Resilience indicator traits in 3 dairy cattle breeds in Baden-Württemberg.

In recent years, research in animal breeding has increasingly focused on the topic of resilience, which is expected to continue in the future due to the need for high-yielding, healthy, and robust animals. In this context, an established approach is the calculation of resilience indicator traits with time series analyses. Examples are the variance and autocorrelation of daily milk yield in dairy cows. We applied this methodology to the German dairy cow population. Data from the 3 breeds (German Holstein, German Fleckvieh, and German Brown Swiss) were obtained, which included 13,949 lactations from 36 farms from the state Baden-Württemberg in Germany working with automatic milking systems. Using the milk yield data, the daily absolute milk yields, deviations between observed and expected daily milk yields, and relative proportions of daily milk yields in relation to lactation performance were calculated. We used the variance and autocorrelation of these data as phenotypes in our statistical analyses. We estimated a heritability of 0.047 for autocorrelation and heritabilities between 0.026 and 0.183 for variance-based indicator traits. Furthermore, significant breed differences could be observed, with a tendency of better resilience in Brown Swiss. The breed differences can be due to both genetic and environmental factors. A high value of a variance-based indicator trait indicates a low resilience. Performance traits were positively correlated with variance-based indicator traits calculated from absolute daily milk yields, but they were negatively correlated with variance-based indicators calculated from relative daily milk yields. Thus, they can be considered as different traits. Although variance-based indicators based on absolute daily milk yields were affected by the performance level, variance-based indicators based on relative daily milk yields were corrected for the performance level and also showed higher heritabilities. Thus, they seem to be more suitable for practical use. Further studies need to be conducted to calculate the correlations between resilience indicators, functional traits, and health traits.

Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica).

A large F2 cross with 920 Japanese quail was used to map QTL for phosphorus utilization, calcium utilization, feed per gain and body weight gain. In addition, four bone ash traits were included, because it is known that they are genetically correlated with the focal trait of phosphorus utilization. Trait recording was done at the juvenile stage of the birds. The individuals were genotyped genome-wide for about 4k SNPs and a linkage map constructed, which agreed well with the reference genome. QTL linkage mapping was performed using multimarker regression analysis in a line cross model. Single marker association mapping was done within the mapped QTL regions. The results revealed several genome-wide significant QTL. For the focal trait phosphorus utilization, a QTL on chromosome CJA3 could be detected by linkage mapping, which was substantiated by the results of the SNP association mapping. Four candidate genes were identified for this QTL, which should be investigated in future functional studies. Some overlap of QTL regions for different traits was detected, which is in agreement with the corresponding genetic correlations. It seems that all traits investigated are polygenic in nature with some significant QTL and probably many other small-effect QTL that were not detectable in this study.

Implementing a genomic rotational crossbreeding scheme to promote local dairy cattle breeds-A simulation study.

In dairy cattle breeding, there is a clear trend toward the use of only a few high-yielding breeds. One main reason is that efficient breeding programs require a certain population size. Since some numerically small breeds are well known for their functional traits, they might be an interesting crossing partner for high-yielding breeds with the aim to utilize heterosis. This simulation study investigated the transition period of a small cattle population for the implementation of genomic selection and rotational crossbreeding with a high-yielding breed. Real SNP chip genotype data from the numerically small red dairy breed Angler and the high-yielding breed Holstein Friesian were used to simulate the base generations, from which rotational crossbreeding was conducted for 10 generations. A polygenic trait with many quantitative trait loci with additive and directional dominance effects was simulated. Different selection methods for Angler sires (purebred performance, crossbred performance, and weighted purebred-crossbred performance) and different sizes and structures of the reference population (Angler, crossbred animals, and Angler plus crossbred animals) were considered. The results showed that the implementation of a genomic rotational crossbreeding scheme is an appealing option to promote the numerically small Angler breed. The growing reference population consisting of Angler and crossbred individuals maximized the genetic gain for Angler and the performance level for the crossbred individuals. Selection for purebred performance, crossbred performance, or a weighted combination of both hardly affected the results, and differences between selection scenarios were observed only in the long term with decreasing purebred-crossbred correlations.

