Should performance at different race lengths be treated as genetically distinct traits in Coldblooded trotters?

Speed, in the form of racing time per kilometre (km), is a performance trait of the Swedish-Norwegian Coldblooded trotter included in the joint Swedish-Norwegian genetic evaluation. A few popular stallions have dominated Coldblooded trotter breeding, which has led to an increasing average relationship between individuals in the population. This study investigated the scope for broadening the breeding goal by selecting for racing time per km over different race lengths (short: 1640 m, medium: 2140 m and long: 2640 m), as this could encourage the use of breeding sires that are less related to the population. Performance data on three- to 12-year-old Coldblooded trotters in all Swedish races run 1995-2021 were obtained from the Swedish Trotting Association. These data consisted of 46,356 observations for 8375 horses in short-distance races, 430,512 observations for 11,193 horses in medium-distance races and 11,006 observations for 3341 horses in long-distance races. Variance components and genetic correlations were calculated using a trivariate animal model with Gibbs sampling from the BLUPF90 suite of programs. Breeding values for the three traits were then estimated using univariate animal models with the same fixed and random effects as in the trivariate model. Heritability estimates of 0.27-0.28 and genetic correlations between racing time per km at the different distances of 0.97-0.99 were obtained. Despite the strong genetic correlation between the traits, there was some re-ranking among the top 10 and top 30 stallions based on distance-specific breeding values. Estimated rank correlation between breeding values for racing time per km in short- and medium-distance races was 0.86, while between short- and long-distance races and between medium- and long-distance races it was 0.61. Mean relationship within the top 10 and top 30 stallions based on breeding values for racing time per km at each distance was 0.31-0.33 and 0.23-0.24 while mean relationship to the rest of the population ranged from 0.17 to 0.18 for all groups, although the 10 and 30 top-ranking stallions differed somewhat in the traits. Estimated average increase in inbreeding was 0.1% per year of birth and 1.2% per generation. The strong genetic correlation between racing time per km at different distances did not support their use as genetically distinct traits. Re-ranking of stallions for racing time per km at different race lengths could favour the use of a larger number of stallions in breeding, but according to our results it would not promote the use of stallions that are less related to the total population. Other traits like longevity or health traits, for example, career length and orthopaedic status, may be more relevant in broadening the breeding goal and preventing a few sires dominating future breeding, and this would be interesting to study further.

Changes in genomic inbreeding and diversity over half a century in Swedish Red and Swedish Holstein dairy cattle.

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.

Milk production performance of Ankole crossbreds and Holstein Friesian cattle in different production environments of Rwanda.

The aim of the study was to assess the productive performance of dairy cattle in three different agro-ecological zones of Rwanda: Congo-Nile/Western (WAZ), Central plateau/Central (CAZ), and Eastern plateau/East Agro-ecological Zones (EAZ). A single-visit multi-subject survey was conducted to obtain information on the dairy cattle performance from 51 farms. The breed groups were classified as Ankole x Holstein Friesian (AF), other Ankole crossbreds (AX), and pure Holstein Friesian (F). The F had higher (p < 0.001) milk yield than AF in all zones except EAZ and AF had higher (p < 0.0001) milk yield than AX in all zones. Across all zones, F produced 9 L more than AX and 6 L more than AF per day. Cows from EAZ had the highest average milk yield; however, it was not significantly different from CAZ. The difference that was observed between AF in EAZ and AF in the other two zones indicates that agro-ecological zones should not only be the target in livestock development activities rather additional factors such as feed availability at farm level, social economic, and market infrastructure should be considered in Rwanda.

The effect of high temperature and humidity on milk yield in Ankole and crossbred cows.

Tropical regions are characterized by high temperature and humidity across the year. At high values of temperature humidity index (THI), there is a risk of heat stress leading to lower milk yield. The objective of this study was to describe the effect of season and the effect of maximum daily THI on milk yield of that day in purebred Ankole and Ankole-Friesian, Ankole-Jersey and Ankole-Sahiwal crosses in a tropical climate. In total, 53,730 records of daily milk yield from 183 cows in Rwanda were analyzed. The results showed that THI had a negative effect on daily milk yield above a threshold, but the effect was small (- 0.11 kg milk/THI unit at most). Purebred Ankole cows had the lowest daily milk yield and the lowest threshold (THI mean 66), as compared to the crossbreds (THI mean 68-69). Ankole-Friesian had a steeper decline in daily milk yield above the threshold than Ankole. The crossbreds, especially Ankole-Friesian, had higher daily milk yield than purebred Ankole also at very high THI. The results indicate some differences between breed groups in the way of coping with a hot and humid climate and raise questions about dairy cows' adaptation to such a climate.

