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Stemming from The Worldwide Donkey Breeds Project, an initiative aiming at connecting international researchers and entities working with the donkey species, molecularly tested pedigree analyses were carried out to study the genetic diversity, structure and historical evolution of the Andalusian donkey breed since the 1980s to infer a model to study the situation of international endangered donkey breeds under the remarkably frequent unknown genetical background status behind them. Demographic and genetic variability parameters were evaluated using ENDOG (v4.8). Pedigree completeness and generation length were quantified for the four gametic pathways. Despite mean inbreeding was low, highly inbred animals were present in the pedigree. Average coancestry, relatedness, and non-random mating degree trends were computed. The effective population size based on individual inbreeding rate was about half when based on individual coancestry rate. Nei’s distances and equivalent subpopulations number indicated differentiated farms in a highly structured population. Although genetic diversity loss since the founder generations could be considered small, intraherd breeding policies and the excessive contribution of few ancestors to the gene pool could lead to narrower pedigree bottlenecks. Long average generation intervals could be considered when reducing inbreeding. Wright’s fixation statistics indicated slight inbreeding between farms. Pedigree shallowness suggested applying new breeding strategies to reliably estimate descriptive parameters and control the negative effects of inbreeding, which could indeed, mean the key to preserve such valuable animal resources avoiding the extinction they potentially head towards, making the present model become an international referent when assessing endangered donkey populations.

Oocyte vitrification allows for the storing of endangered breed female gametes. Cryoprotectant (CPA) concentration and exposure time should ensure cell protection with minimal toxicity. In the present study, a high concentration-rapid exposure (HC-RE) and a low concentration-slow exposure (LC-SE) vitrification protocol, using dimethyl sulfoxide (DMSO) and ethylene glycol (EG) as permeating CPAs, were evaluated on meiotic competence and bioenergetic-oxidative status of pre-pubertal lamb immature COCs after in vitro maturation (IVM). For each protocol, COCs vitrified through a traditional protocol and fresh ones were used as controls. Both protocols allowed COC morphology preservation after vitrification-warming (V-W) and cumulus expansion after IVM. The maturation rate (7% and 14%) was comparable to the vitrified control (13% and 21%) but not satisfactory compared to fresh ones (58% and 64%; p < 0.001). The rate of mature oocytes displaying a perinuclear/subcortical (P/S) mitochondrial distribution pattern, an index of cytoplasmic maturity, was comparable between vitrified and fresh oocytes. The LC-SE vitrification protocol did not affect quantitative bioenergetic-oxidative parameters compared to both controls whereas HC-RE protocol significantly reduced intracellular reactive oxygen species (ROS) levels, indicating cell viability loss. In conclusion, to improve pre-pubertal lamb immature COC vitrification, the combination of low CPA concentrations with prolonged exposure time could be more promising to investigate further.

The Martina Franca (MF) donkey breed (Equus asinus) primarily inhabits the rural areas surrounding the homonymous municipality, as well as neighboring municipalities in the provinces of Bari and Brindisi, all located in the Apulia region of Italy. The objective of this study was to assess the current phenotype through the evaluation of 27 morphologic measurements. The study was conducted on 73 female and 18 male breeding animals from eight different herds located in central and southern Italy. Statistical analysis was performed in order to demonstrate statistical differences between males and females, as well as sexual dimorphism and uniformity of all measurements in both genders. The results demonstrated that the mean of three parameters used for the evaluation of an MF donkey (height at withers, circumference of thorax, and shin circumference) are highly representative of the population, with minimal dispersion Cv^ = 0.05–0.06 up to a maximum of 10%, as evidenced by relatively low standard deviations across observed measurements in both genders. Regarding sexual dimorphism, a statistically significant difference was found between males and females. This dimorphism is linked to reproductive activity and is useful during gestation. Overall, our findings suggest that the MF donkey phenotype has been largely preserved over time with high uniformity in males, slight inhomogeneity in the female population, and less variability in both genders.

Conservation of animal genetic resources requires regular monitoring and interventions to maintain population size and manage genetic variability. This study uses genealogical information to evaluate the impact of conservation measures in Europe, using (i) data from the Domestic Animal Diversity Information System (DAD-IS) and (ii) a posteriori assessment of the impact of various conservation measures on the genetic variability of 17 at-risk breeds with a wide range of interventions. Analysis of data from DAD-IS showed that 68% of national breed populations reported to receive financial support showed increasing demographic trends, v. 51% for those that did not. The majority of the 17 at-risk breeds have increased their numbers of registered animals over the last 20 years, but the changes in genetic variability per breed have not always matched the trend in population size. These differences in trends observed in the different metrics might be explained by the tensions between interventions to maintain genetic variability, and development initiatives which lead to intensification of selection.

This genome-wide association study (GWAS) aimed to identify sequence variants (SVs) and candidate genes associated with fertility and health in endangered German Black Pied cattle (DSN) based on whole-genome sequence (WGS) data. We used 304 sequenced DSN cattle for the imputation of 1797 genotyped DSN to WGS. The final dataset included 11,413,456 SVs of 1886 cows. Cow traits were calving-to-first service interval (CTFS), non-return after 56 days (NR56), somatic cell score (SCS), fat-to-protein ratio (FPR), and three pre-corrected endoparasite infection traits. We identified 40 SVs above the genome-wide significance and suggestive threshold associated with CTFS and NR56, and three important potential candidate genes (ARHGAP21, MARCH11, and ZNF462). For SCS, most associations were observed on BTA 25. The GWAS revealed 61 SVs, a cluster of 10 candidate genes on BTA 13, and 7 pathways for FPR, including key mediators involved in milk fat synthesis. The strongest associations for gastrointestinal nematode and Dictyocaulus viviparus infections were detected on BTA 8 and 24, respectively. For Fasciola hepatica infections, the strongest associated SVs were located on BTA 4 and 7. We detected 200 genes for endoparasite infection traits, related to 16 pathways involved in host immune response during infection.