A Novel Model to Explain Extreme Feather Pecking Behavior in Laying Hens.

Feather pecking (FP) is a serious economic and welfare problem in the domestic fowl. It has recently been shown that the distribution of FP bouts within groups is heterogeneous and contains a sub-population of extreme feather peckers (EFP). The present study proposed a novel model to detect EFP hens. A mixture of two negative binomial distributions was fitted to FP data of a F2 cross of about 960 hens, and, based on the results, a calculation of the posterior probability for each hen belonging to the EFP subgroup (pEFP) was done. The fit of the mixture distribution revealed that the EFP subgroup made up a proportion of one third of the F2 cross. The EFP birds came more frequently into pecking mood and showed higher pecking intensities compared to the remaining birds. Tonic immobility and emerge box tests were conducted at juvenile and adult age of the hens to relate fearfulness to EFP. After dichotomization, all traits were analyzed in a multivariate threshold model and a genomewide association study was performed. The new trait pEFP has a medium heritability of 0.35 and is positively correlated with the fear traits. Breeding for this new trait could be an interesting option to reduce the proportion of extreme feather peckers. An index of fear related traits might serve as a proxy to breed indirectly for pEFP. GWAS revealed that all traits are typical quantitative traits with many genes and small effects contributing to the genetic variance.

Genomic analysis of perinatal sucking reflex in German Brown Swiss calves.

A healthy sucking reflex is essential for newborn calves to ensure sufficient colostrum intake in the first few hours postpartum. In recent decades, European Brown Swiss breeders have repeatedly reported that some calves lack the ability to consume colostrum directly after birth due to an absent sucking reflex. In this study, we collected the phenotypes of more than 5,500 German Brown Swiss calves and performed variance component estimation with sire threshold models using Markov chain Monte Carlo algorithms. The 50K (777K) genotypes of nearly 2,000 (200) calves were collected, and an imputation was performed for all 50K genotypes up to 777K. Genome-wide association studies (GWAS) for the trait sucking reflex were conducted for all 777K genotypes. Depending on the trait coding, a low heritability was estimated to range from 0.08 to 0.11. The GWAS results identified 34 trait-associated SNP on 6 different chromosomes. Post-GWAS analyses showed significant overrepresentation of Gene Ontologies for central nervous development and several regulative processes. Functional annotation clustering and pathway analysis revealed relations to lipid metabolism, immune and endocrine systems, and signal transduction. The results of this study suggest that breeding for an improved sucking reflex is possible but requires large data sets for the estimation of reliable breeding values (either large progeny testing groups or a large reference genome in a genomic selection program).

Mapping QTL for production traits in segregating Piétrain pig populations using genome-wide association study results of F2 crosses.

In this study, genome-wide association study (GWAS) results of porcine F2 crosses were used to map QTL in outcross Piétrain populations. For this purpose, two F2 crosses (Piétrain × Meishan, n = 304; Piétrain × Wild Boar, n = 291) were genotyped with the PorcineSNP60v2 BeadChip and phenotyped for the dressing yield, carcass length, daily gain and drip loss traits. GWASs were conducted in the pooled F2 cross applying single marker mixed linear models. For the investigated traits, between two and five (in total 15) QTL core regions, spanning 250 segregating SNPs around a significant trait-associated peak SNP, were identified. The SNPs within the QTL core regions were subsequently tested for trait association in two outcross Piétrain populations consisting of 771 progeny-tested boars and 210 sows with their own performance records. In the sow (boar) dataset, five (eight) of the 15 mapped QTL were validated. Hence, many QTL mapped in the F2 crosses (with Piétrain as a common founder breed) are still segregating in the current Piétrain breed. This confirms the usefulness of existing F2 crosses for mapping QTL that are still segregating in the recent founder breed generation. The approach utilizes the high power of an F2 cross to map QTL in a breeding population for which it is not guaranteed that they would be found using a GWAS in this population.