Genome-wide association studies for canine hip dysplasia in single and multiple populations - implications and potential novel risk loci.

BACKGROUND: Association mapping studies of quantitative trait loci (QTL) for canine hip dysplasia (CHD) can contribute to the understanding of the genetic background of this common and debilitating disease and might contribute to its genetic improvement. The power of association studies for CHD is limited by relatively small sample numbers for CHD records within countries, suggesting potential benefits of joining data across countries. However, this is complicated due to the use of different scoring systems across countries. In this study, we incorporated routinely assessed CHD records and genotype data of German Shepherd dogs from two countries (UK and Sweden) to perform genome-wide association studies (GWAS) within populations using different variations of CHD phenotypes. As phenotypes, dogs were either classified into cases and controls based on the Fédération Cynologique Internationale (FCI) five-level grading of the worst hip or the FCI grade was treated as an ordinal trait. In a subsequent meta-analysis, we added publicly available data from a Finnish population and performed the GWAS across all populations. Genetic associations for the CHD phenotypes were evaluated in a linear mixed model using 62,089 SNPs. RESULTS: Multiple SNPs with genome-wide significant and suggestive associations were detected in single-population GWAS and the meta-analysis. Few of these SNPs overlapped between populations or between single-population GWAS and the meta-analysis, suggesting that many CHD-related QTL are population-specific. More significant or suggestive SNPs were identified when FCI grades were used as phenotypes in comparison to the case-control approach. MED13 (Chr 9) and PLEKHA7 (Chr 21) emerged as novel positional candidate genes associated with hip dysplasia. CONCLUSIONS: Our findings confirm the complex genetic nature of hip dysplasia in dogs, with multiple loci associated with the trait, most of which are population-specific. Routinely assessed CHD information collected across countries provide an opportunity to increase sample sizes and statistical power for association studies. While the lack of standardisation of CHD assessment schemes across countries poses a challenge, we showed that conversion of traits can be utilised to overcome this obstacle.

Genetic parameters of forage dry matter intake and milk produced from forage in Swedish Red and Holstein dairy cows.

High-yielding dairy cows are often fed high proportions of cereal grain and pulses. For several reasons, it would be desirable to replace these feed sources with forage, which is not suitable for human consumption. Feeding large amounts of forage to dairy cows could also make dairy production more publicly acceptable in the future. In this study, we estimated genetic parameters for total dry matter intake (DMI), DMI from forage (DMIFor), energy-corrected milk (ECM), and ECM produced from forage (ECMFor). A total of 1,177 lactations from 575 cows of Swedish Red (SR) and Holstein (HOL) dairy breeds were included in the study. Mixed linear animal random regression models were used, with fixed effect of calving season and lactation week nested within parity 1 and 2+, fixed effect of calving year, and random regression coefficients for breeding value (up to linear) and permanent environmental effect (up to quadratic) of the cow. Heritability for DMI and DMIFor was generally higher for HOL than for SR in all-parity data and in later parities; however, the opposite was true for first parity. Heritability for DMI and DMIFor during the first 8 wk averaged 0.11 and 0.15, respectively, in all-parity data for the 2 breeds. Corresponding values for ECMFor and ECM were 0.21 and 0.29, respectively. In first parity, values were 0.32, 0.36, 0.28, and 0.51, respectively. The genetic correlation between DMI and DMIFor was high, above 0.83, and fairly constant across the lactation. The genetic correlation between ECMFor and ECM was close to unity in the later part of lactation for both breeds, but was around 0.8 in the early lactation for both breeds; it decreased for HOL to 0.54 in wk 17. The genetic correlations between DMI and ECMFor and between DMIFor and ECMFor were low and negative for HOL (absolute value ∼0.2-0.3), but changed for SR from weakly positive in early lactation to negative values and back to positive toward the end of lactation. For most traits, the correlation between wk 1 and wk 8 into the lactation was very high; the lowest value was for DMI in HOL at 0.81. The genetic correlation between parities was rather high in the first part of the lactation. During the first 8 wk, the correlation was lower for HOL than for SR, except for ECM. We found that DMIFor and ECMFor showed reasonably large heritability, and future work should explore the possibility of genomic evaluations.