Domestic donkeys (Equus africanus asinus) are an important livestock genetic resource that is currently considered at risk. The number of donkey breeds worldwide is declining due to their loss of function as working animals in rural communities. Local breeds with small populations, which are threatened by genetic erosion and are at risk of extinction, require urgent action to characterize and preserve their genetic diversity. As microarrays containing thousands of single-nucleotide polymorphisms (SNPs) are not yet available for these species, traditional molecular markers such as microsatellites and mitochondrial DNA (mtDNA) remain valuable tools for genetic monitoring and management. This study uses different molecular markers to assess and manage genetic variability in endangered Sicilian donkey breeds. This information can support breeding plans and mating schemes, as well as in situ and ex situ conservation programs. The practical application of molecular information in the conservation strategies for these breeds is briefly discussed, and the proposed approach is considered transferable to other threatened breeds.

The preservation of locally endangered breeds is essential for maintaining ecosystem services that benefit both society and the environment. Reproductive fitness becomes a crucial consideration in this context. MicroRNAs (miRNAs) are small non-coding RNA molecules that play a key role in post-transcriptional regulation. Typically, they function within the tissues where they are produced. However, when they are released into extracellular fluid, they are referred to as circulating miRNAs (c-miRNAs). C-miRNAs may serve as potential biomarkers, whose profile changes under different physiological states. The purpose of this study is to establish a connection between distinctive variations in the expression of c-miRNAs and specific estrus cycle phases in Frabosana-Roaschina sheep, an endangered Piedmontese breed. Two trials, each involving 20 ewes with different reproductive efficiencies (nulliparous in the first trial and pluriparous in the second trial), were sampled on alternate days after synchronization for blood, saliva, and feces. Ultrasound scans were performed during the induced estrus cycle. The animals' behaviors were assessed through video recordings. In the first trial, play behaviors were detected without sexual behaviors, whereas in the second trial, sexual behaviors were observed without play behaviors. Based on plasma trends of 17β-estradiol and progesterone and ultrasound images, two moments were identified for miRNAs analyses: the beginning of the follicular phase (day 2) and the beginning of the luteal phase (day 11). C-miRNAs of six representative animals from the second trial were sequenced. Analyses of the sequencing data have identified 12 c-miRNAs that were differentially expressed (DE) when comparing day 11 with day 2: five miRNAs were found to be upregulated, whereas seven miRNAs were downregulated. An enrichment analysis, based on predicted targets, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases was performed. Many of these genes regulate reproductive pathways with the possible involvement of miRNAs. Finally, qRT-PCR was conducted to validate the DE miRNAs in all ewes. Differences in gene expression between the two sampling points and the two trials were observed, in line with existing literature. Investigating the role of these miRNAs in regulating estrus could improve the reproductive performance and welfare of Frabosana-Roaschina ewes.

Various climatological and lunar cycle parameters have a direct impact on animal reproduction, and in the case of the avian species, spermatozoa are extremely sensitive to heat stress. These parameters could influence sperm freezability, which will ultimately affect post-thawing semen quality, being sperm motility in roosters a relevant indicator of this quality as it is highly related to fertility. Therefore, the objective of the present study is to determine which are the climatological and lunar cycle parameters that have a greater effect on sperm freezability in roosters. Sperm was obtained from 16 Utrerana breed roosters and a total of 27 replicates were performed. A pool was made with those ejaculates that met the minimum quality criteria for each replicate, and four freezing-thawing samples per replicate were analyzed. The straws were thawed, and sperm motility was evaluated, classifying the results obtained into four seminal quality groups according to the guidelines of the Food and Agriculture Organization of the United Nations (Group 1: Good, Group 2: Satisfactory, Group 3: Acceptable but undesirable and Group 4: Unsatisfactory). The following traits were recorded for each day of semen collection: maximum temperature, minimum temperature, maximum barometric pressure, minimum barometric pressure, maximum gust, wind direction, mean wind speed, sunshine hours, rainfall, moon phase, and percentage of illuminated lunar surface over the total area. A discriminant canonical analysis was performed to determine which of these parameters offered the most information when classifying an ejaculate in each quality group, with minimum temperature, the new moon as moon phase, minimum barometric pressure, and rainfall being the most significant variables. According to the results obtained, semen quality decreases when temperature and precipitation are lower, pressure is higher, and when there is a new moon phase. Therefore, these environmental conditions should be avoided for sperm collection and processing.

This study evaluates a method to accurately, repeatably, and reliably extract camel zoo-metric data (linear and tridimensional) from 2D digital images. Thirty zoometric measures, including linear and tridimensional (perimeters and girths) variables, were collected on-field with a non-elastic measuring tape. A scaled reference was used to extract measurement from images. For girths and perimeters, semimajor and semiminor axes were mathematically estimated with the function of the perimeter of an ellipse. On-field measurements’ direct translation was determined when Cronbach’s alpha (Cα) > 0.600 was met (first round). If not, Bayesian regression corrections were applied using live body weight and the particular digital zoometric measurement as regressors (except for foot perimeter) (second round). Last, if a certain zoometric trait still did not meet such a criterion, its natural logarithm was added (third round). Acceptable method translation consistency was reached for all the measurements after three correction rounds (Cα = 0.654 to 0.997, p < 0.0001). Afterwards, Bayesian regression corrected equations were issued. This research helps to evaluate individual conformation in a reliable contactless manner through the extraction of linear and tridimensional measures from images in dromedary camels. This is the first study to develop and correct the routinely ignored evaluation of tridimensional zoometrics from digital images in animals.

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.