Inbreeding may affect phenotypic traits in an Italian population of Basset Hound dogs

Multiple congenital ocular anomalies in three related litters of Jack Russell Terrier puppies

OBJECTIVE

To describe multiple congenital ocular anomalies in three litters of Jack Russell Terrier puppies.

ANIMALS STUDIED

Seven purebred Jack Russell Terrier puppies from three related litters and their four parents.

PROCEDURES

Medical records of the puppies and their parents were evaluated. All dogs underwent a complete ophthalmic examination, followed by bilateral ocular ultrasonography in two of the puppies with complete corneal opacity. One eye from an affected puppy was subjected to histopathology. A complete database of pedigrees was built, and individual inbreeding was evaluated.

RESULTS

The most commonly diagnosed ocular anomalies in the puppies were: various anomalies of the fundus (12/14 eyes); microphthalmia (10/14 eyes); sclerocornea (8/14 eyes); and persistent pupillary membranes (7/14 eyes). Six out of seven puppies had at least two ocular abnormalities, and only one puppy was normal. Four out of seven puppies had sclerocornea, a particular corneal opacity to date described only in Spanish Podenco dogs. No ocular abnormalities were found in the parents examined (4/4). Analysis of the pedigrees showed that all the puppies and two parents were inbred, and the individual values of the inbreeding puppies were greater than 6.25% in two litters.

CONCLUSIONS

Inbreeding with closely related Jack Russell Terriers may result in severe congenital eye abnormalities in puppies.

Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review

Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.

Pedigree Analysis of Warmblood Horses Participating in Competitions for Young Horses

The aim of the study was to characterize the population structure and assess the genetic diversity of warmblood horses used in the show jumping discipline. Pedigree data of 1,048 horses participating in the Polish Championships for Young Horses were analyzed. The pedigree of these animals included 12 863 individuals. The study consisted in analysis of the pedigree structure of the horses and characterization of the homozygosity and genetic diversity in the population. It was found that pedigree completeness and depth were sufficient for reliable assessment of the genetic diversity in the analyzed population. Although the average inbreeding coefficient exhibited at an acceptable level (approx. 1.01%), the increasing percentage of inbred animals seems disturbing. The results have shown that modern sport horses are derived from a small number of high-quality sires whose offspring were intensively used for breeding—bottleneck effect. In consequence, a greater part of the genetic variation reduction was observed in the non-founder generations. Given the changes in the studied population, the level of inbreeding in modern sport horses should be monitored, and pedigree data should be effectively used in selection for mating.

Pedigree and Molecular Analyses in the Assessment of Genetic Variability of the Polish Greyhound

Simple Summary

The Polish Greyhound is an old Polish breed. The first descriptions of hunting with greyhounds can be found in the hunting literature of the 16th century, and the first detailed description of a greyhound comes from 1600. The Polish Greyhound probably originates from the Saluki-type Asian greyhounds. The population of this breed is very small and limited mainly to the territory of its country of origin (Poland). Pedigree books were opened for this breed in 1981. The narrow gene pool necessitated mating relatives, resulting in the appearance of various genetic diseases in the breed. The analysis of Polish Greyhound pedigrees registered in the pedigree books from the time of the registration of the breed and molecular tests facilitated calculation of the degree of relatedness in the breed and to design future breeding plans, taking into account that a 2.56% increase in inbreeding per complete generation will be observed if the current breeding program and similar matings are maintained.

Abstract

The aim of the study was to assess the genetic variability of the Polish Greyhound population based on pedigree analysis and molecular DNA testing and to determine the degree of relatedness among individuals in the population. Pedigree data of 912 Polish Greyhounds recorded in pedigree books since they were opened for this breed were analyzed. For molecular testing, DNA was obtained from cheek swabs taken from 235 dogs of the tested breed. A panel of 21 markers (Short Tandem Repeat—STR) was used. The mean inbreeding determined for the Polish Greyhound population based on pedigree analyses was low and amounted to 11.8%, but as many as 872 individuals of the 912 dogs in the studied population were inbred. A total of 83 founders (at least one unknown parent) were identified, among which 27 founders had both unknown parents. Full-sibling groups consisted of 130 individuals, with a minimum and maximum litter size of 2 and 16, respectively. The average litter size was 5.969. Gene diversity calculated based on the mean kinship matrix was 0.862 and the population mean kinship was 0.138. The founder genome equivalent based on the mean kinship matrix was 3.61; the founder genome surviving level was 12.34; the mean Ne was estimated at 21.76; and the Ne/N ratio was 0.135. The FIS inbreeding coefficient for 21 STR was negative, and the mean FIS value for all loci had a low negative value (−0.018). These values suggest a low level of inbreeding in the examined breed as well as the avoidance of mating related animals.

