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In many European warmblood studbooks, clear specialization toward either jumping or dressage horses is evident. The Swedish Warmblood (SWB) is also undergoing such specialization, creating a possible need for separate breeding programs and a discipline-specific Young Horse Test (YHT). This study investigated how far specialization of the SWB breed has proceeded and the potential consequences. Individuals in a population of 122,054 SWB horses born between 1980 and 2020 were categorized according to pedigree as jumping (J), dressage (D), allround (AR), or thoroughbred (Th). Data on 8,713 J horses and 6,477 D horses assessed for eight traits in YHT 1999-2020 were used to estimate genetic parameters within and between J and D horses and between different periods. Future scenarios in which young horses are assessed for either jumping or dressage traits at YHT were also analyzed. More than 80% of horses born in 1980-1985 were found to be AR horses, while 92% of horses born in 2016-2020 belonged to a specialized category. The average relationship within J or D category was found to increase during the past decade, whereas the relationship between these categories decreased. Heritability estimates for gait traits were 0.42-0.56 for D horses and 0.25-0.38 for J horses. For jumping traits, heritability estimates were 0.17-0.26 for J horses and 0.10-0.18 for D horses. Genetic correlations between corresponding traits assessed in J and D horses were within the range 0.48-0.81, with a tendency to be lower in the late study period. In the future scenarios, heritability and genetic variance both decreased for traits that were not assessed in all horses, indicating that estimation of breeding value and genetic progress for these traits could be affected by a specialized YHT. However, ranking of sires based on estimated breeding values (EBVs) and accuracy of EBVs was only slightly altered for discipline-specific traits. With continued specialization in SWB, specialization of the YHT should thus be considered.

In this study, we compared mating allocations in Nordic Red Dairy Cattle using genomic information. We used linear programming to optimize different economic scores within each herd, considering genetic level, semen cost, the economic impact of recessive genetic defects, and genetic relationships. We selected 9,841 genotyped females born in Denmark, Finland, or Sweden in 2019 for mating allocations. We used 2 different pedigree relationship coefficients, the first tracing the pedigree 3 generations back from the parents of the potential mating and the second based on all available pedigree information. We used 3 different genomic relationship coefficients, 1 SNP-by-SNP genomic relationship and 2 based on shared genomic segments. We found high correlations (≥0.83) between the pedigree and genomic relationship measures. The mating results showed that it was possible to reduce the different genetic relationships between parents with minimal effect on genetic level. Including the cost of known recessive genetic defects eliminated expression of genetic defects. It was possible to reduce genomic relationships between parents with pedigree measures, but it was best done with genomic measures. Linear programming maximized the economic score for all herds studied within seconds, which means that it is suitable for implementation in mating software to be used by advisors and farmers.

Swedish Red (SR) and Swedish Holstein (SH) are the dominating commercial dairy cattle breeds in Sweden. Both breeds have undergone substantial changes during the last half century due to intensive selection for breeding goal traits, but also resulting from increased international exchange of breeding animals and genetic drift. The aim of this study was to learn more about changes in genomic diversity and inbreeding in these two breeds over time. Therefore, semen samples from old bulls were genotyped using the 150K Genomic Profiler SNP array and combined with 50K SNP array genotype data, obtained for more recent bulls from the Nordic Cattle Genetic Evaluation. Different measures of level of homozygosity, genomic inbreeding, relatedness and changes in allele frequency were estimated for bulls born during different time periods from the 1950s until 2020. In total, more than 33,000 SNPs for 9737 SR and 5041 SH bulls were included in the analysis using PLINK v1.9. The results showed higher average homozygosity for SR than for SH bulls up to around 2000, but the difference was very small after that. The average inbreeding coefficients based on deviation from expected homozygosity as well as on runs of homozygosity decreased until the early 1980s in both breeds, whereafter they started to increase again for SH, but stayed more stable for SR. From the 1990s onwards, SH displayed higher average inbreeding coefficients than SR. In the last studied birth year group (2015-2020), the mean inbreeding coefficient based on runs of homozygosity was 5.9% for SH and 3.7% for SR. A principal component analysis showed a pattern of genetic relationships related to the birth year period of the bulls, illustrating the gradual change of the genetic material within each breed. The change in allele frequency over time was generally larger for SH than for SR. The results show that the inbreeding level was higher half a century ago than at present, and the inbreeding levels were lower than in some other studied populations. Still, the increase seen for inbreeding coefficients and homozygosity, especially in SH during recent years, should be considered in future breeding strategies.

