Genetic aspects for the behaviour of lactating sows towards humans.

With the keeping of lactating sows in loose housing systems, ensuring work safety for stockpersons is gaining importance. Aim of the present study was to develop tests characterising the behaviour of lactating sows in farrowing environments with more freedom to move. The behaviour towards humans in different management procedures was examined. Emphasis was given to integrate tests into daily routines. The study was conducted in a nucleus herd with 771 purebred Landrace sows. Data were collected from October 2016 until December 2018. Sows were kept in individual indoor pens with movable farrowing crates in which the animals were restrained from 7 days antepartum (ap) to an average of 7 days postpartum (pp). The Dummy Arm Test (DAT; 1444 observations) was used to assess the sows' reaction towards a stockperson handling the piglets around day 4 pp (closed crates). With the Towel Test (TT; 2846 observations), the reaction of sows to a novel object and an unexpected situation was assessed. The Trough Cleaning Test (TCT; 2805 observations) described the sows' response to common procedures such as trough cleaning. TT and TCT were conducted on days 3 pp (closed crates) and 10 pp (open crates). Variance components of behavioural traits were estimated univariately with a linear animal model, and genetic correlations between traits were derived using a multivariate animal model in ASreml 3.0. Most sows showed no or only a slight reaction to human interactions without attempting to attack them. However, a strong defensive reaction of sows was recorded in 4.0% (TCT), 4.5% (TT), and 10.7% (DAT) of observations. This behaviour of sows was observed more frequently in the open than in the closed pen system. Estimates of heritabilities (h2 ± SE) were h2 = 0.17 ± 0.05 for behaviour of sows towards humans (DAT), h2 = 0.19 ± 0.04 for response of sows towards unexpected situations (TT), and h2 = 0.13 ± 0.04 for reactions of animals to TCT. Genetic correlations (rg ± SE) ranged from rg = 0.59 ± 0.37 between TT and TCT to rg = 0.77 ± 0.30 between TT and DAT. Our results show that the developed tests are suitable for assessing the behaviour of sows towards humans. Behavioural traits derived from these tests could be used as new phenotypes for the genetic selection of gentle and easy-to-handle sows. The genetic correlations of all tests studied were positive indicating related reaction patterns.

Single-step genomic best linear unbiased predictor genetic parameter estimations and genome-wide associations for milk fatty acid profiles, interval from calving to first insemination, and ketosis in Holstein cattle.

Milk fatty acids (FA) have been suggested as biomarkers for early-lactation metabolic diseases and for female fertility status. The aim of the present study was to infer associations between FA, the metabolic disorder ketosis (KET), and the interval from calving to first insemination (ICF) genetically and genomically. In this regard, we focused on a single-step genomic BLUP approach, allowing consideration of genotyped and ungenotyped cows simultaneously. The phenotypic data set considered 38,375 first-lactation Holstein cows, kept in 45 large-scale co-operator herds from 2 federal states in Germany. The calving years for these cows were from 2014 to 2017. Concentrations in milk from the first official milk recording test-day for saturated, unsaturated (UFA), monounsaturated (MUFA), polyunsaturated, palmitic, and stearic (C18:0) FA were determined via Fourier-transform infrared spectroscopy. Ketosis was defined as a binary trait according to a veterinarian diagnosis key, considering diagnoses within a 6-wk interval after calving. A subset of 9,786 cows was genotyped for 40,989 SNP markers. Variance components and heritabilities for all Gaussian distributed FA and for ICF, and for binary KET were estimated by applying single-step genomic BLUP single-trait linear and threshold models, respectively. Genetic correlations were estimated in series of bivariate runs. Genomic breeding values for the single-step genomic BLUP estimations were dependent traits in single-step GWAS. Heritabilities for FA were moderate in the range from 0.09 to 0.20 (standard error = 0.02-0.03), but quite small for ICF (0.08, standard error = 0.01) and for KET (0.05 on the underlying liability scale, posterior standard deviation = 0.02). Genetic correlations between KET and UFA, MUFA, and C18:0 were large (0.74 to 0.85, posterior standard deviation = 0.14-0.19), and low positive between KET and ICF (0.17, posterior standard deviation = 0.22). Genetic correlations between UFA, MUFA, and C18:0 with ICF ranged from 0.34 to 0.46 (standard error = 0.12). In single-step GWAS, we identified a large proportion of overlapping genomic regions for the different FA, especially for UFA and MUFA, and for saturated and palmitic FA. One identical significantly associated SNP was identified for C18:0 and KET on BTA 15. However, there was no genomic segment simultaneously significantly affecting all trait categories ICF, FA, and KET. Nevertheless, some of the annotated potential candidate genes DGKA, IGFBP4, and CXCL8 play a role in lipid metabolism and fertility mechanisms, and influence production diseases in early lactation. Genetic and genomic associations indicate that Fourier-transform infrared spectroscopy FA concentrations in milk from the first official test-day are valuable predictors for KET and for ICF.