Milk production and lactation length in Ankole cattle and Ankole crossbreds in Rwanda.

This study assessed daily milk yield (DMY), 100-day (MY100), and 305-day (MY305) milk yield, and lactation length (LL) in purebred Ankole cattle and Ankole crossbreds, and the influence of environmental factors on these traits. Milk yield data were obtained for 865 cows and 1234 lactations and analyzed using a mixed linear model. The overall least squares mean of DMY, MY100, and MY305 across breed groups was 2.7 L (N = 1234, SD = 1.7), 262 L (N = 959, SD = 176), and 759 L (N = 448, SD = 439), respectively, while the average lactation length was 256 days (N = 960, SD = 122). All factors included (breed group, season and year of calving, and parity) were significant for yield traits, except season of calving for MY305. First-parity cows had the lowest milk production, and fourth-parity cows the highest. For all traits, pure Ankole cows had the lowest milk yield. Among the crossbreds, there was no significant difference between Ankole × Friesian, Ankole-Jersey mother × Sahiwal sire, and Ankole-Sahiwal mother × Jersey sire, or between Ankole × Sahiwal and Ankole-Sahiwal mother × Sahiwal sire. It was concluded that Ankole crosses with Friesian or Jersey can be beneficial, even under a management system of limited nutrition as in Rwanda.

Genetic dissection of complex behaviour traits in German Shepherd dogs.

A favourable genetic structure and diversity of behavioural features highlights the potential of dogs for studying the genetic architecture of behaviour traits. However, behaviours are complex traits, which have been shown to be influenced by numerous genetic and non-genetic factors, complicating their analysis. In this study, the genetic contribution to behaviour variation in German Shepherd dogs (GSDs) was analysed using genomic approaches. GSDs were phenotyped for behaviour traits using the established Canine Behavioural Assessment and Research Questionnaire (C-BARQ). Genome-wide association study (GWAS) and regional heritability mapping (RHM) approaches were employed to identify associations between behaviour traits and genetic variants, while accounting for relevant non-genetic factors. By combining these complementary methods we endeavoured to increase the power to detect loci with small effects. Several behavioural traits exhibited moderate heritabilities, with the highest identified for Human-directed playfulness, a trait characterised by positive interactions with humans. We identified several genomic regions associated with one or more of the analysed behaviour traits. Some candidate genes located in these regions were previously linked to behavioural disorders in humans, suggesting a new context for their influence on behaviour characteristics. Overall, the results support dogs as a valuable resource to dissect the genetic architecture of behaviour traits and also highlight the value of focusing on a single breed in order to control for background genetic effects and thus avoid limitations of between-breed analyses.

Genomic relatedness and diversity of Swedish native cattle breeds.

BACKGROUND: Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. RESULTS: We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. CONCLUSIONS: This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

Reproductive performance of Ankole cattle and its crossbreds in Rwanda.

The aim of this study was to assess the reproductive performance of Ankole cattle and its crossbreds with Friesian (F), Jersey (J), and Sahiwal (S). The traits (number of records) studied were calving to first insemination, CFI (797); calving to last insemination, CLI (797); conception rate, CR (4354); number of inseminations, NINS (936); and calving interval, CI (259). The overall means of intervals CFI, CLI and CI, CR, and NINS were 192, 198 and 480 days, 67%, and 1.23 respectively. Breed group was significant (P < 0.05) for all traits except NINS, while season of calving was significant for CFI, CLI, and CI, and season of insemination was significant for CR. The breed group AF had better CR than the purebred Ankole and AS, and AS had lower CR than AJxS and AJ. On the other hand, Ankole (and to some extent AF) had longer CFI and CLI than AJ, AS, and FF. Ankole had 54 days longer CI than all crossbreds taken together. The prolonged intervals CFI, CLI, and CI observed in this study call for proper postpartum anestrus management both in terms of nutrition and calf suckling management.