Assessment protocols to describe the various aspects of conformation, gait and jumping traits on a linear scale were introduced at young horse tests for Swedish Warmblood horses in 2013. The traits scored on a linear scale are assumed to be less subjective and more easily compared across populations than the traditional evaluated traits that are scored relative to the breeding goal. However, the resulting number of traits is considerable, and several of the traits are correlated. The aim of this study was to investigate the interrelationship between the different evaluated and linearly scored traits in Swedish Warmbloods using factor analysis. In total, 20,935 horses born 1996-2017 had information on evaluated traits, and 5450 of these also had linearly scored trait records assessed since 2014 when the protocol was updated. A factor analysis with varimax rotation was performed separately for evaluated and linearly scored traits using the Psych package in R. Height at withers was included in both analyses. A total of four factors for evaluated traits and 14 factors for linearly scored traits were kept for further analysis. Missing values for individual traits in horses with linearly scored trait records were imputed based on correlated traits before factor scores were calculated using factor loadings. Genetic parameters for, and correlations between, the resulting underlying factors were estimated using multiple-trait animal models in the BLUPF90 package. Heritability estimates were on a similar level as for the traits currently used in the genetic evaluation, ranging from 0.05 for the factor for linearly scored traits named L.behaviour (dominated by traits related to behaviour) to 0.59 for the factor for evaluated traits named E.size (dominated by height at withers and conformation). For both types of traits, separate factors were formed for jumping and gait traits, as well as for body size. High genetic correlations were estimated between such corresponding factors for evaluated traits and factors for linearly scored traits. In conclusion, factor analysis could be used to reduce the number of traits to be included in multiple-trait genetic evaluation or in genomic analysis for warmblood horses. It can also contribute to a better understanding of the interrelationships among the assessed traits and be useful to decide on subgroups of traits to be used in several multiple-trait evaluations on groups of original traits.

Equine insect bite hypersensitivity (IBH) is a pruritic skin allergy caused primarily by biting midges, Culicoides spp. IBH susceptibility has polygenic inheritance and occurs at high frequencies in several horse breeds worldwide, causing increased costs and reduced welfare of affected horses. The aim of this study was to identify and validate single nucleotide polymorphisms (SNPs) associated with equine IBH susceptibility. After quality control, 33,523 SNPs were included in a Bayesian genome-wide association study on 177 affected and 178 unaffected Icelandic horses. We report associated regions in E. caballus (ECA) 1, 3, 15 and 18, overlapping with known IBH QTLs in horses, and novel regions containing several genes, together explaining 11.46% of the total genetic variance. For validation, three SNPs on ECA 1 and ECA X (explaining the largest percentage of genetic variance) within 1-mb genomic windows for IBH were genotyped in an independent population of 280 Exmoor ponies. The associated genomic region (152-153 mb) on ECA 1 was confirmed in Exmoor ponies and contains the AQR gene involved in splicing processes and a long non-coding RNA. This study confirms the polygenic nature of IBH susceptibility and suggests a role of transcriptional regulatory mechanisms (e.g., alternative splicing) for IBH predisposition in these horse breeds. ispartof: JOURNAL OF ANIMAL BREEDING AND GENETICS vol:137 issue:2 pages:223-233 ispartof: location:Germany status: published

Fertility, represented by calving interval, has been included in the genetic evaluation of Icelandic cattle since 1993. In spite of this an unfavourable genetic trend is seen and, recent implementation of test-day models for the genetic evaluation of milk production has changed the premise of using calving interval to represent fertility. The aim of this study was to estimate genetic parameters and genetic trends of different female fertility traits in Icelandic dairy cattle and suggest new traits for the genetic evaluation. Insemination records for the first three lactations and the heifer period of 52,951 Icelandic cows were used to analyse the traits: conception rate at first insemination (CR), number of inseminations per service period (AIS), interval first to last insemination (IFL), interval calving to first insemination (ICF), interval calving to last insemination (ICL) and calving interval (CI). Correlations between fertility and production traits were also estimated. Five different linear animal models were used to estimate (co)variance components. Breeding values were compared, and genetic trends of fertility traits were investigated. Estimated heritabilities for the fertility traits were low, ranging from 0.01 (IFL) to 0.08 (ICF). Genetic correlations between heifer and cow performances within traits ranged from 0.23 to 0.81. Between lactations within traits, the genetic correlations ranged from 0.36 to 1.00. Genetic correlations between different heifer traits were strong, and between different cow fertility traits they ranged from weak (-0.17) to very strong (0.97). Genetic correlations between the fertility and production traits were generally unfavourable, but more pronouncedly so for AIS, IFL, ICL and CI than for ICF and CR. Estimated genetic trends seemed unfavourable for the traits AIS, IFL and CI and favourable for ICF and ICL. In a revised genetic evaluation for fertility in Icelandic cattle, the traits ICF and IFL should be included to represent cow fertility, and CR to represent heifer fertility.

Background Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). Conclusions We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.

