Modeling Climate Change Effects on Genetic Diversity of an Endangered Horse Breed Using Canonical Correlations

The historical increase in the occurrence of extreme weather events in Spain during the last thirty years makes it a perfect location for the evaluation of climate change. Modeling the effects of climate change on domestic animals' genetic diversity may help to anticipate challenging situations. However, animal populations' short life cycle and patent lack of historical information during extended periods of time drastically compromise the evaluation of climate change effects. Locally adapted breeds' gene pool is the base for their improved resilience and plasticity in response to climate change's extreme climatic conditions. The preservation of these domestic resources offers selection alternatives to breeders who seek such improved adaptability. The Spanish endangered autochthonous Hispano-Arabian horse breed is perfectly adapted to the conditions of the territory where it was created, developed, and widespread worldwide. The possibility to trace genetic diversity in the Hispano-Arabian breed back around seven decades and its global ubiquity make this breed an idoneous reference subject to act as a model for other international populations. Climate change's shaping effects on the genetic diversity of the Hispano-Arabian horse breed's historical population were monitored from 1950 to 2019 and evaluated. Wind speed, gust speed, or barometric pressure have greater repercussions than extreme temperatures on genetic diversity. Extreme climate conditions, rather than average modifications of climate, may push breeders/owners to implement effective strategies in the short to medium term, but the effect will be plausible in the long term due to breed sustainability and enhanced capacity of response to extreme climate events. When extreme climatic conditions occur, breeders opt for mating highly diverse unrelated individuals, avoiding the production of a large number of offspring. People in charge of domestic population conservation act as catalyzers of the regulatory changes occurring during breeds' climate change adaptive process and may identify genes conferring their animals with greater adaptability but still maintaining enhanced performance. This model assists in determining how owners of endangered domestic populations should plan their breeding strategies, seeking the obtention of animals more resilient and adapted to climate-extreme conditions. This efficient alternative is focused on the obtention of increased profitability from this population and in turn ensuring their sustainability.

Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys

Donkeys (Equus asinus) play a pivotal role as essential livestock in arid and semi-arid regions, serving various purposes such as transportation, agriculture, and milk production. Despite their significance, donkey breeding has often been overlooked in comparison to other livestock species, resulting in limited genetic improvement programs. Preserving donkey genetic resources within each country necessitates the establishment of breed conservation programs, focusing on managing genetic diversity among populations. In recent years, significant strides have been made in sequencing and analyzing complete mitochondrial DNA (mtDNA) molecules in donkeys. Notably, numerous studies have honed in on the mitochondrial D-loop region, renowned for its remarkable variability and higher substitution rate within the mtDNA genome, rendering it an effective genetic marker for assessing genetic diversity in donkeys. Furthermore, genetic markers at the RNA/DNA level have emerged as indispensable tools for enhancing production and reproduction traits in donkeys. Traditional animal breeding approaches based solely on phenotypic traits, such as milk yields, weight, and height, are influenced by both genetic and environmental factors. To overcome these challenges, genetic markers, such as polymorphisms, InDel, or entire gene sequences associated with desirable traits in animals, have achieved widespread usage in animal breeding practices. These markers have proven increasingly valuable for facilitating the selection of productive and reproductive traits in donkeys. This comprehensive review examines the cutting-edge research on mitochondrial DNA as a tool for assessing donkey biodiversity. Additionally, it highlights the role of genetic markers at the DNA/RNA level, enabling the informed selection of optimal production and reproductive traits in donkeys, thereby driving advancements in donkey genetic conservation and breeding programs.