Phenotypic relationships, genetic parameters, genome-wide associations, and identification of potential candidate genes for ketosis and fat-to-protein ratio in German Holstein cows.

Energy demand for milk production in early lactation exceeds energy intake, especially in high-yielding Holstein cows. Energy deficiency causes increasing susceptibility to metabolic disorders. In addition to several blood parameters, the fat-to-protein ratio (FPR) is suggested as an indicator for ketosis, because a FPR >1.5 refers to high lipolysis. The aim of this study was to analyze phenotypic, quantitative genetic, and genomic associations between FPR and ketosis. In this regard, 8,912 first-lactation Holstein cows were phenotyped for ketosis according to a veterinarian diagnosis key. Ketosis was diagnosed if the cow showed an abnormal carbohydrate metabolism with increased content of ketone bodies in the blood or urine. At least one entry for ketosis in the first 6 wk after calving implied a score = 1 (diseased); otherwise, a score = 0 (healthy) was assigned. The FPR from the first test-day was defined as a Gaussian distributed trait (FPRgauss), and also as a binary response trait (FPRbin), considering a threshold of FPR = 1.5. After imputation and quality controls, 45,613 SNP markers from the 8,912 genotyped cows were used for genomic studies. Phenotypically, an increasing ketosis incidence was associated with significantly higher FPR, and vice versa. Hence, from a practical trait recording perspective, first test-day FPR is suggested as an indicator for ketosis. The ketosis heritability was slightly larger when modeling the pedigree-based relationship matrix (pedigree-based: 0.17; SNP-based: 0.11). For FPRbin, heritabilities were larger when modeling the genomic relationship matrix (pedigree-based: 0.09; SNP-based: 0.15). For FPRgauss, heritabilities were almost identical for both pedigree and genomic relationship matrices (pedigree-based: 0.14; SNP-based: 0.15). Genetic correlations between ketosis with FPRbin and FPRgauss using either pedigree- or genomic-based relationship matrices were in a moderate range from 0.39 to 0.71. Applying genome-wide association studies, we identified the specific SNP rs109896020 (BTA 5, position: 115,456,438 bp) significantly contributing to ketosis. The identified potential candidate gene PARVB in close chromosomal distance is associated with nonalcoholic fatty liver disease in humans. The most important SNP contributing to FPRbin was located within the DGAT1 gene. Different SNP significantly contributed to ketosis and FPRbin, indicating different mechanisms for both traits genomically.

Review: Opportunities and challenges for small populations of dairy cattle in the era of genomics.