Recessive lethal variants often segregate at low frequencies in animal populations, such that two randomly selected individuals are unlikely to carry the same mutation. However, the likelihood of an individual inheriting two copies of a recessive lethal mutation is dramatically increased by inbreeding events. Such occurrences are particularly common in domestic animal populations, which are often characterised by high rates of inbreeding and low effective population sizes. To date there have been no published investigations into the presence of specific variants at high frequencies in domestic horse populations. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance.In this study, we scanned genotype data from Thoroughbred horses(n= 526) for adjacent single nucleotide polymorphisms (SNPs) at high heterozygote frequencies, but with a complete absence of homozygotes. Two SNPs that matched these criteria were mapped to an intronic region in theLY49Bgene, indicating that a closely linked mutation may cause lethality in homozygous state. Despite a complete absence of homozygotes, almost 35% of Thoroughbreds included in these analyses were heterozygous for both SNPs. A similar loss or absence of homozygotes was observed in genotype data from other domestic horse breeds (n= 2030). Variant analysis of whole-genome sequence data (n= 90) identified two SNPs in the 3’UTR region of theLY49Bgene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed thatLY49Bis expressed in the trophoblast during placentation stage of development.In this study, a region in theLY49Bgene was identified as a strong candidate for harbouring a variant causing lethality in homozygous state. These findings suggest thatLY49Bmay have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations.Author SummaryRecessive lethal mutations may reach high frequencies in livestock populations due to selective breeding practices, resulting in reduced fertility rates. In this study, we characterise recessive lethal mutations at high frequencies in the Thoroughbred horse population, a breed with high rates of inbreeding and low genetic diversity. We identified a haplotype in theLY49Bgene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Two 3’UTR variants were identified as most likely to cause loss of function in theLY49Bgene, resulting in lethality. This finding provides novel insights into the potential importance ofLY49Bin equine development. Additionally, this study may assist with breeding strategies to improve fertility rates in the Thoroughbred and other domestic horse breeds.

This study investigated different aspects of the trait spirit that is routinely recorded in breeding field tests (BFTs) for Icelandic horses. Genetic parameters were estimated for spirit and six newly introduced temperament suppleness traits assessed by judges and riders in Icelandic BFTs, and for everyday life temperament traits assessed by owners of breeding horses in 2014 and 2015. The findings suggested moderate heritability for some temperament traits assessed by riders in BFTs and showed that the assessment method needs to be improved in order for judges to discern the variation in these traits. Furthermore, according to estimated correlations the score for spirit described only part of the general temperament of the horse, where aspects of general nerve strength was not well covered. Nevertheless, no clearly unfavourable correlations with spirit were found and the majority of horse owners surveyed in this study were satisfied with the assessment for spirit.

The Swedish Mountain (Fjall) cattle and the subpopulation Fjallnara originates from northern Sweden. They are differentiated from both traditional and commercial cattle from southern Sweden. We analysed data from the GGP HD150k SNP array and investigated genetic diversity and differences between Fjall and Fjallnara, and between different groups of Fjallnara. We found that the Fjallnara can be divided into four groups, which are differentiated from each other and from the other Fjall cattle. We also compared allele frequencies between different groups of Fjall and Fjallnara for some of the functional SNPs included in the SNP array. Interestingly, the B allele of Beta lactoglobulin has a very high frequency (94%) in the Fjallnara cattle, which is significantly different from the frequency in the Fjall cattle (60%). Comparing older samples of Fjall cattle with more recent samples, we found a significant increase in the frequency of the B allele in Fjall cattle.

This study compared the abilities of virgin heifer genomically enhanced breeding values (GEBV) and parent average breeding values (PA) to predict future cow performance. To increase confidence in genomic technology among farmers, a clear demonstration of the relationship between genomic predictions and future phenotypes is needed. We analyzed 12 different traits in first parity, including production, conformation, fer-tility, and other functional traits. Phenotype data were obtained from national milk recording schemes and breeding values from the Nordic Cattle Genetic Evalu-ation. Direct genomic breeding values were calculated using genomic BLUP and combined with traditional breeding values, using bivariate blending. The data covered 14,862 Red Dairy Cattle, 17,145 Holstein, and 7,330 Jersey genotyped virgin heifers born between 2013 and 2015 in Denmark, Finland, and Sweden. Phe-notypes adjusted for systematic environmental effects were used as measures of cow performance. Two meth-ods were used to compared virgin heifer GEBV and PA regarding their ability to predict future cow per-formance: (1) correlations between breeding values and adjusted phenotypes, (2) ranking cows into 4 quartiles for their virgin heifer GEBV or PA, and calculating actual cow performance for each quartile. We showed that virgin heifer GEBV predicted cow performance significantly better than PA for the vast majority of analyzed traits. The correlations with adjusted pheno-types were 38 to 136% higher for GEBV than for PA in Red Dairy Cattle, 42 to 194% higher for GEBV in Holstein, and 11 to 78% higher for GEBV in Jersey. The relative change between GEBV bottom and top quartiles compared with that between PA bottom and top quartiles ranged from 9 to 261% for RDC, 42 to 138% for Holstein, and 4 to 90% for Jersey. Hence, farmers in Denmark, Finland, and Sweden can have confidence in using genomic technology on their herds.

The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010–2011, and used Principal Coordinates Analysis and Discriminant Analysis of Principal Components to detect population stratification. Fixation index and Cross Population Extended Haplotype Homozygosity scores were used to scan the genome for potential signatures of selection. In accordance with current breeding practice, this study highlights the development of two separate breed subpopulations with putative signatures of selection in eleven chromosomes. These regions involve genes with known function in, e.g., mentality, endogenous reward system, development of connective tissues and muscles, motor control, body growth and development. This study shows genetic divergence, due to specialization towards different disciplines in SWB horses. This latter evidence can be of interest for SWB and other horse studbooks encountering specialized breeding.

