procedures also allow the inclusion of external evaluations for animals of other breeds. The multi-breed model was applied to a dataset provided by the American Gelbvieh Association. Different analyses were conducted by varying the weights given to the prior literature relative to the information provided by the dataset. Large differences were observed for the heterosis estimates, the BOF x generation group effect estimates, and the predicted breeding values across breeds due to the weights posed on prior literature estimates versus estimates derived directly from data. However, the rankings within breed were observed to be relatively robust to the different weights on prior information.

Genetic parameters for first and second lactation milk yields of Polish black and white cattle with random regression test-day models.

Single- and two-trait random regression models were applied to estimate variance components of test-day records of milk, fat, and protein yields in the first and second lactation of Polish Black and White cattle. The model included fixed herd test-day effect, three covariates to describe lactation curve nested within age-season classes, and random regressions for additive genetic and permanent environmental effects. In two-parity models, each parity was treated as a separate trait. For milk and the two-parity model, heritabilities were in the range of 0.14 to 0.19 throughout first lactation and 0.10 to 0.16 throughout second lactation. For fat, heritabilities were within 0.11 to 0.16 and 0.11 to 0.22 throughout first and second lactations, respectively. For protein in the two-parity model, heritabilities were within 0.10 to 0.15 throughout most of first lactation and within 0.06 to 0.15 throughout the most of second lactation. For milk, genetic correlations between the first and second parities were 0.6 at the beginning of the lactation, rising to 0.9 in the middle, and 0.8 at the end of the lactation. For fat, the corresponding correlations were 0.6, 0.8, and 0.7, respectively, and for protein were 0.6, 0.8, and 0.8, respectively. Heritability estimates for all traits were flatter for the two-parity model. Relatively smooth genetic and permanent environmental variances with the two-parity model indicated that large swings of heritabilities could be artifacts of single-trait random regression models. High correlations between most of test day records across lactations suggested that a repeatability model could be considered as an alternative to a multiple-trait model to analyze multiple parities.

Sperm pre-incubation prior to insemination affects the sex ratio of bovine embryos produced in vitro.

The objective of the present study was to determine whether sperm incubation prior to oocyte insemination in vitro affects the sex ratio of resulting blastocyst. Cumulus-oocyte-complexes (COCs) collected from slaughterhouse ovaries were matured in vitro and inseminated with frozen-thawed semen of three proven artificial insemination (AI) bulls pre-incubated in vitro in Sperm-Talp for 6 and 24 h. On day-9 blastocysts were collected and processed for sex determination. More than 80% of blastocyst were successfully sexed. There were no significant differences in cleavage and blastocyst rates using sperm pre-incubated for 6 h as compared with the 0-h pre-incubation control group. The cleavage and blastocyst rates were significantly lower in the 24-h pre-incubation group. The male to female ratio, when compared with the theoretical 1 : 1, differed significantly in favour of females among hatched (viable) blastocysts derived from sperm pre-incubated for 24 h prior to insemination as well as among all blastocytsts in the 6-h group. Moreover, when the sperm treatment was considered, the sex ratio was affected only among hatched blastocysts in 24-h pre-incubation group. It was concluded that prolonged sperm pre-incubation influences the rate of development and the sex ratio among hatched blastocysts.

Strategies for estimating the parameters needed for different test-day models.

Currently, most analyses of parameters in test-day models involve two types of models: random regression, where various functions describe variability of (co)variances with regard to days in milk, and multiple traits, where observations in adjacent days in milk are treated as one trait. The methodologies used for estimation of parameters included Bayesian via Gibbs sampling, and REML in the form of derivative-free, expectation-maximization, or average-information algorithms. The first method is simpler and uses less memory but may need many rounds to produce posterior samples. In REML, however, the stopping point is well established. Because of computing limitations, the largest estimations of parameters were on fewer than 20,000 animals. The magnitude and pattern of heritabilities varied widely, which could be caused by simplifications in the model, overparameterization, small sample size, and unrepresentative samples. Patterns of heritability differ among random regression and multiple-trait models. Accurate parameters for large multi-trait random regression models may be difficult to obtain at the present time. Parameters that are sufficiently accurate in practice may be obtained outside the complete prediction model by a constructive approach, where parameters averaged over the lactation would be combined with several typical curves for (co)variances for days in milk. Obtained parameters could be used for any model, and could also aid in comparison of models.

Short communication: effect of leptin gene polymorphisms on breeding value for milk production traits.

New molecular techniques focused on genome analysis open new possibilities for complex evaluation of economically important traits in farm animals. Milk production traits are typical quantitative characteristics controlled by a number of genes. Mutations in their sequences may alter animal performance as well as their breeding values. In this study, we investigated the effect of 3 restriction fragment length polymorphisms (RFLP): HphI, Kpn2I, and Sau3AI in the leptin gene, on bull breeding values for milk, fat, and protein yield, and fat and protein content. One hundred seventeen Polish Black and White AI bulls were genotyped. Pedigree analysis indicated a relatively close relationship between the bulls. Statistical analysis indicated that the HphI polymorphism has a significant effect on milk and protein yield. Animals with the TT genotype had approximately 2x higher estimated breeding values for milk and protein yields. No effect was found for the other 2 polymorphisms.