In modern dairy cattle breeding, genomic breeding programs have the potential to increase efficiency and genetic gain. At the same time, the requirements and the availability of genotypes and phenotypes present a challenge. The set-up of a large enough reference population for genomic prediction is problematic for numerically small breeds but also for hard to measure traits. The first part of this study is a review of the current literature on strategies to overcome the lack of reference data. One solution is the use of combined reference populations from different breeds, different countries, or different research populations. Results reveal that the level of relationship between the merged populations is the most important factor. Compiling closely related populations facilitates the accurate estimation of marker effects and thus results in high accuracies of genomic prediction. Consequently, mixed reference populations of the same breed, but from different countries are more promising than combining different breeds, especially if those are more distantly related. The use of female reference information has the potential to enlarge the reference population size. Including females is advisable for small populations and difficult traits, and maybe combined with genotyping females and imputing those that are un-genotyped. The efficient use of imputation for un-genotyped individuals requires a set of genotyped related animals and well-considered selection strategies which animals to choose for genotyping and phenotyping. Small populations have to find ways to derive additional advantages from the cost-intensive establishment of genomic breeding schemes. Possible solutions may be the use of genomic information for inbreeding control, parentage verification, within-herd selection, adjusted mating plans or conservation strategies. The second part of the paper deals with the issue of high-quality phenotypes against the background of new, difficult and hard to measure traits. The use of contracted herds for phenotyping is recommended, as additional traits, when compared to standard traits used in dairy cattle breeding can be measured at set moments in time. This can be undertaken even for the recording of health traits, thus resulting in complete contemporary groups for health traits. Future traits to be recorded and used in genomic breeding programs, at least partly will be traits for which traditional selection based on widespread phenotyping is not possible. Enabling phenotyping of sufficient numbers to enable genomic selection will rely on cooperation between scientists from different disciplines and may require multidisciplinary approaches.

Investigating the genetic background of bovine digital dermatitis using improved definitions of clinical status.

Bovine digital dermatitis (DD) is an increasing claw health problem in all cattle production systems worldwide. The objective of this study was to evaluate the use of an improved scoring of the clinical status for DD via M-scores accounting for the dynamics of the disease; that is, the transitions from one stage to another. The newly defined traits were then subjected to a genetic analysis to determine the genetic background for susceptibility to DD. Data consisted of 6,444 clinical observations from 729 Holstein heifers in a commercial dairy herd, collected applying the M-score system. The M-score system is a classification scheme for stages of DD that allows a macroscopic scoring based on clinical inspections of the bovine foot, thus it describes the stages of lesion development. The M-scores were used to define new DD trait definitions with different complexities. Linear mixed models and logistic models were used to identify fixed environmental effects and to estimate variance components. In total, 68% of all observations showed no DD status, whereas 11% were scored as infectious for and affected by DD, and 21% of all observations exhibited an affected but noninfectious status. For all traits, the probability of occurrence and clinical status were associated with age at observation and period of observation. Risk of becoming infected increased with age, and month of observation significantly affected all traits. Identification of the optimal month concerning DD herd status was consistent for all trait definitions; the last month of the trial was identified. In contrast, months exhibiting the highest least squares means of transformed scores differed depending on trait definition. In this respect, traits that can distinguish between healthy, infectious, and noninfectious stages of DD can account for the infectious potential of the herd and can serve as an alert tool. Estimates of heritabilities of traits studied ranged between 0.19 (±0.11) and 0.52 (±0.17), revealing a tendency for higher values for more complex trait definitions. In terms of genetic selection, all trait definitions identified the best (i.e., most resistant) animals, but only the new trait definitions were able to distinguish between animals with average and high predispositions for DD. Considering repeated measurements resulted in heritability estimates ranging between 0.13 (±0.05) and 0.29 (±0.10).

Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs.

The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.

A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits.