The aims of this study were to investigate variation and clustering in breeding goal trait preferences among Norwegian dairy farmers and to identify factors with a systematic influence on their preferences. An internet-based questionnaire was sent out to dairy farmers connected to the Norwegian co-operative breeding organization Geno (N = 8222), of which 10.8% answered (N = 888). Of the 15 suggested traits fertility had the highest overall ranking, while parasite resistance and methane emission had the lowest. Four distinct preference clusters were identified by the means of cluster analysis, of which two had a high preference for milk production. Differences in terms of farm and herd characteristics between clusters suggests a mixture of systematic and intrinsic effects on breeding goal trait priorities. This study shows that Norwegian dairy farmers' preferences for breeding goal traits fall into four distinct clusters, both affected by herd and farm characteristics along with intrinsic values.

There is substantial international influence on the Swedish Warmblood (SWB) sport horse population. The SWB Association suspects that imported horses are pre-selected based on their anticipated performance level, which could lead to biased estimated breeding values (EBVs) for stallions. This study examined different strategies to handle records for imported horses in the genetic evaluation. The stallions were evaluated for 10 traits using 3 different EBV estimation methods that were compared based on ranking comparisons of stallions, accuracy, correlations and absolute differences between EBVs. The results showed that the stallions’ EBVs were affected by imported offspring which, as a group, had higher average scores than horses born in Sweden. Sire EBVs differed by up to 0.6 genetic standard deviation of the trait between methods for stallions with >50% imported offspring. Excluding imported offspring lowered the accuracies and caused larger re-ranking compared with including a fixed effect of or...

Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses. Results We investigated the patterns, population variation and gene annotation of CNV using the Axiom® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~ 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value Conclusions This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.

Cryptorchidism is a defect in males where one or both testes fail to descend normally into the scrotum. If both testes are retained, the stallion will be infertile. There are few studies of the prevalence of the condition in horses based on field data, and heritability estimates for equine cryptorchidism are lacking. The objective of this study was to provide data on prevalence and heritability of cryptorchidism in Icelandic horses born in Sweden. A questionnaire was sent to breeders, asking whether or not stallions born at the farm had both testes present in the scrotum at the age of 1, 6 and 12 months. Fixed effects were analysed using logistic regression and genetic parameters were estimated using linear animal models. Information about 595 yearling stallions born 1997–2011 was used in the analyses. Close to 9% of the yearlings did not have both testes in the scrotum. Probability of cryptorchidism in yearlings was significantly influenced by farm and time period of birth. Heritability estimates for cryptorchidism ranged from 0.12 to 0.32 (SE 0.08–0.12) on the observable scale, and from 0.35 to 0.96 (SE 0.24–0.40) when transformed to the underlying continuous scale. The results support that equine cryptorchidism is heritable. Further studies with more individuals included would be needed to confirm this.

A linear profiling protocol was introduced in 2013 at tests for 3-year-old Swedish Warmblood horses. In this protocol, traits are subjectively described on a nine-point linear scale from one biological extreme to the other. This complements the traditional scoring where horses are evaluated in relation to the breeding objective. This study aimed to investigate the suitability of the linear information for genetic evaluation. Data on 22 conformation traits, 17 movement traits, 14 jumping traits and one temperament trait from 3,410 horses tested between 2013 and 2016 were analysed using an animal model. For conformation traits, the heritabilities ranged from 0.10 for description of hock joint from behind to 0.52 for shape of the neck. For movement traits, the highest heritability (0.54) was estimated for elasticity in trot and the lowest (0.08) for energy in walk. The heritabilities for jumping traits ranged from 0.05 for the ability to focus on the assignment to 0.57 for scope. Genetic correlations between linear traits and corresponding traditionally scored traits were strong (-0.37 to in many cases

The hot topic of genetic modification and genome editing is sometimes presented as a rapid solution to various problems in the field of animal breeding and genetics. These technologies hold potential for future use in agriculture but we need to be aware of difficulties in large-scale application and integration in breeding schemes. In this review, we discuss applications of both classical genetic modifications (GM) using vectors and genome editing in dairy cattle breeding. We use an interdisciplinary approach considering both ethical and animal breeding perspectives. Decisions on how to make use of these techniques need to be made based not only on what is possible, but on what is reasonable to do. Principles of animal integrity, naturalness, risk perception, and animal welfare issues are examples of ethically relevant factors to consider. These factors also influence public perception and decisions about regulations by authorities. We need to acknowledge that we lack complete understanding of the genetic background of complex traits. It may be difficult, therefore, to predict the full effect of certain modifications in large-scale breeding programs. We present 2 potential applications: genome editing to dispense with dehorning, and insertion of human genes in bovine genomes to improve udder health as an example of classical GM. Both of these cases could be seen as beneficial for animal welfare but they differ in other aspects. In the former case, a genetic variant already present within the species is introduced, whereas in the latter case, transgenic animals are generated-this difference may influence how society regards the applications. We underline that the use of GM, as well as genome editing, of farm animals such as cattle is not independent of the context, and should be considered as part of an entire process, including, for example, the assisted reproduction technology that needs to be used. We propose that breeding organizations and breeding companies should take an active role in ethical discussions about the use of these techniques and thereby signal to society that these questions are being responsibly addressed.