Growth traits of crossbreds of Ankole with Brown Swiss, Holstein Friesian, Jersey, and Sahiwal cattle in Rwanda.

The objective of the study was to compare body weights and growth from birth to 18 months of age of various groups of crossbred cattle born from 1999 to 2007, being crossbreds of Ankole (A) with Brown Swiss (B), Holstein Friesian (F), Jersey (J), and Sahiwal (S). Average weights were 26.5 kg at birth, 161 kg at weaning, and 226 kg at 18 months. Both season and sex significantly affected birth weight (BW), weight at 8 and 18 months (W8 and W18), and average daily gain from weaning to 18 months (ADG18) and, unlike season, sex significantly affected average daily gain to 8 months and weaning age. The general trend was that average daily gain attained a maximum before weaning and thereafter decreased until 18 months. Least square means for AB and AF calves were comparable and significantly differed only for W18 and ADG18. AJ had the lowest BW but was comparable with AS, AJxS, and ASxJ for W8, age-adjusted weaning weight, and W18. Generally, AF was heavier than other breed groups, but the difference was smaller than expected probably because environmental conditions did not allow full expression of genetic potential for growth.

Seasonality of fertility measured by physical activity traits in Holstein cows.

Seasonality of female fertility traits, including the interval from calving to first high activity (CFHA), duration of high activity episode (DHA), and strength of high activity episode (SHA) of first estrus, were studied. The physical activity traits were derived from electronic activity tags for 20,794 Holstein cows in 135 commercial Holstein herds in Denmark. Data were categorized in 3 ways: (1) into 4 seasons of calving: winter (January-March), spring (April-June), summer (July-September), and fall (October-December); (2) into 2 seasons: a cold season (October-March) and a warm season (April-September); and (3) into an increasing light season (IL; January-June), where daylight hours gradually increased, and a decreasing light season (DL; July-December), where daylight hours gradually decreased. At the phenotypic level, least squares means of CFHA were highest at 55d for cows calving in December and lowest at 31d for cows calving in September. The highest least squares means of DHA and SHA were recorded for cows calving in November and lowest for cows calving in May and June. Genetic parameters for all traits were estimated using average information-REML in a bivariate animal model that treated the same trait in different calving seasons as different traits. Heritability estimates for CFHA were highest for the winter season (0.13) and low for the other seasons (0.03-0.04), whereas heritability estimates for DHA and SHA were lowest for winter and highest for fall. Heritability estimates for CFHA for the cold season (0.17) was higher than that for the warm season (0.10). Heritability estimates of CFHA for the IL season (0.12) was higher than for the DL season (0.07), but the opposite pattern was found for DHA and SHA. Genetic correlations (rA) of CFHA between winter and summer (rA=0.34 ± 0.27), and winter and fall (rA=0.65 ± 0.20) were significantly lower than unity. The corresponding correlations of DHA and SHA between seasons were all close to unity, except for the correlation of SHA between winter and fall (rA=0.36 ± 0.34). When the year was split into only 2 seasons, the genetic correlation of CFHA between cold and warm seasons was only moderate (rA=0.46 ± 0.15) but was slightly stronger between IL and DL seasons (rA=0.63 ± 0.16); both significantly deviated from unity. These results indicate the existence of a genotype by environment interaction for CFHA regardless of calving season classification.

Genotype by environment interaction for the interval from calving to first insemination with regard to calving month and geographic location in Holstein cows in Denmark and Sweden.

