D-loop haplotype diversity in Brazilian horse breeds

Landscape Genetics for Brazilian Equines

Optimization of DNA collection for National gene bank and conservation programs requires information on spatial and genetic distribution of animals countrywide. The relationship between genetic and geographic distances were examined in 8 Brazilian horse breeds (Baixadeiro, Crioulo, Campeiro, Lavradeiro, Marajoara, Mangalarga Marchador, Pantaneiro and Puruca) using Single Nucleotide Polymorphism markers and collection point locations. Mantel correlations, Genetic Landscape Shape Interpolation, Allelic Aggregation Index Analyses and Spatial autocorrelation tests indicated a nonrandom distribution of horses throughout the country. Minimum collection distances for the national Gene Bank should be 530km, with clear divisions seen in genetic structure of horse populations in both North/South and East/West directions. Comparing Pantaneiro and North/Northeastern breeds, physical distance is not necessarily the defining factor for genetic differentiation. This should be considered when sampling these local breeds. These data can help optimise GenBank collection routines and conservation strategies for these breeds.

Low transmission rates of Equine infectious anemia virus (EIAV) in foals born to seropositive feral mares inhabiting the Amazon delta region despite climatic conditions supporting high insect vector populations

Background

Marajó Island, within in the Amazon River Delta, supports numerous bands of feral equids including the genetically distinct Marajoara horses. Approximately 40% of the equids on the island are infected with Equine infectious anemia virus (EIAV). This high seropositivity rate coupled with the need to preserve rare breeds such as the Marajoara horse precludes euthanasia as the primary means for controlling EIAV in this region. In the absence of iatrogenic transmission, spread of this lentivirus is mediated primarily by hematophagous insects, whose year-round prevalence on the island is supported by favorable climatic conditions. In addition, cases of vertical EIAV transmission have been observed suggesting inclusion of seropositive mares in restorative breeding programs could result in their progeny becoming infected with this virus either pre-parturition or post-partum via hematophagous insects. Therefore, the aim of this study was to evaluate EIAV vertical and post-partum insect-mediated transmission rates among foals born to seropositive feral mares until natural weaning. Serum samples from foals born to seropositive feral mares within the Soure municipality, of Marajó Island, were collected to investigate their serological status, using an indirect ELISApgp45, with positive samples confirmed using the classical agar gel immunodiffusion (AGID) assay.

Results

The serological status of 28 foals were monitored over a 2-year period with some subjects, depending on their date of birth, being sampled up to six times. All foals remained with their respective mares until fully weaned at approximately 10 months of age. Only 2 foals (7.14%) in the study group became seropositive against EIAV.

Conclusion

The results demonstrate that in most cases it is possible to obtain seronegative foals born to and eventually weaned by EIA positive mares, even in equatorial regions where substantial rainfall and high temperatures favor the proliferation of insect vectors.

Selection signatures for heat tolerance in Brazilian horse breeds

Since domestication, horse breeds have adapted to their environments and differentiated from one another. This paper uses two methods to detect selection signatures in 23 horse breeds, eight of which are Brazilian (610 animals), both cold-blooded and warm-blooded, from temperate and tropical regions. These animals were genotyped using the GGP Equine BeadChip and we analysed the data by Principal Component Analysis (PCA). The samples were separated into groups based on their geographical area of origin and PCA results studied. The genomic regions under selection were detected by hapFLK and PCAdapt methodologies, identifying six regions under selection with at least one Brazilian horse breed. These regions contain genes associated with heat tolerance, skin colour, body size, energy production/metabolism, genes involved in protein degradation/turnover/DNA repair, genes reducing the impact of oxidative stress/cellular repair, and transcriptional regulation. This work confirmed LCORL and NCAPG gene regions in previous studies associated with body size on Equine Chromosome Autosome 3 (ECA3). On the same ECA3, a region implicating genes linked to coat colour was identified, also previously related to heat stress. Regions with genes coding heat shock proteins were found on ECA1 and 2, and many candidate genes for oxidation-reduction which are a natural response to heat stress. However, a larger sample size and whole-genome SNPs are needed to understand better and identify new candidate regions as well as their functional relation with heat tolerance.