Previous research has found that a quantitative trait locus exists affecting calving and conformation traits on Bos taurus autosome 18 that may be related to increased calf birth weights, which are not routinely recorded in the United States. Birth weight data from large, intensively managed dairies in eastern Germany with management systems similar to those commonly found in the United States were used to develop a selection index predictor for predicted transmitting ability (PTA) of birth weight. The predictor included body depth, rump width, sire calving ease, sire gestation length, sire stillbirth, stature, and strength. Genetic and phenotypic correlations and heritabilities from the United States were substituted for the German values, and birth weight PTA predicted for 31,984 bulls with US genetic evaluations. A genome-wide association study was conducted on the predicted birth weight PTA with the 2-step genomic BLUP procedure used for routine evaluations in the United States. Allele substitution effects were predicted for 43,188 single nucleotide polymorphisms (SNP). Genotypes were available for 53,644 predictor animals. Gene set enrichment analysis was performed on the 100 SNP that had the largest effects expressed in additive genetic standard deviations. Several SNP related to growth and development were found among the 25 SNP with the largest effects, including markers located within or near (≤ 100 kbp) ABCA12, FLRT2, LHX4, MAP3K5, NRAC, NTNG1, PIGN, and ZNF75A. The gene set enrichment analysis identified the Kyoto Encyclopedia of Genes and Genomes "Regulation of actin cytoskeleton" pathway (bta04810) as being enriched. That pathway includes the ROCK gene, which is involved in placental function in the human, as well as other developmental genes (e.g., FAK and PAK). Prediction equations derived from one population are useful for identifying genes and gene networks associated with phenotypes that are not directly measured in a second population. This approach will identify only genes associated with the traits used to construct the birth weight predictor, and not loci that affect only birth weight.

A study based on records taken at time of hoof trimming reveals a strong association between the IQ motif-containing GTPase-activating protein 1 (IQGAP1) gene and sole hemorrhage in Holstein cattle.

Feet and leg problems have a major effect on the well-being and lifespan of the dairy cow and thus are economically important to the dairy farmer. Apart from approaches using genetic selection for classical traits from conformation scoring, attempts for genetic improvement can be based either on records of individual disease cases or on records of disorder status at time of hoof trimming. In this study, 1,962 first-lactation cows were subjected to hoof trimming with an assessment of disorder status for sole hemorrhage as a binary trait. Cows were from 7 large commercial herds in Mecklenburg-Western Pomerania (northeastern Germany) that had similar housing with cubicles, slatted flooring, little use of straw for bedding, and total mixed ration feeding. Cows were trimmed and assessed once, focusing on cows in the first half of the lactation. Herds were visited at intervals to enable recording of cohorts at a similar stage of lactation. Each cohort or herd-visit included between 31 and 165 cows. Additional measurements included body weight, back fat thickness, and body condition at time of trimming. Further data on dairy production, conformation scores, and reproductive performance were merged after collection of records had finished. The DNA extracted from blood of 1,183 cows was used for analysis with a custom-made array of 384 single nucleotide polymorphisms (SNP). The SNP were selected according to results from the literature for effects in classical conformation traits, from biochemical pathway analysis, and from comparative analysis of putative candidate genes in cattle, pigs, and sheep. Selection of cohorts of cows for SNP chip analysis was such that cohorts with extreme frequencies of disorders and cohorts with slightly deviating housing systems were excluded in this first step. The results from a mixed threshold model analysis with genotype included as a fixed effect and accounting for relationships among animals revealed that the intronic SNP rs29017173 (A/G) within the IQ motif-containing GTPase-activating protein 1 (IQGAP1, Bos taurus autosome 21) was significantly associated with disorder status. Back-transformed means of disorder status for the 3 genotypes were 0.37 (AA), 0.52 (AG), and 0.56 (GG). Using the full data set of 1,962 cows, including the less-suitable cohorts, gave back-transformed means of 0.51 (AA), 0.58 (AG), and 0.62 (GG). As SNP rs29017173 is included on the Illumina BovineSNP50 DNA Analysis BeadChip (Illumina Inc., San Diego, CA), a sample of 2,394 artificial insemination sires from the German calibration sample for genomic selection from birth years 1998 to 2003 was studied for possible correlated effects. The A/G polymorphism of SNP rs29017173 studied here was also associated with substantial effects for feet and leg traits from the classical conformation score system. Selection using this polymorphism will be facilitated by the fact that the same allele is favored for all traits with substantial effects.

Relationships between bovine hoof disorders, body condition traits, and test-day yields.

