Suitability of AFLP markers for the study of genetic relationships among Korean native dogs

The genetic audiogenic seizure hamster from Salamanca: The GASH:Sal

The hamster has been previously described as a paroxysmal dystonia model, but our strain is currently recognized as a model of audiogenic seizures (AGS). The original first epileptic hamster appeared spontaneously at the University of Valladolid, where it was known as the GPG:Vall line, and was transferred to the University of Salamanca where a new strain was developed, named GASH:Sal. By testing auditory brainstem responses, the GASH:Sal exhibits elevated auditory thresholds that indicate a hearing impairment. Moreover, amplified fragment length polymorphism analysis distinguished genetic differences between the susceptible GASH:Sal hamster strain and the control Syrian hamsters. The GASH:Sal constitutes an experimental model of reflex epilepsy of audiogenic origin derived from an autosomal recessive disorder. Thus, the GASH:Sal exhibits generalized tonic-clonic seizures, characterized by a short latency period after auditory stimulation, followed by wild running, a convulsive phase, and finally stupor, with origin in the brainstem. The seizure profile of the GASH:Sal is similar to those exhibited by other models of inherited AGS susceptibility, which decreases after six months of age, but the proneness across generations is maintained. The GASH:Sal can be considered a reliable model of audiogenic seizures, suitable to investigate current antiepileptic pharmaceutical treatments as well as novel therapeutic drugs. This article is part of a Special Issue entitled "Genetic and Reflex Epilepsies, Audiogenic Seizures and Strains: From Experimental Models to the Clinic".

Effect of Acteoside as a Cell Protector to Produce a Cloned Dog

Somatic cell nuclear transfer (SCNT) is a well-known laboratory technique. The principle of the SCNT involves the reprogramming a somatic nucleus by injecting a somatic cell into a recipient oocyte whose nucleus has been removed. Therefore, the nucleus donor cells are considered as a crucial factor in SCNT. Cell cycle synchronization of nucleus donor cells at G0/G1 stage can be induced by contact inhibition or serum starvation. In this study, acteoside, a phenylpropanoid glycoside compound, was investigated to determine whether it is applicable for inducing cell cycle synchronization, cytoprotection, and improving SCNT efficiency in canine fetal fibroblasts. Primary canine fetal fibroblasts were treated with acteoside (10, 30, 50 μM) for various time periods (24, 48 and 72 hours). Cell cycle synchronization at G0/G1 stage did not differ significantly with the method of induction: acteoside treatment, contact inhibition or serum starvation. However, of these three treatments, serum starvation resulted in significantly increased level of reactive oxygen species (ROS) (99.5 ± 0.3%) and apoptosis. The results also revealed that acteoside reduced ROS and apoptosis processes including necrosis in canine fetal fibroblasts, and improved the cell survival. Canine fetal fibroblasts treated with acteoside were successfully arrested at the G0/G1 stage. Moreover, the reconstructed embryos using nucleus donor cells treated with acteoside produced a healthy cloned dog, but not the embryos produced using nucleus donor cells subjected to contact inhibition. In conclusion, acteoside induced cell cycle synchronization of nucleus donor cells would be an alternative method to improve the efficiency of canine SCNT because of its cytoprotective effects.

Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress

BACKGROUND

The Sapsaree (Canis familiaris) is a Korean native dog that is very friendly, protective, and loyal to its owner, and is registered as a natural monument in Korea (number: 368). To investigate large-scale gene expression profiles and identify the genes related to exercise-induced stress in the Sapsaree, we performed whole-transcriptome RNA sequencing and analyzed gene expression patterns before and after exercise performance.

RESULTS

We identified 525 differentially expressed genes in ten dogs before and after exercise. Gene Ontology classification and KEGG pathway analysis revealed that the genes were mainly involved in metabolic processes, such as programmed cell death, protein metabolic process, phosphatidylinositol signaling system, and cation binding in cytoplasm. The ten Sapsarees could be divided into two groups based on the gene expression patterns before and after exercise. The two groups were significantly different in terms of their basic body type (p ≤ 0.05). Seven representative genes with significantly different expression patterns before and after exercise between the two groups were chosen and characterized.

CONCLUSIONS

Body type had a significant effect on the patterns of differential gene expression induced by exercise. Whole-transcriptome sequencing is a useful method for investigating the biological characteristics of the Sapsaree and the large-scale genomic differences of canines in general.

Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Behavior in Sapsaree Dog (Canis familiaris)

The purpose of this study was to characterize genetic architecture of behavior patterns in Sapsaree dogs. The breed population (n = 8,256) has been constructed since 1990 over 12 generations and managed at the Sapsaree Breeding Research Institute, Gyeongsan, Korea. Seven behavioral traits were investigated for 882 individuals. The traits were classified as a quantitative or a categorical group, and heritabilities (h(2)) and variance components were estimated under the Animal model using ASREML 2.0 software program. In general, the h(2) estimates of the traits ranged between 0.00 and 0.16. Strong genetic (r G ) and phenotypic (r P ) correlations were observed between nerve stability, affability and adaptability, i.e. 0.9 to 0.94 and 0.46 to 0.68, respectively. To detect significant single nucleotide polymorphism (SNP) for the behavioral traits, a total of 134 and 60 samples were genotyped using the Illumina 22K CanineSNP20 and 170K CanineHD bead chips, respectively. Two datasets comprising 60 (Sap60) and 183 (Sap183) samples were analyzed, respectively, of which the latter was based on the SNPs that were embedded on both the 22K and 170K chips. To perform genome-wide association analysis, each SNP was considered with the residuals of each phenotype that were adjusted for sex and year of birth as fixed effects. A least squares based single marker regression analysis was followed by a stepwise regression procedure for the significant SNPs (p<0.01), to determine a best set of SNPs for each trait. A total of 41 SNPs were detected with the Sap183 samples for the behavior traits. The significant SNPs need to be verified using other samples, so as to be utilized to improve behavior traits via marker-assisted selection in the Sapsaree population.