Maternal Phylogenetic Relationships and Genetic Variation among Rare, Phenotypically Similar Donkey Breeds

The mitochondrial DNA (mtDNA) D-loop of endangered and critically endangered breeds has been studied to identify maternal lineages, characterize genetic inheritance, reconstruct phylogenetic relations among breeds, and develop biodiversity conservation and breeding programs. The aim of the study was to determine the variability remaining and the phylogenetic relationship of Martina Franca (MF, with total population of 160 females and 36 males), Ragusano (RG, 344 females and 30 males), Pantesco (PT, 47 females and 15 males), and Catalonian (CT) donkeys by collecting genetic data from maternal lineages. Genetic material was collected from saliva, and a 350 bp fragment of D-loop mtDNA was amplified and sequenced. Sequences were aligned and evaluated using standard bioinformatics software. A total of 56 haplotypes including 33 polymorphic sites were found in 77 samples (27 MF, 22 RG, 8 PT, 19 CT, 1 crossbred). The breed nucleotide diversity value (π) for all the breeds was 0.128 (MF: 0.162, RG: 0.132, PT: 0.025, CT: 0.038). Principal components analysis grouped most of the haplogroups into two different clusters, I (including all haplotypes from PT and CT, together with haplotypes from MF and RG) and II (including haplotypes from MF and RG only). In conclusion, we found that the primeval haplotypes, haplogroup variability, and a large number of maternal lineages were preserved in MF and RG; thus, these breeds play putative pivotal roles in the phyletic relationships of donkey breeds. Maternal inheritance is indispensable genetic information required to evaluate inheritance, variability, and breeding programs.

Genetics, Evolution, and Physiology of Donkeys and Mules

The genus Equus is made up of donkeys, horses, and zebras. Despite significant variation in chromosome number across these species, interspecies breeding results in healthy, although infertile, hybrid offspring. Most notable among these are the horse-donkey hybrids, the mule and hinny. Donkeys presently are used for everything from companion animals to beasts of burden. Although closely related from an evolutionary standpoint, differences in anatomy and physiology preclude the assumption that they can be treated identically to the domestic horse. Veterinarians should be aware of these differences and adjust their practice accordingly.

First attempts for vitrification of immature oocytes in donkey (Equus asinus): Comparison of two vitrification methods

Most wild donkey breeds are severely threatened by poaching for meat, habitat loss, and competition with livestock for food resources. Moreover, due to the mechanization in agriculture and in transport, most domestic donkey breeds are at risk of extinction. Considering the importance of biodiversity and preservation of genetic resources, the creation of genetic banks for endangered donkey breeds is urgently needed. Cryopreservation of immature jennies oocytes would be an efficient tool to allow storage of female genetics. The aim of the present study was to establish conditions for immature donkey oocyte vitrification, using equine oocytes as a control. Asine and equine immature cumulus-oocyte complexes were collected by transvaginal ultrasound-guided follicular aspiration and flushed to obtain oocytes surrounded by only corona radiata. Oocytes were vitrified after exposure to increasing concentrations of dimethyl sulfoxide, ethylene glycol and sucrose as cryoprotectants in a solution of INRA-Freeze™ medium or TCM199-Hepes supplemented with bovine serum albumin. Oocytes were warmed in decreasing concentrations of sucrose and processed for in vitro maturation. The recovery rate was 48% for jennies oocytes (4.8 oocyte per female) and 42% for mares oocytes (3.5 oocyte per female). When oocytes were exposed to cryoprotectants in INRA-Freeze™ medium none of the jennies re-warmed oocytes matured, whereas 24% of the mares re-warmed oocytes reached metaphase II after in vitro maturation. When oocytes were exposed to cryoprotectants in TCM199-Hepes-BSA medium, 33% of the jennies re-warmed oocytes matured. In conclusion, we developed a method for the vitrification of immature oocytes from jennies that allows in vitro maturation of the vitrified-warmed asine oocytes. Their competence for fertilization and development has to be ascertain.

Genetic parameter and breeding value estimation of donkeys' problem-focused coping styles

Donkeys are recognized therapy or leisure-riding animals. Anecdotal evidence has suggested that more reactive donkeys or those more easily engaging flight mechanisms tend to be easier to train compared to those displaying the natural donkey behaviour of fight. This context brings together the need to quantify such traits and to genetically select donkeys displaying a neutral reaction during training, because of its implication with handler/rider safety and trainability. We analysed the scores for coping style traits from 300 Andalusian donkeys from 2013 to 2015. Three scales were applied to describe donkeys' response to 12 stimuli. Genetic parameters were estimated using multivariate models with year, sex, husbandry system and stimulus as fixed effects and age as a linear and quadratic covariable. Heritabilities were moderate, 0.18 ± 0.020 to 0.21 ± 0.021. Phenotypic correlations between intensity and mood/emotion or response type were negative and moderate (-0.21 and -0.25, respectively). Genetic correlations between the same variables were negative and moderately high (-0.46 and -0.53, respectively). Phenotypic and genetic correlations between mood/emotion and response type were positive and high (0.92 and 0.95, respectively). Breeding values enable selection methods that could lead to endangered breed preservation and genetically selecting donkeys for the uses that they may be most suitable.