Linkage disequilibrium pattern and genome-wide association mapping for meat traits in multiple porcine F2 crosses.

In the present study, data from four F2 crosses were analysed and used to study the linkage disequilibrium (LD) structure within and across the crosses. Genome-wide association analyses (GWASes) for conductivity and dressing out meat traits were conducted using single-marker and Bayesian multi-marker models using the pooled data from all F2 crosses. Porcine F2 crosses generated from the distantly related founder breeds Wild Boar, Piétrain and Meishan, as well as from a porcine F2 cross from the closely related founder breed Piétrain and an F1 Large White × Landrace cross were pooled. A total of 2572 F2 animals were genotyped using a 62K SNP chip. The positions of the SNPs were based on genome assembly Sscrofa11.1. After post-alignment and genotype filtering, approximately 50K SNPs were usable for LD studies and GWASes. The main findings of the present study are that the breakdown of LD was faster in crosses from closely related founder breeds compared to crosses from distantly related founders. The fastest breakdown of LD was observed by pooling the data. Based on the single-marker results and LD structure, clusters and windows were built for 1-Mb intervals. For conductivity and dressing out, 183 and 191 nominal significant associations respectively and six and five clusters respectively were found. Dominance was important for conductivity, and considering dominance in GWASes improved the mapping signals. Most clear signals were found for conductivity on SSC6, 8 and 15 and for dressing out on SSC2 and 7. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. However, further research is needed to investigate if dominance is also important in crossbreed pig breeding schemes.

Estimation of relative economic weights and the marginal willingness to pay for breeding traits of Brown Swiss cattle using discrete choice experiments.

Breeding traits are usually combined in a total merit index according to their economic weights to maximize genetic gain based on economic merit. However, this maximization may not always be the aim of the selection decisions by farm managers. A discrete choice experiment was used to evaluate the importance of traits in terms of the selection decisions of farm managers operating in different environments. Six trait complexes, the semen price, the interactions between these traits, and significant characteristics of the farms were included in a conditional logit model to estimate relative economic weights and the marginal willingness to pay for all traits. Milk value, conformation/udder, and fitness were the most important traits for the farmers, and significant interactions indicated that fitness is of greater importance on organically managed farms than on conventional farms. Farm managers with an advanced education placed more weight on the milk value trait than farm managers without advanced education. On conventional farms, managers weighted the traits milk value and conformation/udder highly. The conformation/udder and fitness trait complexes were important on organic farms. A new trait called perinatal sucking behavior of newborn calves should be included in the total merit index.

Inferring relationships between Phosphorus utilization, feed per gain, and bodyweight gain in an F2 cross of Japanese quail using recursive models.

Phosphorus utilization (PU) has received considerable attention in poultry nutrition. However, reliable estimates of genetic parameters for PU and related traits have largely not been reported until now; however, these are needed to assess whether selection for an improved PU would result in selection response. A large Japanese quail F2 cross was generated and 888 F2 individuals were phenotyped for PU, bodyweight gain (BWG), and feed per gain (F:G). Because it can reasonably be assumed that the interrelationships between these traits are complex, structural equation models were used. The structural coefficient λij describes the rate of change of trait I with respect to trait j for a model with a recursive effect of trait j on trait i Three recursive structural coefficients (λF:G,PU,λBWG,PU,λBWG,F:G) were selected a priori based on biological knowledge. The model was fitted using ASReml software. Standard errors of estimated variance components and genetic parameters were approximated using the delta method. The heritability of PU, F:G, and BWG were 0.136, 0.118, and 0.092. The structural coefficient[Formula: see text]indicates that an increase in PU leads to reduced and thus improved F:G. The estimate[Formula: see text]indicates that improved F:G leads to an increase in BWG. The overall effect of PU on BWG was[Formula: see text]i.e. an increase in PU of 1% leads to an increase of BWG of 0.374 g in the data collection period, which spanned five days. The phenotypic and genetic correlations were negative between PU and F:G as well as between BWG and F:G and were positive between PU and BWG. These correlations are driven by direct genetic effects (pleiotropic genes or genes being in linkage disequilibrium) as well as by indirect genetic effects (genes affecting trait j affected indirectly trait i). The application of structural equation models contributed to our understanding of the complex biological relationship between PU, F:G, and BWG in quails. PU shows a heritability that is sufficient to achieve a selection response when breeding for this very-hard-to-measure trait.