In a previous study it was shown that a nonsense mutation in the DMRT3 gene alters the pat- tern of locomotion in horses and that this mutation has a strong positive impact on trotting performance of Standardbreds. One aim of this study was to test if rac- ing performance and trotting technique in the Nordic (Coldblood) trotters are also influenced by the DMRT3 genotype. Another aim was to further investigate the effect of the mutation on performance in Standardbreds, by using a within-family analysis and genotype-pheno- type correlations in a larger horse material than in the previous study. We genotyped 427 Nordic trotters and 621 Standardbreds for the DMRT3 nonsense mutation and a SNP in strong linkage disequilibrium with it. In Nordic trotters, we show that horses homozygous for the DMRT3 mutation (A) had significantly higher EBV for trotting performance traits than heterozygous (CA) or homozygous wild-type (CC) horses (P = 0.001). Furthermore, AA homozygotes had a higher propor- tion of victories and top 3 placings than horses het- erozygous or homozygous wild-type, when analyzing performance data for the period 3 to 6 yr of age (P = 0.06 and P = 0.05, respectively). Another finding in the Nordic trotters was that the DMRT3 mutation influ- enced trotting technique (P = 2.1 × 10 -8 ). Standardbred horses homozygous AA had significantly higher EBV for all traits than horses with at least 1 wild-type allele (CA and CC; P = 1.6 × 10 -16 ). In a within-family anal- ysis of Standardbreds, we found significant differences in several traits (e.g., earnings, P = 0.002; number of entered races, P = 0.004; and fraction of offspring that entered races, P = 0.002) among paternal half-sibs with genotype AA or CA sired by a CA stallion. For most traits, we found significant differences at young ages. For Nordic trotters, most of the results were signifi- cant at 3 yr of age but not for the older ages, and for the Standardbreds most of the results for the ages 3 to 5 were significant. For Nordic trotters, the proportion of victories and placings were the only traits that were significant for other ages than 3 yr.

While susceptibility to hypersensitive reactions is a common problem amongst humans and animals alike, the population structure of certain animal species and breeds provides a more advantageous route to better understanding the biology underpinning these condi- tions. The current study uses Exmoor ponies, a highly inbred breed of horse known to fre- quently suffer from insect bite hypersensitivity, to identify genomic regions associated with a type I and type IV hypersensitive reaction. A total of 110 cases and 170 controls were gen- otyped on the 670K Axiom Equine Genotyping Array. Quality control resulted in 452,457 SNPs and 268 individuals being tested for association. Genome-wide association analyses were performed using the GenABEL package in R and resulted in the identification of two regions of interest on Chromosome 8. The first region contained the most significant SNP identified, which was located in an intron of the DCC netrin 1 receptor gene. The second region identified contained multiple top SNPs and encompassed the PIGN , KIAA1468 , TNFRSF11A , ZCCHC2 , and PHLPP1 genes. Although additional studies will be needed to validate the importance of these regions in horses and the relevance of these regions in other species, the knowledge gained from the current study has the potential to be a step forward in unraveling the complex nature of hypersensitive reactions ispartof: PLoS One vol:11 issue:4 ispartof: location:United States status: published

Summary The genetic evaluation of Icelandic horses is currently based on results from breeding field tests of riding ability and conformation. The effect of integrating competition traits and/or test status into the genetic evaluation was studied concerning estimation bias, predictive ability, accuracy, correlations between breeding values and ranking of sires. Breeding field test data included 19 954 records from horses assessed in 11 countries during 1994–2008. Competition data included 44 160 records from 7687 horses competing in Iceland and Sweden in 1998–2008. Test status was defined as attendance of horses born in Iceland at breeding field tests and/or in competition. Overall, there were trivial differences between different genetic evaluation models regarding estimation bias and predictive ability. Very strong correlations were estimated between breeding values for combined indexes of conformation, riding ability and total score from different models. Higher accuracy was achieved for most of the traits when competition traits and/or test status were added to the model. Sires ranked differently when the new traits were added to the genetic evaluation model. It was concluded that competition traits should be integrated into the genetic evaluation. Further analyses on genetic parameters for test status and its relationship with the other traits are needed for future inclusion of test status in the genetic evaluation.

The consequences of assuming a zero environmental covariance between a binary trait 'test-status' and a continuous trait on the estimates of genetic parameters by restricted maximum likelihood and Gibbs sampling and on response from genetic selection when the true environmental covariance deviates from zero were studied. Data were simulated for two traits (one that culling was based on and a continuous trait) using the following true parameters, on the underlying scale: h² = 0.4; r(A) = 0.5; r(E) = 0.5, 0.0 or -0.5. The selection on the continuous trait was applied to five subsequent generations where 25 sires and 500 dams produced 1500 offspring per generation. Mass selection was applied in the analysis of the effect on estimation of genetic parameters. Estimated breeding values were used in the study of the effect of genetic selection on response and accuracy. The culling frequency was either 0.5 or 0.8 within each generation. Each of 10 replicates included 7500 records on 'test-status' and 9600 animals in the pedigree file. Results from bivariate analysis showed unbiased estimates of variance components and genetic parameters when true r(E) = 0.0. For r(E) = 0.5, variance components (13-19% bias) and especially (50-80%) were underestimated for the continuous trait, while heritability estimates were unbiased. For r(E) = -0.5, heritability estimates of test-status were unbiased, while genetic variance and heritability of the continuous trait together with were overestimated (25-50%). The bias was larger for the higher culling frequency. Culling always reduced genetic progress from selection, but the genetic progress was found to be robust to the use of wrong parameter values of the true environmental correlation between test-status and the continuous trait. Use of a bivariate linear-linear model reduced bias in genetic evaluations, when data were subject to culling.