The objectives of this study were to investigate genotype by environment interaction effects, with environments defined as calving month and geographic location, on the interval from calving to first insemination (CFI) of Holstein cows in Denmark and Sweden. The data set included 811,285 records on CFI for first-parity cows from January 2010 to January 2014 housed in 7,458 herds. The longest mean CFI was 84.7 d for cows calving in April and the shortest was 76.3 d for cows calving in September. The longest mean CFI of 87.1 d was recorded at the northernmost location (LOC-8), whereas the shortest mean CFI of 73.5 d was recorded at the southernmost location (LOC-1). The multiple trait approach, in which CFI values in different calving months and different geographic locations were treated as different traits, was used to estimate the variance components and genetic correlations for CFI by using the average information (AI)-REML procedure in a bivariate sire model. Estimates of genetic variance and heritability were highest for January calvings and 3 times smaller for June calvings. Location 2 had the highest heritability and LOC-8 the lowest, with heritability estimates decreasing from LOC-2 to LOC-8. Genetic correlations of CFI between calving months were weakest between cold months (December and January) and warm months (June, August, and September); the lowest estimate was found between January and September calvings. Genetic correlations of CFI between the different geographic locations were generally strong, and the weakest correlation was between LOC-3 and LOC-8. These results indicate a genotype by environment interaction for CFI primarily regarding seasons described by calving months. The effect of geographic location was less important, mostly producing a scaling effect of CFI in different locations. We concluded that CFI is more sensitive to seasonal effects than geographic locations in Denmark and Sweden.

Genotype by environment interaction for activity-based estrus traits in relation to production level for Danish Holstein.

The objective of this study was to investigate whether genotype by environment interaction exists for female fertility traits and production of energy-corrected milk at 70d in milk (ECM70). Fertility traits considered were the activity-based estrus traits interval from calving to first high activity (CFHA), duration of high activity episode (DHA), as an indicator for first estrus duration, and strength of high activity episode (SHA), as an indicator for first estrus strength. The physical activity traits were derived from electronic activity tags for 11,522 first-parity cows housed in 125 commercial dairy herds. Data were analyzed using a univariate random regression animal model (URRM), by regressing the phenotypic performance on the average herd ECM70 as an environmental gradient. Furthermore, the genetic correlations between CFHA and ECM70 as a function of production level were estimated using a bivariate random regression animal model (BRRM). For all traits, heterogeneity of additive genetic variances and heritability estimates was observed. The heritability estimate for CFHA decreased from 0.25 to 0.10 with increasing production level and the heritability estimate for ECM70 decreased from 0.35 to 0.15 with increasing production level using URRM. The genetic correlation of the same trait in low and high production levels was around 0.74 for CFHA and 0.80 for ECM70 using URRM, but when data were analyzed using the multiple-trait analysis (MT), genetic correlation estimates between low and high production levels were not significantly different from unity. Furthermore, the genetic correlation of SHA between low and high production level was 0.22 using URRM, but the corresponding correlation estimate had large standard error when data were analyzed using MT. The genetic correlation between CFHA and ECM70 as a function of production environment was weak but unfavorable and decreased slightly from 0.09 to 0.04 with increasing production level using BRRM. Moreover, the same trend was observed when the data were analyzed using MT where the genetic correlation between CFHA and ECM70 in the low production environment was 0.29 compared with -0.13 in the high production environment, but these estimates had large standard errors. In conclusion, regardless of the trait used, in relation to average herd ECM70 production, the results indicated no clear evidence of strong genotype by environment interaction that would cause significant re-ranking of sires between low and high production environments.

Participatory definition of breeding objectives for sheep breeds under pastoral systems--the case of Red Maasai and Dorper sheep in Kenya.

Crossing local breeds with exotic breeds may be an option for increased livestock productivity. However, there is a risk for endangerment of the local breeds. One such case is in Kenya where the imported Dorper breed is used for crossbreeding with Red Maasai sheep. The aim of this study was to investigate farmers' trait preferences as a basis for determination of breeding objectives for Red Maasai and Dorper sheep at two sites, Amboseli and Isinya, in Kenya. Within their own flock, each farmer identified three ewes representing the best, average and poorest within each breed group: Red Maasai, Dorper and Crosses. Farmers gave reasons for their ranking. Body measurements and weights were also taken. At the harshest site, Amboseli, differences between breed groups in body weight were small and breeds were equally preferred. In Isinya, where environmental conditions are better and farmers are more market oriented, Dorper and Crosses had significantly higher body weights and market prices and were thus preferred by the farmers. Red Maasai were preferred for their maternal and adaptive traits. Breeding objectives should emphasize growth traits and milk production in both breeds at both sites. Body condition needs to be specifically considered in the breeding objectives for sheep in Amboseli, whereas adaptive traits need to be generally emphasized in Dorper.