Short communication: Importance of introgression for milk traits in the German Vorderwald and Hinterwald cattle.

The subject of the present study was to analyze the influence of genetic introgression on milk yield performance of the German local Vorderwald and Hinterwald cattle breeds. Deviations of milk yield, fat yield, and protein yield of cows as well as pedigree information were analyzed. A sire model was used to estimate genetic trend and effects of the migrant breeds. Migrant contributions to Vorderwald cattle were high and have been rising even in the recent past. The effects of these breeds on milk yield performance were positive. Montbéliarde cattle not only had the largest effect on milk production of Vorderwald cattle but also the highest genetic contribution to this breed. Genetic introgression with Montbéliarde continued until recently. This suggests that introgression of high-yielding breeds is still a preferred method for genetic improvement of local breeds, even though it diminishes their value for conservation. Hence, the current population management has too little focus on the preservation of genetic uniqueness. In comparison, migrant breed contributions to the Hinterwald cattle, a breed with a unique phenotype and an own niche, were moderate and almost constant over the time. For the Hinterwald cattle, no significant effect of migrant breeds could be detected, which suggests that population management has different priorities in different endangered breeds. We conclude that not only the registration of animals from local breeds but also the breeding programs themselves should be supported and need to be controlled.

Estimation of ancestral inbreeding effects on stillbirth, calving ease and birthweight in German Holstein dairy cattle.

In this study, the effect of different measurements of ancestral inbreeding on birthweight, calving ease and stillbirth were analysed. Three models were used to estimate the effect of ancestral inbreeding, and the estimated regression coefficient of phenotypic data on different measurements of ancestral inbreeding was used to quantify the effect of ancestral inbreeding. The first model included only one measurement of inbreeding, whereas the second model included the classical inbreeding coefficients and one alternative inbreeding coefficient. The third model included the classical inbreeding coefficients, the interaction between classical inbreeding and ancestral inbreeding, and the classical inbreeding coefficients of the dam. Phenotypic data for this study were collected from February 1998 to December 2008 on three large commercial milk farms. During this time, 36,477 calving events were recorded. All calves were weighed after birth, and 8.08% of the calves died within 48 h after calving. Calving ease was recorded on a scale between 1 and 4 (1 = easy birth, 4 = surgery), and 69.95, 20.91, 8.92 and 0.21% of the calvings were scored with 1, 2, 3 and 4, respectively. The average inbreeding coefficient of inbred animals was 0.03, and average ancestral inbreeding coefficients were 0.08 and 0.01, depending on how ancestral inbreeding was calculated. Approximately 26% of classically non-inbred animals showed ancestral inbreeding. Correlations between different inbreeding coefficients ranged between 0.46 and 0.99. No significant effect of ancestral inbreeding was found for calving ease, because the number of animals with reasonable high level of ancestral inbreeding was too low. Significant effects of ancestral inbreeding were estimated for birthweight and stillbirth. Unfavourable effects of ancestral inbreeding were observed for birthweight. However, favourable purging effects were estimated for stillbirth, indicating that purging could be partly beneficial for genetic improvement of stillbirth.