The aim of this study was to compare different scenarios for bull dam selection in a nucleus herd. A deterministic simulation study using selection index methodology was undertaken. In the scenarios studied, differing amounts of information on functional traits were available when bull dams were selected, and the resulting genetic responses in these traits were compared. Field-recorded fertility traits used in the scenarios were available as progeny test results of artificial insemination bulls: these included pregnant at first insemination (PFI), interval between calving and first insemination (CFI), and cases of reproductive disorders (RD). Similarly, field-recorded cases of clinical mastitis (CM), lactation somatic cell score (LSCS), and protein yield (PY) were included for pedigree selection. In the scenarios, heat intensity score and progesterone levels were treated as new indicator traits of fertility recorded in the nucleus herd. Traits CFI and LSCS were assumed to be better recorded with higher heritability in the nucleus herd than in ordinary herds. Economic weights currently used in Nordic Cattle Genetic Evaluation (NAV) were adapted and used in the scenarios. The results showed that these weights, if used in multiple trait genetic evaluation, would lead to undesirable genetic changes in functional traits for the bull dam selection path in a nucleus environment. More frequent recording of additional traits failed to improve selection for functional traits, as did more frequent recording of ordinary traits. Restriction index methodology was used to derive the bull dam total weights that gave no unfavorable response (i.e., zero genetic change) in traits PFI, CFI, and CM. When summarized over lactations, the new bull dam total weights, when additional records from nucleus were used, had to be 12 to 23 times higher for fertility, and 3 times higher for mastitis, than the presently used NAV weights, if these traits were to remain unchanged through the bull dam selection path. Thus, nucleus herd selection of bull dams is questionable for low heritability traits that are already recorded in the field.

Genetic evaluation of Icelandic horses is currently based on results from breeding field tests where riding ability and conformation of the horses are evaluated over the course of 1-2 days. Only a small part of registered horses attend these field tests, and it can be assumed that these are not a random sample of the population. In this study, the trait test status was introduced, describing whether a horse was assessed in a breeding field test. This trait was analysed to find out whether it has a genetic variation and how it correlates genetically to other traits in the breeding goal. Breeding field test data included 39,443 mares born in Iceland in 1990-2001, of which 7431 were assessed in the period 1994-2007. The trait was defined in relation to age, gender and stud of horses. Variance and covariance components were estimated using the Markov Chain Monte Carlo method by applying the Gibbs sampler procedure in the DMU program. Three multivariate analyses were performed where the test status trait was analysed with breeding field test traits. Animal models and sire models were applied. Based on estimated heritabilities (0.51-0.67) and genetic correlations (0.00-0.87), the test status trait showed significant genetic variation and was strongly correlated to some traits. The test status trait reflects preselection in the breeding field test traits and should be included in the genetic evaluation to enhance the procedure, reduce selection bias and increase accuracy of the estimation.

Many genes are known to have an influence on conformation and performance traits; however, the role of one gene, Myostatin (MSTN), has been highlighted in recent studies on horses. Myostatin acts as a repressor in the development and regulation of differentiation and proliferative growth of skeletal muscle. Several studies have examined the link between MSTN, conformation, and performance in racing breeds, but no studies have investigated the relationship in Icelandic horses. Icelandic horses, a highly unique breed, are known both for their robust and compact conformation as well as their additional gaits tolt and pace. Three SNPs (g.65868604G>T [PR8604], g.66493737C>T [PR3737], and g.66495826A>G [PR5826]) flanking or within equine MSTN were genotyped in 195 Icelandic horses. The SNPs and haplotypes were analyzed for association with official estimated breeding values (EBV) for conformation traits (n = 11) and gaits (n = 5). The EBV for neck, withers, and shoulders was significantly associated with both PR8604 and PR3737 (P < 0.05). PR8604 was also associated with EBV for total conformation (P = 0.05). These associations were all supported by the haplotype analysis. However, while SNP PR5826 showed a significant association with EBVs for leg stance and hooves (P < 0.05), haplotype analyses for these traits failed to fully support these associations. This study demonstrates the possible role of MSTN on both the form and function of horses from non-racing breeds. Further analysis of Icelandic horses as well as other non-racing breeds would be beneficial and likely help to completely understand the influence of MSTN on conformation and performance in horses.