Estrus traits derived from activity measurements are heritable and closely related to the time from calving to first insemination.

The aim of this study was to estimate genetic parameters for estrus-related traits that could improve selection for increased fertility due to improved ability of the cow to return to cycling and go into heat after calving. We compared the time from calving to first insemination (CFI) to 3 physical activity traits: the interval from calving to first high activity (CFHA), estrus duration (ED), and estrus strength (ES). We calculated CFI based on data from commercial Holstein herds that included the insemination dates for 11,363 cows. The CFHA, ED, and ES traits were derived from electronic activity tags for 3,533 Holstein cows. Estimates of heritability were 0.07 for CFI, 0.16 for CFHA, 0.02 for ED, and 0.05 for ES. We found a strong genetic correlation between CFI and CFHA (0.96). Genetic correlations between ED and CFI and CFHA were -0.37 and -0.68, respectively. Genetic correlations between ES and CFI and CFHA were -0.50 and -0.58, respectively. The heritability of CFHA and its strong genetic correlation with CFI suggest that including CFHA in the genetic evaluation of female cow fertility could improve the effectiveness of selection, because CFHA reflects the ability to return to cyclicity and go into heat after calving.

Genome wide association study in Swedish Labrador retrievers identifies genetic loci associated with hip dysplasia and body weight.

Genome wide association studies (GWAS) have been utilized to identify genetic risk loci associated with both simple and complex inherited disorders. Here, we performed a GWAS in Labrador retrievers to identify genetic loci associated with hip dysplasia and body weight. Hip dysplasia scores were available for 209 genotyped dogs. We identified a significantly associated locus for hip dysplasia on chromosome 24, with three equally associated SNPs (p = 4.3 × 10-7) in complete linkage disequilibrium located within NDRG3, a gene which in humans has been shown to be differentially expressed in osteoarthritic joint cartilage. Body weight, available for 85 female dogs, was used as phenotype for a second analysis. We identified two significantly associated loci on chromosome 10 (p = 4.5 × 10-7) and chromosome 31 (p = 2.5 × 10-6). The most associated SNPs within these loci were located within the introns of the PRKCE and CADM2 genes, respectively. PRKCE has been shown to play a role in regulation of adipogenesis whilst CADM2 has been associated with body weight in multiple human GWAS. In summary, we identified credible candidate loci explaining part of the genetic inheritance for hip dysplasia and body weight in Labrador retrievers with strong candidate genes in each locus previously implicated in the phenotypes investigated.

Estimation of genetic variance for macro- and micro-environmental sensitivity using double hierarchical generalized linear models.

BACKGROUND: Genetic variation for environmental sensitivity indicates that animals are genetically different in their response to environmental factors. Environmental factors are either identifiable (e.g. temperature) and called macro-environmental or unknown and called micro-environmental. The objectives of this study were to develop a statistical method to estimate genetic parameters for macro- and micro-environmental sensitivities simultaneously, to investigate bias and precision of resulting estimates of genetic parameters and to develop and evaluate use of Akaike's information criterion using h-likelihood to select the best fitting model. METHODS: We assumed that genetic variation in macro- and micro-environmental sensitivities is expressed as genetic variance in the slope of a linear reaction norm and environmental variance, respectively. A reaction norm model to estimate genetic variance for macro-environmental sensitivity was combined with a structural model for residual variance to estimate genetic variance for micro-environmental sensitivity using a double hierarchical generalized linear model in ASReml. Akaike's information criterion was constructed as model selection criterion using approximated h-likelihood. Populations of sires with large half-sib offspring groups were simulated to investigate bias and precision of estimated genetic parameters. RESULTS: Designs with 100 sires, each with at least 100 offspring, are required to have standard deviations of estimated variances lower than 50% of the true value. When the number of offspring increased, standard deviations of estimates across replicates decreased substantially, especially for genetic variances of macro- and micro-environmental sensitivities. Standard deviations of estimated genetic correlations across replicates were quite large (between 0.1 and 0.4), especially when sires had few offspring. Practically, no bias was observed for estimates of any of the parameters. Using Akaike's information criterion the true genetic model was selected as the best statistical model in at least 90% of 100 replicates when the number of offspring per sire was 100. Application of the model to lactation milk yield in dairy cattle showed that genetic variance for micro- and macro-environmental sensitivities existed. CONCLUSION: The algorithm and model selection criterion presented here can contribute to better understand genetic control of macro- and micro-environmental sensitivities. Designs or datasets should have at least 100 sires each with 100 offspring.