Genome-wide association analysis for growth, muscularity and meat quality in Piétrain pigs.

Improvement in growth and meat quality is one of the main objectives in sire line pig breeding programmes. Mapping quantitative trait loci for these traits using experimental crosses and a linkage-based approach has been performed frequently in the past. The Piétrain breed often was involved as a founder breed to establish the experimental crosses. This breed was selected for muscularity and leanness but shows relatively poor meat quality. It is frequently used as a sire line breed. With the advent of genome-wide and dense SNP chips in pig genomic research, it is possible to also conduct genome-wide association studies within the Piétrain breed. In this study, around 500 progeny-tested sires were genotyped with 60k SNPs. Data filtering showed that around 48k SNPs were useable in this sample. These SNPs were used to conduct a genome-wide association study for growth, muscularity and meat quality traits. Because it is known that a mutation in the RYR1 gene located on chromosome 6 shows a major effect on meat quality, this mutation was included in the models. Single-marker and multimarker association analyses were performed. The results revealed between zero and eight significant associations per trait with P < 5 × 10(-5) . Of special interest are SNPs located on SSC6, SSC10 and SSC15.

Bos indicus introgression into (peri-)alpine cattle breeds - evidence from the analysis of bovine whey protein variants.

The major bovine whey proteins, α-lactalbumin (α-LA) and ß-lactoglobulin (ß-LG), exhibit breed-specific genetic variation. The aim of this study was to identify possible new protein variants and determine the distribution of variants across a variety of 18 taurine and indicine cattle breeds applying a DNA-based sequencing approach. To this end, the open reading frames of the respective genes (LALBA and LGB) were sequenced in 476 animals. Within the LALBA gene, a previously unknown synonymous and a previously undesignated non-synonymous nucleotide exchange were identified. Furthermore, two known α-LA variants (A and B) and four known ß-LG variants (A, B, C and W) were determined. The occurrence of typical indicine variants in some taurine cattle breeds, such as Suisse Eringer, German Hinterwälder and Hungarian Grey Steppe, further supports the hypothesis of ancient Bos indicus introgression into (peri-)alpine cattle breeds.

The contribution of migrant breeds to the genetic gain of beef traits of German Vorderwald and Hinterwald cattle.

During the past decades, migrant contributions have accumulated in many local breeds. Cross-breeding was carried out to mitigate the risk of inbreeding depression and to improve the performance of local breeds. However, breeding activities for local breeds were not as intensive and target oriented as for popular high-yielding breeds. Therefore, even if performance improved, the gap between the performance of local and popular breeds increased for many traits. Furthermore, the genetic originality of local breeds declined due to the increasing contributions of migrant breeds. This study examined the importance of migrant breed influences for the realization of breeding progress of beef traits of German Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. The effect of the French cattle breed Montbéliard (p-value 0.014) on daily gain of Vorderwald bulls at test station was positive. The effects of Vorderwald ancestors (p-value for daily gain 0.007 and p-value for net gain 0.004) were positive for both traits under consideration in the population of Hinterwald cattle. Additionally, the effect of remaining breeds (p-value 0.030) on net gain of Hinterwald cattle in the field was also positive. The estimated effect of Fleckvieh ancestors on net gain of Hinterwald cattle was even larger but not significant. Breeding values adjusted for the effects of the migrant breeds showed little genetic trend.

Investigations on the pattern of linkage disequilibrium and selection signatures in the genomes of German Piétrain pigs.