A designed field study was conducted on 1,962 first-lactation Holstein cows kept on 7 large-scale dairy farms in Germany, in loose-housing systems on standard slatted flooring. Records of hoof disorders at trimming composed of subclinical as well as clinical cases were combined with body measurements and body condition scores, test-day records, and further individual cow data. The 6 most frequent disorders were laminitis, also known as sole hemorrhage (57.3% of all cows), dermatitis digitalis (17.0%), dermatitis interdigitalis (7.9%), white line disease (12.6%), sole ulcer (7.1%), and interdigital hyperplasia (5.5%). The most important environmental effects were herd-visit date and stage of lactation. Heifers between 50 and 99 d in milk had the highest frequencies for laminitis. Lighter cows were less susceptible to laminitis and white line disease, but had a higher prevalence of interdigital hyperplasia. Relationships between stature and white line disease as well as relationships between body condition score and dermatitis digitalis were nonlinear, resulting in an improved disorder status of cows with an intermediate condition score and average stature. Increased biomechanical stress caused by different factors (weight, social rank, standing time) is a presumed effect that leads to an increased susceptibility for hoof diseases. From a management perspective, under- and overconditioning should be avoided. Milk production traits differed between cows with and without laminitis-related claw horn lesions. Fat percentage and fat-to-protein ratio in the first month before trimming were significantly decreased for cows with a positive laminitis status. Hence, this finding points to metabolic disorders being associated with a higher risk for hoof diseases. Estimates of heritabilities for laminitis, dermatitis digitalis, dermatitis interdigitalis, white line disease, and sole ulcer were 0.09, 0.14, 0.10, 0.11, and 0.06 when applying a threshold model with a probit link function.

Short communication: A comparison between purebred Holstein and Brown Swiss × Holstein cows for milk production, somatic cell score, milking speed, and udder measurements in the first 3 lactations.

Brown Swiss × Holstein (BS × HO) crossbred cows (n = 55) and purebred Holstein (HO) cows (n = 50) were compared for milk yield, fat and protein production, somatic cell score, milking speed, and udder measurements for the first 3 lactations. Cows from a designed experiment were housed in a freestall barn at the experimental station of the federal state of Saxony-Anhalt, Germany, and calved from July 2005 to August 2008. Best prediction was used to determine actual production for 305-d lactations from test-day observations. For the first 3 lactations, BS × HO cows and HO cows were not significantly different for milk yield, fat and protein production, or SCS. Average milking time was significantly longer for BS × HO cows than for HO cows for first, second, and third lactations by 35, 51, and 30s, respectively. Average milking speed expressed as average yield per minute was significantly lower for BS × HO cows than for HO cows for the first 3 lactations by 0.19, 0.35, and 0.19 kg/min, respectively. Front and rear teats were significantly longer for BS × HO cows than for HO cows. Furthermore, front and rear udder clearance was significantly lower for BS × HO cows compared with HO cows in first and second lactations.

Optimal strategies for the use of genomic selection in dairy cattle breeding programs.

The objective of the present study was to conduct a stochastic simulation study on the possible benefits of an application of genomic selection in dairy cattle breeding programs according to a variety of selection schemes. In addition, the heritability of the trait in question, the accuracy of genomic breeding values, and the number of animals to be genotyped were varied. Specifically, the question of genotyping males, females, or both, was addressed. Selection schemes were compared with a young bull breeding program. The main criterion for comparison was the average of true breeding values of selected young males to be used as replacements for artificial insemination bulls. Stochastic simulations were run with 50 repetitions each to generate individuals with phenotypes, breeding values estimated by BLUP, and true breeding values. Genomic breeding values were generated from true breeding values with defined accuracy. Examined scenarios included a group of selection schemes that featured genotyping of parents of future bulls only. Such schemes can be viewed as improvements of young bull programs, and they were found to be competitive with or superior to a classical young bull program. However, a genomic breeding program usually involves at least genotyping young male candidates. A second group of selection schemes reflected this requirement. Scenarios in this group were found to be superior over the young bull program by 1.0 to 1.2 standard deviations of the average true breeding value of young male candidates. Within this group of scenarios, one scheme referred to an ideal situation under which genotypes for male calves were available without limitation. Using the average of true breeding values as the criterion for comparison, this idealistic scenario was competitive with other scenarios only if the reliability of genomic breeding values was larger than 0.50. Conventionally, not all males available will have genotypes, and the 2 most promising scenarios included a preselection step for dams of future bulls. This preselection step can be based on conventional BLUP estimated breeding values for bull dams, because differences with a scheme under which both parents and the resulting male offspring are genotyped were marginal. Genotyping of young male candidates should be the focus of activities of today's breeding organizations.

