Breeding Strategies for Weather Resilience in Small Ruminants in Atlantic and Mediterranean Climates

Identifying selection strategies based on the practices and preferences of small ruminant farmers to improve the sustainability of their breeding systems

Small ruminant farming is of socio-economic and environmental importance to many rural communities around the world. The SMARTER H2020 project aims to redefine genetic selection criteria to increase the sustainability of the sector. The objective of this study was to analyse the selection and breeding management practices of small ruminant producers and breeders, linked with socio-technical elements that shape them. The study is based on farm surveys using semi-structured interviews conducted in five countries (France, Spain, Italy, Greece, and Uruguay) across 272 producers and breeders of 13 sheep and goat breeds, and 15 breed × system combinations. The information was collected in four sections. The first and second sections dealt with general elements of structure and management of the system and the flock/herd. The third section focused on selection and breeding management practices: criteria for culling and replacement of females, selection criteria for males, use of estimated breeding values and global indexes, and preferences for indexing new traits to increase the sustainability of their system. The fourth section aimed to collect socio-technical information. We used a data abstraction method to standardise the representation of these data. A mixed data factor analysis followed by a hierarchical ascending classification allowed the characterisation of three profiles of selection and breeding management: (1) a profile of producers (n = 93) of small flocks/herds, with little knowledge or use of genetic selection and improvement tools (selection index, artificial insemination, performance recording); these farmers do not feel that new traits are needed to improve the sustainability of their system. (2) a profile of producers (n = 34) of multibreed flocks/herds that rely significantly on grazing; they are familiar with genetic tools, they currently use AI; they would like the indexes to include more health and robustness characteristics, to make their animals more resistant and to increase the sustainability of their system. And (3) a profile of producers or breeders (n = 145) of large flocks/herds, with specific culling criteria; these farmers are satisfied with the current indexes to maintain the sustainability of their system. These results are elements that can be used by private breeding companies and associations to support the evolution of selection objectives to increase the resilience of animals and to improve the sustainability of the small ruminant breeding systems.

Are farmers motivated to select for heat tolerance? Linking attitudinal factors, perceived climate change impacts, and social trust to farmers' breeding desires

This study provides an understanding of dairy farmers' willingness to include heat tolerance in breeding goals and the modulating effect of sociopsychological factors and farm profile. A survey instrument including a choice experiment was designed to specifically address the trade-off between heat tolerance and milk production level. A total of 122 farmers across cattle, goat, and sheep farms were surveyed face-to-face. The results of the experiment show that most farmers perceive that heat stress and climate change are increasingly important problems, and that farming communities should invest more in generating knowledge and resources on mitigation strategies. However, we found limited initial support for selection for heat tolerance. This attitude changed when farmers were presented with objective information on the benefits and limitations of the different breeding choices, after which most farmers supported selection for heat tolerance, but only if doing so would compromise milk production gains to a small extent. Our results show that farmers' selection choices are driven by the interactions between heat stress risk perception, attitudes toward breeding tools, social trust, the species reared, and farm production level. In general, farmers willing to support selection of heat-tolerant animals are those with positive attitudes toward genetic values and genomic information and a strong perception of climate change and heat stress impacts on farms. On the contrary, negative support for selection for heat tolerance is found among farmers with high milk production levels; high trust in farming magazines, livestock farmers' associations, and veterinarians; and low trust in environmental and animalist groups.