In a study of the possibility of using competition data in the genetic evaluation of Icelandic horses, data from competitions held in Iceland between 1999 and 2004 and in Sweden between 1998 and 2004 were analyzed to estimate the genetic parameters of competition performance traits. The data-sets from both countries included 18 982 records of 3790 horses in 379 different events. Two types of competition were included: sport competitions and gaeðinga competitions performed on oval tracks and on a straight track. Each type of competition involves several disciplines in which the horses are ridden in the various gaits. The traits analyzed were two different measures of four-gait, five-gait and tolt, and one pace trait. In both the four-gait and five-gait tests the gaits walk, trot, tolt and gallop are exhibited. In the five-gait test, pace is also exhibited. The traits tolt and pace are performances of these single gaits. Highly correlated and similar traits were combined, and three new traits relating to tolt, four-gait and five-gait were formed. No large differences in means or standard deviations of traits were found between countries. All traits were approximately normally distributed. Genetic parameters were estimated using linear animal models including the fixed effects of sex, age and event for all traits, and the level of discipline was included for some traits. Random permanent environmental effects were also included. Estimated heritabilities were moderate to high, ranging from 0.18 to 0.21 for sport-competition traits, from 0.33 to 0.35 for gaeðinga-competition traits and from 0.19 to 0.22 for combined traits. Estimated genetic correlations between different sport-competition traits varied from 0.63 to 0.96, and between the two gaeðinga-competition traits it was estimated at 0.43. Genetic correlations between sport- and gaeðinga-competition traits ranged from − 0.42 to 1.00. It was concluded that competition traits are suitable to include in genetic evaluations.

This thesis reports on an investigation of the mechanisms of edge wicking in retortable paperboard. Retortable board is used for packaging preserved food, a process which requires that the package and its contents be sterilised by exposure to high temperature steam for up to three hours. The board used must thus have higher water repellence than traditional liquid packaging. Water vapour that condenses on the cut edges on the outside of the board causes particular concern. The paperboards studied were made from refined and unrefined bleached softwood kraft pulp and from refined unbleached softwood kraft pulp in one or two plies with different sizing levels and structures. Samples of each of the boards were immersed in a water bath at 95 °C. Other samples from the same boards were exposed to a combination of saturated steam at 130 °C and condensed steam in a special apparatus developed for this purpose. The board samples were placed on a cooling plate to simulate the temperature gradient when a container of cold food is sterilised with heated steam. Still other samples were exposed to heated steam in the absence of condensation by hanging them freely in the apparatus. The extent of edge wicking in the boards was determined by gravimetric measurements and also by near-infrared (NIR) spectroscopy, a technique that yields more information about the moisture content profiles and the mechanisms of liquid sorption. The moisture content profiles of boards exposed to saturated steam in the absence of condensation show more uniform water uptake. This phenomenon can be explained by rapid vapour phase transport throughout the pore structure, followed by slower water uptake in the fibres. By contrast, in samples exposed to both heated steam and condensed steam, there was both liquid sorption in the fibre network and rapid vapour phase transport of the steam. The moisture content in those samples was much higher close to the edge and lower behind the liquid frontier. The edge wicking of high temperature water was greatest in board that was not fully sized, in low density board, and in board made from unrefined pulp. The greater edge wicking in board made from unbleached pulp can be accounted for in terms of its greater swelling potential. In the low density board and the board made from unrefined pulp, the lumens at the unsized edge and the weaker bonding strength are suggested to affect the results. Capillary sorption takes place in lumens and delaminated bonds at the edge and then any further propagation takes place entirely by fibre diffusion. Capillary sorption may also be important in damaged areas where broken fibre-fibre bonds are exposed to liquid. The weaker bonded area in low density board therefore also contributes to water sorption. Edge wicking in the boards placed on the cooling plate and exposed to a combination of saturated and condensed steam was of a different nature. For these samples, density was not an important factor. The difference is due to the different mechanism at work in this case, where the relative area of the edge exposed to condensed steam was larger in the high density boards than in the low density boards. In the high density boards, condensed steam was sorbed in the structure by diffusion in the fibre structure, whereas in low density boards, the dominant effect was vapour phase transport in the void spaces followed by water uptake in the fibres.

Frequencies of polymorphisms in myostatin vary in Icelandic horses according to the use of the horses

The objective of this study was to estimate genetic correlations between calving difficulty score and carcass traits in Charolais and Hereford cattle, treating first and later parity calvings as different traits. Genetic correlations between birth weight and carcass traits were also estimated. Field data on 59,182 Charolais and 27,051 Hereford calvings, and carcass traits of 5,260 Charolais and 1,232 Hereford bulls, were used in bivariate linear animal model analyses. Estimated heritabilities were moderate to high (0.22 to 0.50) for direct effects on birth weight, carcass weight, and (S)EUROP (European Community scale for carcass classification) grades for carcass fleshiness and fatness. Heritabilities of 0.07 to 0.18 were estimated for maternal effect on birth weight, and for direct and maternal effects on calving difficulty score at first parity. Lower heritabilities (0.01 to 0.05) were estimated for calving difficulty score at later parities. Carcass weight was positively genetically correlated (0.11 to 0.53) with both direct and maternal effects on birth weight and with direct effects on calving difficulty score. Carcass weight was, however, weakly or negatively (-0.70 to 0.07) correlated with maternal calving difficulty score. Higher carcass fatness grade was genetically associated with lower birth weight, and in most cases, also with less difficult calving. Genetic correlations with carcass fleshiness grade were highly variable. Moderately unfavorable correlations between carcass fleshiness grade and maternal calving difficulty score at first parity were estimated for both Charolais (0.42) and Hereford (0.54). This study found certain antagonistic genetic relationships between calving performance and carcass traits for both Charolais and Hereford cattle. Both direct and maternal calving performance, as well as carcass traits, should be included in the breeding goal and selected for in beef breeds.