The aim of this study was to study the population structure, to characterize the LD structure and to define core regions based on low recombination rates among SNP pairs in the genome of Piétrain pigs using data from the PorcineSNP60 BeadChip. This breed is a European sire line and was strongly selected for lean meat content during the last decades. The data were used to map signatures of selection using the REHH test. In the first step, selection signatures were searched genome-wide using only core haplotypes having a frequency above 0.25. In the second step, the results from the selection signature analysis were matched with the results from the recently conducted genome-wide association study for economical relevant traits to investigate putative overlaps of chromosomal regions. A small subdivision of the population with regard to the geographical origin of the individuals was observed. The extent of LD was determined genome-wide using r(2) values for SNP pairs with a distance ≤5 Mb and was on average 0.34. This comparable low r(2) value indicates a high genetic diversity in the Piétrain population. Six REHH values having a p-value < 0.001 were genome-wide detected. These were located on SSC1, 2, 6 and 17. Three positional candidate genes with potential biological roles were suggested, called LOC100626459, LOC100626014 and MIR1. The results imply that for genome-wide analysis especially in this population, a higher marker density and higher sample sizes are required. For a number of nine SNPs, which were successfully annotated to core regions, the REHH test was applied. However, no selection signatures were found for those regions (p-value < 0.1).

A pilot study of the genetic variation of phosphorus utilization in young Japanese quail (Coturnix japonica).

This study estimated the genetic variance components of P utilization in Japanese quail. A parental generation was assembled from an unselected random-bred Japanese fattening quail line. Seven sires and 14 dams were randomly selected, and each sire was paired with 2 dams to produce full and half sibs. A total of 200 unsexed 1-d-old quail with known pedigree were wing-banded and raised during the first 4 d posthatch in groups in floor pens on wood shavings and fed a preexperimental diet that was adequate in all nutrients. Starting on d 5, quail were individually housed in metabolic compartments on P-free filter paper. This started a balance trial with 5 d of adaption and 5 d of total excreta collection. During this balance period, all quail were fed a low-P (3.9 g/kg of DM) corn-soybean meal-based diet with a Ca:P ratio of 1.6:1.0. Phosphorus and Ca utilization were determined individually using the difference in P or Ca intake and the total P or Ca excretion. The average P utilization was 72% and the average Ca utilization was 63%, each with very high variation. Heritabilities were estimated to be 0.09 (SE = 0.09) for P utilization and 0.09 (SE = 0.09) for Ca utilization. Heritabilities were close to the values reported in the literature for broilers and suggest that quail are suitable as a model animal. The SE of the heritability estimates were large. This implies that further studies with a larger sample size are needed to identify genetic and physiological mechanisms that influence P and Ca utilization in Japanese quail.

Genetic parameters for feather pecking and aggressive behavior in a large F2-cross of laying hens using generalized linear mixed models.

Feather pecking and aggressive pecking is a well-known problem in egg production. In the present study, genetic parameters for 4 feather-pecking-related traits were estimated using generalized linear mixed models. The traits were bouts of feather pecking delivered (FPD), bouts of feather pecking received (FPR), bouts of aggressive pecking delivered (APD), and bouts of aggressive pecking received (APR). An F2-design was established from 2 divergent selected founder lines. The lines were selected for low or high feather pecking for 10 generations. The number of F2 hens was 910. They were housed in pens with around 40 birds. Each pen was observed in 21 sessions of 20 min, distributed over 3 consecutive days. An animal model was applied that treated the bouts observed within 20 min as repeated observations. An over-dispersed Poisson distribution was assumed for observed counts and the link function was a log link. The model included a random animal effect, a random permanent environment effect, and a random day-by-hen effect. Residual variance was approximated on the link scale by the delta method. The results showed a heritability around 0.10 on the link scale for FPD and APD and of 0.04 for APR. The heritability of FPR was zero. For all behavior traits, substantial permanent environmental effects were observed. The approximate genetic correlation between FPD and APD (FPD and APR) was 0.81 (0.54). Egg production and feather eating records were collected on the same hens as well and were analyzed with a generalized linear mixed model, assuming a binomial distribution and using a probit link function. The heritability on the link scale for egg production was 0.40 and for feather eating 0.57. The approximate genetic correlation between FPD and egg production was 0.50 and between FPD and feather eating 0.73. Selection might help to reduce feather pecking, but this might result in an unfavorable correlated selection response reducing egg production. Feather eating and feather pecking are genetically correlated and this needs further investigation.