Analysis of reproduction success, growth and milk trajectories and response to nutritional challenge in two Alpine goat lines selected on divergent longevity

This study aims to investigate whether the variation in reproduction success, growth, and milk trajectories is associated with different adaptive strategies in the short term (response to an acute nutritional challenge), using two Alpine goat lines. A total of 382 Alpine goats (179 low longevity (low_LGV) and 203 high longevity (high_LGV)), selected for divergent functional longevity from a commercial population, were monitored for 4 years and recorded for BW, reproduction and milking performance. Every year, an average of fifty primiparous goats were exposed to a 2-d nutritional challenge in early lactation. A polynomial model was used to analyse the lifetime trajectory of lactation and BW. A piecewise model was used to analyse the individual milk yield and responses of milk components to the nutritional challenges. The statistical analysis revealed that the two lines had a similar performance for total milk yield in the first lactation, BW at birth and at first kidding, litter size and weight, kidding interval and interval from the first insemination to conception. BW trajectories revealed that low_LGV goats had a greater BW in pregnancy but then lost more weight in early lactation compared to high_LGV goats, which showed a greater BW after kidding. Milk trajectories showed that the high_LGV goats had a higher initial milk yield, an earlier but less marked lactation peak and more persistency in milk production in late lactation than low_LGV goats. Except for milk protein content, quite similar response and recovery profiles of milk yield and milk fat content were observed during the challenge for both lines. The response to the challenge was positively correlated to the initial level of milk production in early lactation but negatively correlated with milk production decline after the peak. This finding suggests that the low_LGV goats were more adapted to allocate resources to meet an expected physiological change such as gestation and lactation. However, high_LGV goats allocate more than low_LGV goats for structural mass and may better cope with an unexpected environmental change such as nutritional deficit.

Relationship between Vaccine Application and Climate Factors in Sheep and Goat Farms in Greece

The objectives of the present study were (a) to evaluate the importance of climate-related variables in the vaccination patterns applied in sheep and goat farms in Greece and (b) to assess potential interactions between these factors and previously established important health management- and human resources-related factors applied in the farms. Vaccination patterns against chlamydial abortion, clostridial infections, contagious agalactia, contagious ecthyma, foot-rot, paratuberculosis, pneumonia or staphylococcal mastitis were assessed. Climatic variables (2010–2019 and 2018–2019) were obtained for 444 locations with small ruminant farms throughout Greece. Patterns of vaccine administration in the farms were obtained through interviews with farmers. The following nine outcomes were considered: ‘vaccination against chlamydial abortion’, ‘vaccination against clostridial infections’, ‘vaccination against contagious agalactia’, ‘vaccination against contagious ecthyma’, ‘vaccination against foot-rot’, ‘vaccination against paratuberculosis’, ‘vaccination against bacterial pneumonia’, ‘vaccination against staphylococcal mastitis’ and ‘total number of optional vaccines administered’. Univariable and multivariable analyses were first performed to establish associations of each of the above outcomes with climatic variables. Then, the same approach was employed to assess the importance of climatic variables against health management- and human resources-related factors in the administration of vaccines in the farms of the study. Climatic variables had a higher association with vaccinations against infections in sheep flocks (26 associations) than in goat herds (9 associations) (p = 0.002) and in farms with semi-extensive or extensive management (32 associations) than in farms with intensive or semi-intensive management (8 associations) (p < 0.0001). In 26 cases (38.8% of all analyses evaluated), the climatic variables overshadowed the management- and human resources-related variables assessed as significant predictors for vaccination. In most cases, these referred to sheep flocks (nine cases) and farms with semi-extensive or extensive management (eight cases). For all eight infections, there were changes in the climatic variables found to be significant predictors from the 10-year dataset to the 2-year dataset. The results indicated that, in some cases, climate factors overshadowed factors traditionally considered for the formulation of vaccination programs. This points out the significance of taking into account climate conditions in the health management of small ruminant farms. Future studies can be focused on formulating vaccination programs in accordance with climate factors and also on setting the optimum season(s) for vaccination of animals based on the circulation of the pathogens, the risks for the development of diseases and the stage within the annual production cycle of the animals.