The aim of this study was to estimate direct and maternal genetic parameters for calving difficulty score, stillbirth, and birth weight at first and later parities for Charolais and Hereford cattle in Sweden. Calving traits have long been recorded for pure-bred beef cattle in Sweden, but only birth weight has been used in the selection in order to avoid calving difficulties. Linear animal model analyses included records on birth weight for 60,309 Charolais and 30,789 Hereford calves born from 1980 to 1999, and calving traits for 74,538 Charolais and 37,077 Hereford calves born from 1980 to 2001. The frequencies of difficult calvings and stillbirths were approximately 6% at first and 1 to 2% at later parities for both breeds. Fewer than half the stillborn calves were born from difficult calvings. Heritabilities estimated for birth weight in different univariate and bivariate analyses for Charolais and Hereford calves born at first and later parities ranged from 0.44 to 0.51 for direct effects and 0.06 to 0.15 for maternal effects. Heritabilities on the observable scale for calving difficulty score of Charolais and Hereford, scored in three classes, ranged from 0.11 to 0.16 for direct and 0.07 to 0.12 for maternal effects at first parity, and lower at later parities. All estimated heritabilities for stillbirth were very low (0.002 to 0.016 on the observable scale). Direct-maternal genetic correlations were negative, with few exceptions. Genetic correlations between the traits and between parities within traits were generally moderate to high and positive. Calving difficulty score should be included in the genetic evaluation of beef breeds in Sweden, whereas progeny groups in Swedish beef populations are too small for stillbirth to be considered directly.

To investigate the possibility of using carcass data from commercial slaughterhouses for the genetic evaluation of beef cattle, genetic parameters for carcass traits and their correlations with field-recorded growth traits were estimated. The data comprised information on carcass weight (CWT), carcass fleshiness (FLESH) and carcass fatness grade (FAT) according to the (S)EUROP scale for 5870, 1509 and 1119 young bulls of the Charolais, Hereford and Simmental breeds, respectively. In addition, information on field-recorded pre-weaning gain (WG) and post-weaning gain (PWG) was available for more than 23 200 and 15 700 bulls, respectively. The breeds were analysed separately using BLUP animal models. The results showed that it is feasible to include field-recorded carcass traits in the genetic evaluation. The estimated direct heritabilities of FLESH, FAT, CWT, WG and PWG were in the ranges 0.21–0.39, 0.23–0.45, 0.42–0.70, 0.31–0.41 and 0.29–0.42, respectively. The genetic correlations differed between breeds, though for all breeds studied the genetic correlations with pre-weaning gain were weaker for FAT and FLESH than for CWT. The effect of selection on pre-weaning gain appeared to be stronger for CWT than for the other traits.

Insect bite hypersensitivity (IBH) is the most common allergic skin disease in horses and is caused by biting midges, mainly of the genus Culicoides. The disease predominantly comprises a type I hypersensitivity reaction, causing severe itching and discomfort that reduce the welfare and commercial value of the horse. It is a multifactorial disorder influenced by both genetic and environmental factors, with heritability ranging from 0.16 to 0.27 in various horse breeds. The worldwide prevalence in different horse breeds ranges from 3% to 60%; it is more than 50% in Icelandic horses exported to the European continent and approximately 8% in Swedish-born Icelandic horses. To minimize the influence of environmental effects, we analyzed Swedish-born Icelandic horses to identify genomic regions that regulate susceptibility to IBH. We performed a genome-wide association (GWA) study on 104 affected and 105 unaffected Icelandic horses genotyped using Illumina® EquineSNP50 Genotyping BeadChip. Quality control and population stratification analyses were performed with the GenABEL package in R (λ = 0.81). The association analysis was performed using the Bayesian variable selection method, Bayes C, implemented in GenSel software. The highest percentage of genetic variance was explained by the windows on X chromosomes (0.51% and 0.36% by 73 and 74 mb), 17 (0.34% by 77 mb), and 18 (0.34% by 26 mb). Overlapping regions with previous GWA studies were observed on chromosomes 7, 9, and 17. The windows identified in our study on chromosomes 7, 10, and 17 harbored immune system genes and are priorities for further investigation.

Summary Breeding programmes for warmblood sport horses are similar in the Nordic countries Sweden, Denmark, Finland and Norway, and stallions of same origin are used. The aim was to investigate whether a joint Nordic genetic evaluation based on lifetime competition performance is feasible and beneficial for breeding competitive sport horses in the Nordic countries. Results for almost 45 000 horses in show jumping and 30 000 horses in dressage were available. The larger populations in Sweden and Denmark contributed with 85% of the results. Heritabilities and genetic correlations between performances in the different countries were estimated, and comparisons of accuracies of estimated breeding values (EBVs) and number of stallions with EBVs based on national or joint data were studied. The heritabilities ranged between 0.25 and 0.42 for show jumping and between 0.14 and 0.55 for dressage. The genetic correlations between competition performances in the Nordic countries were estimated to 0.63–1.00. EBVs based on joint data increased accuracies for EBVs for stallions by 38–81% and increased the number of available stallions with EBVs by 40–288%, compared to EBVs based on national data only. A joint Nordic genetic evaluation for sport horses is recommended.