Genomic Characterization of the Istrian Shorthaired Hound

Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there is no data on genetic diversity, population structure, and degree of inbreeding that could be used for advanced management and conservation of this breed. Our study aimed to provide a high-resolution population structure of the Istrian shorthaired hound using a 220K HD SNP array, to compare the obtained data with the genealogical records and to place the breed in a broader context of world dog populations. Relatively high population size and low inbreeding coefficient estimated from genealogical data indicate a preserved genetic diversity in this breed. The principle component analysis, the NeighborNet network, and TreeMix were used to determine the genetic relationship between the Istrian shorthaired hound and other breeds. The Istrian shorthaired hound was found to be genetically related to Italian hunting dogs sharing the same branch with the Segugio Italiano a Pelo Raso and Segugio Italiano a Pelo Forte. The ADMIXTURE analysis indicated that the Istrian shorthaired hound could be involved in the development of some other hunting dog breeds. The estimated effective population size (Ne) based on SNP data was similar to Ne calculated from genealogical data indicating the absence of bottlenecks and well-balanced use of breeding animals. The low genomic inbreeding coefficient, together with the higher number of short runs of homozygosity, observed in the Istrian shorthaired hound, confirms the ancient origin of the breed based on historical documents. The analysis of selective sweeps identified genomic regions with the strongest selection signals in the vicinity of the genes associated with cognitive performance and behavior. Genome analysis proved to be a useful tool for estimating population parameters and can be implemented in the conservation plan for this indigenous breed.

Impact of breeding for coat and spotting patterns on the population structure and genetic diversity of an islander endangered dog breed

First references of the endangered autochthonous Majorcan Ca Mè dog date from the 13th century and enhance its skills and adaptability to the orography. Genealogical historical records were traced back to founders. Founder number in the reference population (397), maximum generations traced, and average number of complete generations were 32, 5, and 2.75, respectively. Structure assessment revealed the existence of subpopulations regarding criteria such as owners (402), breeders (55), coat colours (liver, lemon, black and orange) and spotting patterns (piebald, roan, solid colour, tie or star presence). Average inbreeding (F) within colour groups ranged from 6.3-10.4%, for orange and black populations, respectively. F ranged from 9.43-12.22% for roan patterns and star presence, respectively. Tan point markings showed an F coefficient of 5.85%. The study of genetic diversity revealed a slightly different genetic background between subpopulations. Average coancestry between and within coat colours suggested orange and roan traits could be ascribed to the original nuclei, without omitting the high relationships among other subpopulations. Breeding strategy should select breeding pairs holding a relatedness coefficient below 15%. Hence, coat patterns in dog breeds can help preserving the genetic diversity in endangered dogs, even when these are geographically isolated.

Inbreeding depression causes reduced fecundity in Golden Retrievers

Inbreeding depression has been demonstrated to impact vital rates, productivity, and performance in human populations, wild and endangered species, and in recent years, the domestic species. In all cases, standardized, high-quality phenotype data on all individuals are invaluable for longitudinal analyses such as those required to evaluate vital rates of a study cohort. Further, many investigators agree upon the preference for and utility of genomic measures of inbreeding in lieu of pedigree-based estimates of inbreeding. We evaluated the association of measures of reproductive fitness in 93 Golden Retrievers enrolled in the Golden Retriever Lifetime Study with a genomic measurement of inbreeding, F_ROH. We demonstrate a statistically significant negative correlation between fecundity and F_ROH. This work sets the stage for larger scale analyses to investigate genomic regions associated with fecundity and other measures of fitness.