Genetic variation in competition traits at different ages and time periods and correlations with traits at field tests of 4-year-old Swedish Warmblood horses

For many years, the breeding value estimation for Swedish riding horses has been based on results from Riding Horse Quality Tests (RHQTs) of 4-year-olds only. Traits tested are conformation, gaits and jumping ability. An integrated index including competition results is under development to both get as reliable proofs as possible and increases the credibility of the indexes among breeders, trainers and riders. The objectives of this study were to investigate the suitability of competition data for use in genetic evaluations of horses and to examine how well young horse performance agrees with performance later in life. Competition results in dressage and show jumping for almost 40 000 horses from the beginning of the 1960s until 2006 were available. For RHQT data of 14 000 horses judged between 1988 and 2007 were used. Genetic parameters were estimated for accumulated competition results defined for different age groups (4 to 6 years of age, 4 to 9 years of age and lifetime), and for different birth year groups. Genetic correlations were estimated between results at RHQT and competitions with a multi-trait animal model. Heritabilities were higher for show jumping than dressage and increased with increasing age of the horse and amount of information. For dressage, heritabilities increased from 0.11 for the youngest group to 0.16 for lifetime results. For show jumping corresponding values increased from 0.24 to 0.28. Genetic correlations between competition results for the different age groups were highly positive (0.84 to 1.00), as were those between jumping traits at RHQT and competition results in show jumping (0.87 to 0.89). For dressage-related traits as 4-year-old and dressage competition results the estimated genetic correlations were between 0.47 and 0.77. We suggest that lifetime results from competitions should be integrated into the genetic evaluation system. However, genetic parameters showed that traits had changed during the over 35-year period covered due to the development of the sport, which needs to be considered in future genetic evaluations

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

Heritability and Genetic Correlations of Fear-Related Behaviour in Red Junglefowl–Possible Implications for Early Domestication

Domesticated species differ from their wild ancestors in a number of traits, generally referred to as the domesticated phenotype. Reduced fear of humans is assumed to have been an early prerequisite for the successful domestication of virtually all species. We hypothesized that fear of humans is linked to other domestication related traits. For three generations, we selected Red Junglefowl (ancestors of domestic chickens) solely on the reaction in a standardized Fear of Human-test. In this, the birds were exposed for a gradually approaching human, and their behaviour was continuously scored. This generated three groups of animals, high (H), low (L) and intermediate (I) fearful birds. The birds in each generation were additionally tested in a battery of behaviour tests, measuring aspects of fearfulness, exploration, and sociality. The results demonstrate that the variation in fear response of Red Junglefowl towards humans has a significant genetic component and is genetically correlated to behavioural responses in other contexts, of which some are associated with fearfulness and others with exploration. Hence, selection of Red Junglefowl on low fear for humans can be expected to lead to a correlated change of other behavioural traits over generations. It is therefore likely that domestication may have caused an initial suite of behavioural modifications, even without selection on anything besides tameness

Relevance of the production system for the sustainability of conservation and breeding programs for the Creole cattle in Pasorapa, Bolivia

Local livestock breeds play an important role in the food security of smallholders in developing countries in the Global South. They are also a reservoir of potentially valuable genes for adaptation of global animal genetic resources. The Creole cattle population from Pasorapa, Bolivia, is threatened by effects of climate change and unplanned crossbreeding. The aim of this study was to assess the current situation in this population and to evaluate factors to be considered before implementing conservation and genetic improvement programs in order to achieve the sustainable development goals 1, 2, 13 and 15, which refer to no poverty, zero hunger, climate change and life on land, respectively. We examined and analyzed the most important elements related to the production system and farmers' perceptions that could affect the design of such programs. Open-ended and closed-ended questionnaires and interviews were performed with 81 smallholders from 11 communities in Pasorapa. A rearing system based on two stages and animals feeding mainly on native plants during both, involves a strong interaction between the environment and the production system. A survey of farmers' perceptions about diseases, mortality causes, and selection criteria revealed that farmers in Pasorapa consider coat color an important trait when selecting breeding and replacement animals. Half of all interviewees perceived an association between coat color and traits such as temperament, milk yield, and beef production. In a SWOT analysis we discussed the vulnerability of the system to climate change impacts and the contribution of this traditional system to rural mitigation. Overall, this work revealed the importance of this local ecotype and identified key factors to consider when developing breeding and conservation programs

Genetic evaluation of mastitis liability and recovery through longitudinal analysis of transition probabilities

BACKGROUND: Many methods for the genetic analysis of mastitis use a cross-sectional approach, which omits information on, e.g., repeated mastitis cases during lactation, somatic cell count fluctuations, and recovery process. Acknowledging the dynamic behavior of mastitis during lactation and taking into account that there is more than one binary response variable to consider, can enhance the genetic evaluation of mastitis. METHODS: Genetic evaluation of mastitis was carried out by modeling the dynamic nature of somatic cell count (SCC) within the lactation. The SCC patterns were captured by modeling transition probabilities between assumed states of mastitis and non-mastitis. A widely dispersed SCC pattern generates high transition probabilities between states and vice versa. This method can model transitions to and from states of infection simultaneously, i.e. both the mastitis liability and the recovery process are considered. A multilevel discrete time survival model was applied to estimate breeding values on simulated data with different dataset sizes, mastitis frequencies, and genetic correlations. RESULTS: Correlations between estimated and simulated breeding values showed that the estimated accuracies for mastitis liability were similar to those from previously tested methods that used data of confirmed mastitis cases, while our results were based on SCC as an indicator of mastitis. In addition, unlike the other methods, our method also generates breeding values for the recovery process. CONCLUSIONS: The developed method provides an effective tool for the genetic evaluation of mastitis when considering the whole disease course and will contribute to improving the genetic evaluation of udder health

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

Seasonality of fertility measured by physical activity traits in Holstein cows

AbstractSeasonality 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

Association of genomically enhanced and parent average breeding values with cow performance in Nordic dairy 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

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 Federation 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

Unravelling selection signatures in a single dog breed suggests recent selection for morphological and behavioural traits

Strong selection has resulted in substantial morphological and behavioral diversity across modern dog breeds, which makes dogs interesting model animals to study the underlying genetic architecture of these traits. However, results from between-breed analyses may confound selection signatures for behavior and morphological features that were coselected during breed development. In this study, we assess population genetic differences in a unique resource of dogs of the same breed but with systematic behavioral selection in only one population. We exploit these different breeding backgrounds to identify signatures of recent selection. Selection signatures within populations were found on chromosomes 4 and 19, with the strongest signals in behavior-related genes. Regions showing strong signals of divergent selection were located on chromosomes 1, 24, and 32, and include candidate genes for both physical features and behavior. Some of the selection signatures appear to be driven by loci associated with coat color (Chr 24; ASIP) and length (Chr 32; FGF5), while others showed evidence of association with behavior. Our findings suggest that signatures of selection within dog breeds have been driven by selection for morphology and behavior. Furthermore, we demonstrate that combining selection scans with association analyses is effective for dissecting the traits under selection