Brown Swiss × Holstein crossbreds compared with pure Holsteins for calving traits, body weight, backfat thickness, fertility, and body measurements.

Brown Swiss × Holstein crossbred cows and pure Holstein cows were compared in a designed experiment. All cows were housed in a freestall barn at the experimental station of the federal state of Saxony-Anhalt, Germany, and calved from July 2005 to August 2008. Brown Swiss × Holstein crossbred cows were mated to Holstein AI bulls for first calving and mated to Fleckvieh artificial insemination (AI) bulls for second and third calvings. Pure Holstein cows were consistently mated to Holstein AI bulls. At first calving, Holstein-sired calves from Brown Swiss × Holstein crossbred dams (282 d) had longer gestation length than Holstein-sired calves from Holstein dams (280 d). For second and third calvings, gestation length was significantly longer for Fleckvieh-sired calves from Brown Swiss × Holstein crossbred dams (284 d) than for Holstein-sired calves from Holstein dams (278 d). Holstein-sired calves from Brown Swiss × Holstein crossbred dams (43 kg) and Holstein-sired calves from pure Holstein dams (42 kg) were not significantly different for calf weight at birth for first calving. For second and third calvings, Fleckvieh-sired calves from Brown Swiss × Holstein crossbred dams (50 kg) had significantly heavier calf weight at birth than Holstein-sired calves from pure Holstein dams (44 kg). For calving difficulty and stillbirth, Brown Swiss × Holstein crossbred cows were not different from pure Holstein cows at first calving or at second and third calving. Brown Swiss × Holstein crossbred cows (71 d) were not significantly different from pure Holstein cows (75 d) for days to first breeding during first lactation; however, Brown Swiss × Holstein crossbred cows (81 d) had significantly fewer days to first breeding than pure Holstein cows (89 d) during second lactation, and the crossbred cows (85 d) tended to have fewer days to first breeding than pure Holstein cows (92 d) during third lactation. For days open, Brown Swiss × Holstein crossbred cows were not significantly different than pure Holstein cows during any of the first 3 lactations. For body weight, Brown Swiss × Holstein crossbred cows were significantly heavier than pure Holstein cows during first lactation (621 kg versus 594 kg) and second lactation (678 kg versus 656 kg). Also, Brown Swiss × Holstein crossbred cows (18.20mm) had significantly more backfat thickness than pure Holstein cows (15.81 mm) during first lactation. Brown Swiss × Holstein crossbred cows (48 cm) had significantly greater chest width than pure Holstein cows (46 cm). Furthermore, Brown Swiss × Holstein crossbred cows had significantly longer front heel walls (5.2 cm versus 5.0 cm), significantly longer rear heel walls (4.2 cm versus 4.0 cm), and significantly more depth of the front heel (4.4 cm vs. 4.1cm) than pure Holstein cows. This study has shown that F(1) of Brown Swiss × Holstein cows are competitive with pure Holstein cows for all traits analyzed here. For fertility, crossbred Brown Swiss × Holstein cows exhibited fewer days to first breeding during second lactation than pure Holstein cows.

Application of selection index calculations to determine selection strategies in genomic breeding programs.