A novel heterozygote allele in caprine melanocortin 1 receptor (MC1R) gene: an association with heat stress traits

Climate change negatively influences the productive and reproductive abilities of goats. There is a need to understand the relationship between heat stress and genes that may aid in the development of climate-resilient goats. Melanism variation in goats plays a role in thermoregulation, in which the melanogenic genes have a pleiotropic effect on the regulation of physiological responses and behavior that are altered due to heat stress in the animals. Thus, the present study was conducted to establish a possible association between the coat color gene (MC1R) and heat stress characteristics. The physiological responses and cortisol levels were recorded in forty different coat-colored goats. The genotyping of the animals revealed four SNPs at the 183^rd (C/T), 332^nd (C/G), 748^th (G/T), and 801^st (C/G) positions, among which the black and brown goat populations had novel SNPs at the 332^nd position. Eight haplotypes were constructed, and an association study revealed that haplotypes (CCGG, TCGG, and CCTC) that were linked to white animals had lower cortisol values, rectal temperature, skin temperature, and respiration rate. The multivariate and cluster analyses revealed that the white goats were distinct from the rest of the goats. In addition, the docking results revealed the residues that were forming the interaction complex, which could play a role in melanogenesis in the animals and, in turn, the heat stress ability of the goats. Altogether, the results of the present study could pave the way for more research into coat color genes and their relationship with heat stress traits.

Identification of Selection Signals on the X-Chromosome in East Adriatic Sheep: A New Complementary Approach

Sheep are one of the most important livestock species in Croatia, found mainly in the Mediterranean coastal and mountainous regions along the East Adriatic coast, well adapted to the environment and mostly kept extensively. Our main objective was therefore to map the positive selection of the X-chromosome (18,983 SNPs that passed quality control), since nothing is known about the adaptation genes on this chromosome for any of the breeds from the Balkan cluster. Analyses were performed on a sample of eight native Croatian breeds (101 females and 100 males) representing the East Adriatic metapopulation and on 10 mouflons (five females and males), all sampled in Croatia. Three classical within-population approaches (extreme Runs of Homozygosity islands, integrated Haplotype Score, and number of Segregating Sites by Length) were applied along with our new approach called Haplotype Richness Drop (HRiD), which uses only the information contained in male haplotypes. We have also shown that phylogenetic analyses, such as the Median-joining network, can provide additional information when performed with the selection signals identified by HRiD. Our new approach identifies positive selection signals by searching for genomic regions that exhibit a sudden decline in haplotype richness. In total, we identified 14 positive selection signals, 11 using the classical approach and three using the HRiD approach, all together containing 34 annotated genes. The most reliable selection signal was mapped by all four approaches in the same region, overlapping between 13.17 and 13.60 Mb, and assigned to the CA5B, ZRSR2, AP1S2, and GRPR genes. High repeatability (86%) of results was observed, as 12 identified selection signals were also confirmed in other studies with sheep. HRiD offers an interesting possibility to be used complementary to other approaches or when only males are genotyped, which is often the case in genomic breeding value estimations. These results highlight the importance of the X-chromosome in the adaptive architecture of domestic ruminants, while our novel HRiD approach opens new possibilities for research.

Long-Term Climatic Changes in Small Ruminant Farms in Greece and Potential Associations with Animal Health

The objectives of this work were (a) to present the changes in climatic parameters from 1989 to 2019, in 444 locations throughout Greece, where small ruminant farms have been based and (b) to present associations of the changes in the climatic parameters with clinical data related to small ruminant health. Climatic variables (1989–2019) were obtained for 444 locations with small ruminant farms throughout Greece. During this period, significant increases were noted in temperature-related parameters (annually 0.05 °C for average temperature and 0.14 °C for temperature range) and precipitation (annually 0.03 mm). There were significant differences in climatic conditions between locations of farms in accord with the management system applied therein, as well as in accord with the breed of animals on the farms (e.g., higher average temperature in locations with Greek breeds, higher temperature range in locations with imported breeds). There were significant associations of temperature-related parameters with the annual frequency of cases of neonatal hypothermia seen at a veterinary teaching hospital, as well as with the average proportion of Haemonchus contortus larvae in faecal samples and the frequency of cases of H. contortus resistance reported by a veterinary parasitology laboratory.