Integration of epidemiology into the genetic analysis of mastitis in Swedish Holstein.

Heritability of mastitis (and diseases in general) tends to be low. One possible cause is that no clear distinction can be made between resistant and nonresistant animals, because healthy animals include animals that have not been exposed to pathogens and resistant animals. To account for this, we quantified the prevalence of clinical mastitis (CM) and subclinical mastitis (SCM) in 2,069 Swedish Holstein herds as a measure of exposure. Herd prevalence averaged 26.5% for SCM and 6.4% for CM; 61% of the first lactations of 177,309 cows were classified as having at least one case of SCM and 10% as having CM. In a reaction norm approach, heritability of (S)CM was quantified as a function of herd prevalence of (S)CM. The best-fitting model was a second-order polynomial of first-lactation cow SCM as a function of herd prevalence SCM, and a first-order (linear) polynomial of first-lactation cow CM as a function of CM herd prevalence. Heritability for SCM ranged from 0.069 to 0.105 and for CM from 0.016 to 0.032. For both, we found no clear effect of herd prevalence on their heritability. Genetic correlations within traits across herd prevalences were all greater than 0.92. Whether relationships among prevalence, exposure, disease, and genetics were as expected is a matter of discussion, but reaction norm analyses may be a valuable tool for epidemiological genetics.

Heritability and genetic trend of body weight in dogs of different breeds in Sweden.

High body weight (BW) in dogs has been associated with developmental as well as degenerative diseases, but the heritability of BW in dog breeds is largely unknown. The aim of the current study was to estimate heritability and genetic change (genetic trend) for BW in a range of dog breeds in Sweden. Body weight registrations from 19 dog breeds (with n ranging from 412 to 4,710) of varying body size, type and usage were collected from 2007 to 2016. The average BW of the breeds was 8 to 56 kg. The BW registrations were performed when the dogs were 12 to 24 mo of age (18 to 30 mo for one large-sized breed) in connection with an official radiographic screening program for hip dysplasia. Collected weight records were used to estimate heritability and genetic trends for BW. Several statistical models were used. The preliminary model included the fixed effects of breed (P < 0.001), sex (P < 0.001), year of screening (P < 0.001), litter size (P = 0.06), parity of the dam (P = 0.03) and linear regression on age at screening (P < 0.001), the latter five effects all nested within breed, and the random effects of litter and dam. Season of birth and the quadratic effect of age were also tested, but were not significant (P > 0.10). For the genetic analysis, various mixed linear models were tested within breed with different combinations of random effects; the most complex model included random effects of litter, direct additive, and maternal genetic effects, and maternal permanent environmental effects. The average heritability for BW over all 19 breeds was 51%, with a range of 35% to 70%, and the additive genetic coefficient of variance was around 9%. Maternal heritability was 5% to 9% and litter variance was below 10% with one exception (15% in Shetland Sheepdogs). For nine breeds, there was a genetic trend of increasing BW, whereas seven breeds had a genetic trend of decreasing BW. The largest absolute genetic change over a 10-yr period was around 0.6 kg or about 2% of the mean. In conclusion, given the small genetic changes in spite of the high heritability, it seems that there is generally a very weak selection, if any, for BW in the included dog breeds.

High body weight in dogs is often considered to cause problems, for instance, resulting in hip and elbow diseases. Furthermore, there is a huge variation in body conformation and size between different dog breeds, which is related to breeding for specific appearances and genetic traits. The aim of this study was to investigate the genetic variation of body weight within different dog breeds. To study this, we examined 19 dog breeds with an average body weight of 8 to 56 kg. We found that on average about 50% of the total variation in body weight between dogs, within a breed, depends on genetic differences, but with a range from 35% to 70% depending on breed. There were rather small changes over time in the genetic predisposition for high or low body weight; the largest changes were 0.6 kg over a 10-yr period.