Reviewing population studies for forensic purposes: Dog mitochondrial DNA

The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework.

Canine behavioral problems and their effect on relinquishment of the Jindo dog

The purpose of this study was to evaluate behavior problems of the Jindo dog, the native dog of Korea, based on an owner's survey and their effect on pet relinquishment. To live a better life with their own pet and prevent relinquishment, it is important to understand the innate behavior characteristics of dog breed and the potential causes of relinquishment. Information concerning various factors and demonstration of the five most common behavior problems was collected via 189 completed questionnaires. No factors significantly affected the demonstration of behavior problem. A total 151 of 189 dogs had behavior problems (79.9%) and 38 dogs did not have behavior problems (20.1%). Among 151 dogs, 139 dogs showed single behavior problem (92.1%). They were 'excessive excitability' (46.8%), 'excessive vocalization' (30.2%), 'inappropriate elimination' (17.3%), 'destructive behavior' (4.3%), and 'aggressive behavior' (1.4%), respectively. In addition, 12 dogs showed two concurrent behavior problems (7.9%) According to the results, the relinquishment of Jindo dogs was not significantly associated with canine behavior problems, which is the single greatest risk factor of relinquishment in general. The possible reasons for potential behavior problems include improper raising, lack of socialization, and insufficient dog training classes, therefore canine behavior would be improved by owner education.

Genetic variation among isolates of Sarcocystis neurona, the agent of protozoal myeloencephalitis, as revealed by amplified fragment length polymorphism markers

Sarcocystis neurona causes serious neurological disease in horses and other vertebrates in the Americas. Based on epidemiological data, this parasite has recently emerged. Here, the genetic diversity of Sarcocystis neurona was evaluated using the amplified fragment length polymorphism (AFLP) method. Fifteen S. neurona taxa from different regions collected over the last 10 years were used; six isolates were from clinically diseased horses, eight isolates were from wild-caught opossums (Didelphis virginiana), and one isolate was from a cowbird (Molothrus ater). Additionally, four outgroup taxa were also fingerprinted. Nine primer pairs were used to generate AFLP patterns, with a total number of amplified fragments ranging from 30 to 60, depending on the isolate and primers tested. Based on the presence/absence of amplified AFLP fragments and pairwise similarity values, all the S. neurona isolates tested were clustered in one monophyletic group. No significant correlation could be found between genomic similarity and host origin of the S. neurona isolates. AFLP revealed significant intraspecific genetic variations, and S. neurona appeared as a highly variable species. Furthermore, linkage disequilibrium analysis suggested that S. neurona populations within Michigan have an intermediate type of population structure that includes characteristics of both clonal and panamictic population structures. AFLP is a reliable molecular technique that has provided one of the most informative approaches to ascertain phylogenetic relationships in S. neurona and its closest relatives, allowing them to be clustered by relative similarity using band matching and unweighted pair group method with arithmetic mean analysis, which may be applicable to other related protozoal species.

Genetic variation in an endemic salamander, Salamandra atra, using amplified fragment length polymorphism

The pattern of genetic differentiation of the endemic alpine salamander, Salamandra atra, has been studied using amplified fragment length polymorphism (AFLP) from 11 populations throughout the range of the two currently recognized subspecies, atra and aurorae. Five different primer combinations produced 706 bands and were analyzed by constructing a phylogenetic tree using NJ and principal component analysis. Significant genetic variation was revealed by AFLP between and within populations but, our results show a lack of genetic structure. AFLP markers seems to be unsuitable to investigate complex and recent diversification.

Standardisation of nomenclature for dog mtDNA D-loop: a prerequisite for launching a Canis familiaris database

Domestic dogs are increasingly involved, often as protagonists, in the forensic scene. Acknowledging this fact and benefiting from the accumulated experience on human mitochondrial DNA (mtDNA) analyses, we propose a standard for Canis familiaris mtDNA sequences as a prerequisite for the launching of the corresponding database.

Assessment of genetic diversity of Korean native pig (Sus scrofa) using AFLP markers

In order to assess the genetic diversity and genetic relationships among the six commercial pig breeds including the Korean native pig, we performed an amplified fragment length polymorphism (AFLP) analysis. Applying the three EcoRI/TagI primer combinations to 54 individual pig samples out of six breeds, a total of 186 AFLP bands were generated, 67 (36%) of which were identified as polymorphic bands. From these polymorphic bands, the three estimates (percentage of polymorphic loci, Neis heterozygosity and Shannon index) of genetic diversity, G(ST) estimates, Neis unbiased genetic distance and two indices of genetic similarity were calculated. From all the calculations of genetic diversity, the lowest genetic diversity was exhibited in the Korean native pig, and the highest in the Chinese Yanbian pig. Given the mean G(ST) value (G(ST) = 0.390) across all pigs examined, levels of apparent breed subdivision were considerable. A UPGMA tree of individuals based on Jaccards similarity index showed that the Korean native pig formed a distinct cluster from the other five pigs. In addition, the tree displayed that all the individuals except for six individuals were grouped into their breeds. Principal component analysis based on the binary data matrix of either presence or absence confirmed the distinctness of the Korean native pig from the other pigs. Our results indicate that the Korean native pig has a low level of genetic diversity and is distinct from the five pig breeds, confirming the results from previous microsatellite data. The findings also suggest that AFLP analysis may be a valuable tool for revealing genetic relationships and genetic diversity among different pig breeds.