Investigation of genetic diversity and inbreeding in a Japanese native horse breed for suggestions on its conservation

Because native breeds can serve as genetic resources for adapting to environment changes, their conservation is important for future agroecosystems. Using pedigree analysis, we investigated genetic diversity and inbreeding in Japanese Hokkaido native horses, which have adapted to a cold climate and roughage diet. Genetic diversity was measured as the number of founders and the effective number of founders, ancestors and genomes. All metrics imply a decrease in genetic diversity. A comparison of these metrics suggested that pedigree bottlenecks contributed more than did random gene losses to the reduction of genetic diversity. Estimates of marginal contributions of ancestors suggest that the bottlenecks arose mainly because related stallions had been used for breeding. A tendency for an increase in inbreeding coefficients was observed. F-statistics revealed that a small effective population size majorly contributed to this increase, although non-random mating in particular regions also contributed. Because the bottlenecks are thought to have reduced the effective population size, our results imply that mitigation of bottlenecks is important for conservation. To this end, breeding should involve genetically diverse stallions. In addition, to prevent non-random mating observed in particular regions, efforts should be made to plan mating with consideration of kinships.

A model to infer the demographic structure evolution of endangered donkey populations

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.

Mitochondrial DNA genetic diversity in six Italian donkey breeds (Equus asinus)

Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.

Status of the genetic diversity and population structure of the Pêga donkey

Pedigree analysis was extended to the Pêga donkey population in order to evaluate the status of genetic diversity and population structure. All parameters were computed for three reference populations of animals born between 2004 and 2014: all animals, animals with mouse gray coat color, and animals with roan coat color. Although the average inbreeding coefficient observed was low (about 3 %), highly inbred animals are present in the current population. The effective population size based on the individual inbreeding rate was 35, while the effective population size based on the individual coancestry rate was about three times higher. The number of equivalent subpopulations was at around three, indicating that the Pêga donkey population is highly structured. There is no evidence of differentiation between subpopulations based on the coat color of the animals (Nei's minimum distance 0.10 %). The breeding policy of Pêga donkeys is predominantly intra-herd. The loss of genetic diversity since the founder generations can be considered small in Pêga donkeys (1.25 %). The excessive contribution of few ancestors to the gene pool may lead to narrower bottlenecks in the pedigree of this population in the future. The long generation interval in Pêga donkeys (10.7 years) may be considered an advantage to reduce the increase in inbreeding and to maintain the genetic diversity of these animals.

Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms

Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

Pedigree and herd characterization of a donkey breed vulnerable to extinction

Most donkey and local horse breeds are vulnerable to extinction as mechanization of agriculture progress throughout the world. The present study analyzed the pedigree and herd records of the donkey Asinina de Miranda breed (RAM), identifying genealogical and human factors that may affect the breed genetic diversity in the future and suggesting suitable strategies to breed preservation, early on the conservation program. The breeding rate was very low, with a ratio of foaling/live animals of 0.23 (178/760). The estimated number of founders and ancestors contributing to the reference population was 128 and 121. The number of founder herds in the reference population was 64, with an effective number of founder herds for the reference population of 7.6. The mean age of herd owners was 65.50 ± 0.884 years, with a negative association among the herd size and owner's age (P<0.001). In contrast, the size of the herd and the ownership of a male were both positively associated (P<0.001) with the herd number of in-born foals. Both the owners' age and the herd location (RAM home region v. dispersal region) were negatively associated with the foaling number (P<0.001). The main identified risk factors were: low breeding rates; low number of males and their unequal contribution to the genetic pool; unequal contribution of the herds to genetic pool; and advanced age of herd owners.