The availability of genomic estimated breeding values (GEBV) allows for possible modifications to existing dairy cattle breeding programs. Selection index calculations including genomic and phenotypic observations as index sources were used to determine the optimal number of offspring per genotyped sire with a focus on functional traits and the design of cooperator herds, and to evaluate the importance of a central station test for genotyped bull dams. Evaluation criteria to compare different breeding strategies were correlations between index and aggregate genotype (r(TI)), and the relative selection response percentage (RSR) of an index without single nucleotide polymorphism information in relation to a single nucleotide polymorphism-based index. The number of required daughter records per sire to achieve a predefined r(TI) strongly depends on the accuracy of GEBV (r(mg)) and the heritability of the trait. For a desired r(TI) of 0.8, h(2) = 0.10, and r(mg) = 0.5, at least 57 additional daughters have to be included in the genetic evaluation. Daughter records of genotyped sires are not necessary for optimal scenarios where r(mg) is greater than or equal to r(TI). There still is a substantial need for phenotypic daughter records, especially for low-heritability functional traits and r(mg) < 0.7. Phenotypic records from genotyped potential bull dams have no relevance for increasing r(TI), even with a low value for r(mg) of 0.5. Hence, genomic breeding programs should focus on recording functional traits within progeny groups, preferably in cooperator herds. For low-heritability traits and with r(mg) > 0.7, the RSR of conventional breeding programs was only 10% of RSR from genomic breeding strategies. As shown in scenarios including 2 traits in the index as well as in the aggregate genotype, the availability of highly accurate GEBV for production traits and low-accuracy GEBV for functional traits increased the risk of widening the gap between selection responses in production and functionality. Counteractions are possible, such as via higher economic weights for low-heritability functional traits. Finally, an alternative selection strategy considering only 2 pathways of selection for genotyped male calves and for cow dams was evaluated. This strategy is competitive with a 4-pathway genomic breeding program if the fraction of selected male calves for the artificial insemination program is below 1% and if selection is focused on functionality, thus pointing to substantial insufficiencies caused by low reliabilities of breeding values for cows for such traits in conventional bull dam selection schemes.

Evaluation of MAFbx expression as a marker for congenital splay leg in piglets.

Splay leg is a hereditary syndrome observed in highly varying frequency in newborn piglets. Although the phenotype indicates a muscular weakness, the etiology is still poorly understood. Only recently, the gene expression of muscle atrophy F-box (MAFbx; FBXO32) was proposed as being of diagnostic value for splay leg in piglet. In this study, total RNA from three healthy and three affected male piglets was isolated. Samples were collected from M. gracilis, Mm. adductores, and M. sartorius. Further samples were taken for histological and biochemical analyses. Expression of MAFbx was analysed by real-time RT-PCR and with the GeneChip" Porcine Genome Array (Affymetrix). No significant differences (p>0.05) were observed in relative MAFbx expression, either between the three muscles or between splay leg and healthy piglets for each muscle. The expression of further atrophy-related genes was unchanged, indicating that splay leg is not characterized by general muscular atrophy in the affected hind limbs. This is supported by histological and biochemical data that does not demonstrate signs of atrophy in splay leg muscles. We conclude that the diagnostic value of MAFbx expression for congenital splay leg in piglets is doubtful and that the disease is characterized by heterogeneous alterations in skeletal muscle.

A general method to validate breeding value prediction software.

The validity of national genetic evaluations depends on the quality of input data, on the model of analysis, and on the correctness of genetic evaluation software. A general strategy was developed to validate national breeding value prediction software: performances from a real data file were replaced with simulated ones, created from simulated fixed and random effects and residuals in such a way that BLUP estimates from the evaluation software must be equal to the simulated effects. This approach was implemented for a multiple-trait model and a random regression test-day model. An example was presented on test-day observations analyzed with a random regression animal model including a lactation curve described as a sum of fixed polynomial regression and fixed spline regression on days in milk, and with genetic and permanent environmental effects modeled by using Legendre polynomials of order 2. Residuals had heterogeneous variances, and phantom parent groups were included. This method can be easily extended to other linear models. The comparison of genetic evaluation results with simulated true effects is used to demonstrate the great efficiency and usefulness of the proposed method.

Exclusion of NFYB as candidate gene for congenital splay leg in piglets and radiation hybrid mapping of further five homologous porcine genes from human chromosome 12 (HSA12).