Genetic analysis of phenotypic indicators for heat tolerance in crossbred dairy cattle.

Climate change-induced rise in global temperatures has intensified heat stress on dairy cattle and is contributing to the generally observed low milk productivity. Selective breeding aimed at enhancing animals' ability to withstand rising temperatures while maintaining optimal performance is crucial for ensuring future access to dairy products. However, phenotypic indicators of heat tolerance are yet to be effectively factored into the objectives of most selective breeding programs. This study investigated the response of milk production to changing heat load as an indication of heat tolerance and the influence of calving season on this response in multibreed dairy cattle performing in three agroecological zones Kenya. First-parity 7-day average milk yield (65 261 milk records) of 1 739 cows were analyzed. Based on routinely recorded weather data that were accessible online, the Temperature-Humidity Index (THI) was calculated and used as a measure of heat load. THI measurements used represented averages of the same 7-day periods corresponding to each 7-day average milk record. Random regression models, including reaction norm functions, were fitted to derive two resilience indicators: slope of the reaction norm (Slope) and its absolute value (Absolute), reflecting changes in milk yield in response to the varying heat loads (THI 50 and THI 80). The genetic parameters of these indicators were estimated, and their associations with average test-day milk yield were examined. There were no substantial differences in the pattern of milk yield response to heat load between cows calving in dry and wet seasons. Animals with ≤50% Bos taurus genes were the most thermotolerant at extremely high heat load levels. Animals performing in semi-arid environments exhibited the highest heat tolerance capacity. Heritability estimates for these indicators ranged from 0.06 to 0.33 and were mostly significantly different from zero (P < 0.05). Slope at THI 80 had high (0.64-0.71) negative correlations with average daily milk yield, revealing that high-producing cows are more vulnerable to heat stress and vice versa. A high (0.63-0.74) positive correlation was observed between Absolute and average milk yield at THI 80. This implied that low milk-producing cows have a more stable milk production under heat-stress conditions and vice versa. The study demonstrated that the slope of the reaction norms and its absolute value can effectively measure the resilience of crossbred dairy cattle to varying heat load conditions. The implications of these findings are valuable in improving the heat tolerance of livestock species through genetic selection.

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

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

Genome-wide association analysis to identify genotype × environment interaction for milk protein yield and level of somatic cell score as environmental descriptors in German Holsteins.

Genotype by environment interaction (G × E) has been widely reported in dairy cattle. If the environment can be measured on a continuous scale, reaction norms can be applied to study G × E. The average herd milk production level has frequently been used as an environmental descriptor because it is influenced by the level of feeding or the feeding regimen. Another important environmental factor is the level of udder health and hygiene, for which the average herd somatic cell count might be a descriptor. In the present study, we conducted a genome-wide association analysis to identify single nucleotide polymorphisms (SNP) that affect intercept and slope of milk protein yield reaction norms when using the average herd test-day solution for somatic cell score as an environmental descriptor. Sire estimates for intercept and slope of the reaction norms were calculated from around 12 million daughter records, using linear reaction norm models. Sires were genotyped for ~54,000 SNP. The sire estimates were used as observations in the association analysis, using 1,797 sires. Significant SNP were confirmed in an independent validation set consisting of 500 sires. A known major gene affecting protein yield was included as a covariable in the statistical model. Sixty (21) SNP were confirmed for intercept with P ≤ 0.01 (P ≤ 0.001) in the validation set, and 28 and 11 SNP, respectively, were confirmed for slope. Most but not all SNP affecting slope also affected intercept. Comparison with an earlier study revealed that SNP affecting slope were, in general, also significant for slope when the environment was modeled by the average herd milk production level, although the two environmental descriptors were poorly correlated.