Variability analyses of the maternal lineage of horses and donkeys

Equid breeds originating from the Iberian Peninsula and North Africa are believed to have genetically contributed to the formation of breeds and ecotypes from Brazil. The country has numerous breeds and ecotypes of horses and donkeys but there are no extensive studies on maternal genetic diversity and their origins. This study reports the results of the first genetic analysis of all horse and donkey breeds/ecotypes from Brazil based on sequences of the mitochondrial DNA control region (D-loop) whose main objective was to characterize the genetic variation in these animals. These analyses will contribute to the understanding of the current population structure and diversity of breeds/ecotypes of horses and donkeys raised in the Brazil. We analyzed 310 D-loop sequences representing 41 breeds/ecotypes of Equus caballus and Equus asinus, including 14 native horse breeds/ecotypes, 3 native donkey breeds/ecotypes and 24 cosmopolite horse breeds. The results revealed that the breeds are well structured genetically and that they comprise different groups. A total of 80 and 14 haplotypes were identified for horses and donkeys, respectively. Most of the horse mtDNA haplotypes were shared by many breeds, whereas donkey mtDNA haplotypes seemed to be more group-especif. Some groups presented a low intrabreed distance and/or a low haplotype/nucleotide diversity such as Lavradeiro, Crioulo, Piquira and Percheron horses and Brazilian donkey. Thus, specific actions must be designed for each population. The different levels of genetic diversity provided important information for conservation resource management of adapted groups as well as for mating orientation of breed associations. Some autochthonous ecotypes require attention because of their low genetic variability.

Mitochondrial DNA variation in the Italian Heavy Draught Horse

Background

In the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook.

Methodology

To provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds.

Results

Among the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices.

Genetic Diversity and Structure of Iranian Horses' Population Based on Mitochondrial Markers

The source and history of horse domestication have been studied for decades in biology and archeology. The aim of this study was to evaluate the genetic structure and the genetic relationship between six breeds of native horses using mitochondrial D-loop region. Blood samples were collected from 96 horses. Total DNA was extracted, and 430 bp of D-Loop region (hyper variable) was amplified and sequenced using Sanger sequencing methods. The analysis of data led to identify 48 polymorphic sites that create 52 haplotypes. The plotted phylogenic tree for haplotypes of Iranian native horses is placed in the 11 haplogroups including A, B, C, E, G, I, L, M, N, P, and Q. Genetic and haplotype diversity values obtained were 0.0233 and 0.980, respectively. Nucleotide diversity (Pi) was observed between 0.0172 and 0.0242 in populations. In addition, the average number of nucleotide differences (k) ranged from 6.0 (Darehshori or Qashqai horse [DAH]) to 8.5 (Kord horse [KOH]) with an average value of 7.8. The highest and lowest genetic differentiates were observed between KOH and DAH (Fst = 0.193) and between North West native horse and horse riding club in North West (Fst = 0.003), respectively. Tajima D of 0.441 was obtained for all samples which was not significant (P > .01). The results indicate high genetic variety and numerous maternal lines in native horses of Iran.

Genetic analysis of maternal and paternal lineages in Kabardian horses by uniparental molecular markers

Studies of mitochondrial DNA (mtDNA) as well as the non-recombining part of the Y chromosome help to understand the origin and distribution of maternal and paternal lineages. The Kabardian horse from Northern Caucasia which is well-known for strength, stamina and endurance in distance riding has a large gap in its breeding documentation especially in the recent past. A 309 bp fragment of the mitochondrial D-loop (156 Kabardian horses) and six mutations in Y chromosome (49 Kabardian stallions), respectively, were analyzed to get a better insight into breeding history, phylogenetic relationship to related breeds, maternal and paternal diversity and genetic structure. We found a high mitochondrial diversity represented by 64 D-loop haplotypes out of 14 haplogroups. The most frequent haplogroups were G (19.5%), L (12.3%), Q (11.7%), and B (11.0%). Although these four haplogroups are also frequently found in Asian riding horses (e.g. Buryat, Kirghiz, Mongolian, Transbaikalian, Tuvinian) the percentage of the particular haplogroups varies sometimes remarkable. In contrast, the obtained haplogroup pattern from Kabardian horse was more similar to that of breeds reared in the Middle East. No specific haplotype cluster was observed in the phylogenetic tree for Kabardian horses. On Kabardian Y chromosome, two mutations were found leading to three haplotypes with a percentage of 36.7% (haplotype HT1), 38.8% (haplotype HT2) and 24.5% (haplotype HT3), respectively. The high mitochondrial and also remarkable paternal diversity of the Kabardian horse is caused by its long history with a widely spread maternal origin and the introduction of Arabian as well as Thoroughbred influenced stallions for improvement. This high genetic diversity provides a good situation for the ongoing breed development and performance selection as well as avoiding inbreeding.