Nuclear transcription factor Y, beta (NFYB) was evaluated as candidate gene for congenital splay leg in piglets based on data from differential display and QTL analysis. We mapped NFYB to pig chromosome 5 (SSC5). By assigning further five porcine genes from the corresponding region on human chromosome (HSA) 12q23.3--> q24.11 to SSC5 and 14 we could confine an evolutionary breakpoint from an interval of more than 10 Mb to less than 400 kb. Comparative sequence analysis of the coding region of NFYB in healthy and splay leg piglets revealed no polymorphism. Inter-species conservation of the codons ranges from 87% to 95% between pig, human, cow, dog, rat and mouse, respectively. The expression of NFYB in M. biceps femoris was not different between healthy and splay leg piglets. However, healthy male piglets had a significantly higher expression than females. Our results exclude NFYB as candidate gene for congenital splay leg but provide a basis for selection of further candidates for the disease from SSC5.

Identification and analysis of putative regulatory sequences for the MYF5/MYF6 locus in different vertebrate species.

The myogenic factors (MYF) 5 and 6 are integral to the initiation and development of skeletal muscle and to the maintenance of its phenotype. Thus, they are candidate genes for growth- and meat quality-related traits. We performed a comparative sequence analysis of the MYF5/MYF6 locus in swine, cattle, dog, chicken and zebrafish on the basis of structural and functional information from human and mouse. Beside the characterization of upstream regulatory elements recently identified in mice, we demonstrate the existence of further highly conserved elements (E1 to E4) which may play a role in the regulation of MYF5 and MYF6 expression. Comparative sequence analysis of putative regulatory sequences in swine revealed a total of 21 single nucleotide polymorphisms (SNP) including 1 and 6 SNPs new for the promoters of MYF5 and MYF6, respectively. The conserved organization of the locus in vertebrates indicates a common basic mechanism of muscle development. However, the existence of numerous regulatory elements at large distances to MYF5 and MYF6 points to a very complex pattern of the gene regulation with significant differences between species.

Association of a melanocortin 4 receptor (MC4R) polymorphism with performance traits in Lithuanian White pigs.

The melanocortin 4 receptor is expressed in virtually all brain regions of mammals and plays an important role in energy homeostasis. Polymorphisms in this gene may thus be related to growth and obesity. In pigs, a non-synonymous polymorphic site was described (Asp298Asn) and demonstrated to affect cAMP production and to alter adenylyl cyclase signalling. Association studies revealed significant linkage of this mutation with production trait in pigs. In this study, 207 Lithuanian White pigs were genotyped at the MC4R locus and analysed on relationships between genotype and breeding values for several performance traits. The observed allele and genotype frequencies did not deviate significantly from Hardy-Weinberg equilibrium (wildtype allele 0.59; mutant allele 0.41) and are comparable with those described in other Large White populations. The mutant Asn298 allele of the MC4R gene was significantly associated with increased test daily gain, higher lean meat percentage and lower backfat thickness. There was a trend towards an improved feed conversion ratio (p = 0.065) in animals with the mutant allele whereas no significant effect was found on lifetime daily gain. These results indicate that the MC4R polymorphism should be integrated in selection programmes in the Lithuanian White to improve carcass composition.

Genetic relationships for dairy performance between large-scale and small-scale farm conditions.

Genotype by environment interaction can be detected via the estimation of genetic correlations between environments under an animal model based on data comprising genetic links between the strata. Genetic correlations were estimated for protein yield of Holstein cows within and across regions of Germany using REML under an animal model for lactation and test-day records. Subsets of the entire data were created, stratified by region or herd size within region, and comprised between 16,307 and 132,972 cows with first-lactation records. Substantial heterogeneity exists between regions in Western and Eastern Germany. In Western states, most farms are small, with typical herd sizes of 30 to 60 cows, whereas in Eastern states, mostly large herds with herd sizes of 500 to 2000 cows are common. The results show drastic differences for residual and permanent environmental variance components between Eastern and Western regions with increases of around 30% for Eastern regions. Additive genetic variances were of similar magnitude in both regions. Genetic correlations between Eastern and Western states were between 0.90 and 0.95 but dropped to 0.79 when data from an Eastern state were reduced to contain large herds only. The results indicate that differences in herd size account for more of the differences in genetic correlation than do geographic regional differences.