Search Results (11)

Autosomal trisomy, a genetic disorder characterized by the presence of an extra autosome, is a rare but important chromosomal abnormality in horses, often associated with infertility, developmental abnormalities, and reduced life expectancy. This study represents the largest population-level screening for autosomal trisomy in horses; the analysis used single nucleotide polymorphism (SNP) panel genotype intensity data from 17,078 horses, 6601 of which were juveniles (i.e., ≤12 months of age) when genotyped. Using methodologies adapted from similar screening studies in cattle, the only aneuploidy detected was trisomy 27 in two juvenile male Irish Sport Horses (ISH) (0.03% prevalence among juveniles or 0.01% prevalence in the overall population). One ISH colt was cytogenetically confirmed and displayed no overt external phenotypic abnormalities, while cytogenetics was not undertaken on the other ISH colt, nor was it phenotypically assessed. Parentage analysis revealed that one ISH colt inherited two different copies of chr27 from the sire, demonstrating heterodisomy, likely due to a nondisjunction event during meiosis I in the sire. The other ISH colt inherited two different copies of chr27 from the dam, also indicating heterodisomy; the dam was 23 years of age when the colt was born. Based on the observed prevalence of autosomal trisomy, it can be estimated that at least 3 foals per 10,000 live births are likely to have autosomal trisomy. Though, given that only 74 (i.e., 0.004%) of horses were genotyped within a month of birth, this is likely an underestimate. The economic consequence of undiagnosed trisomy in high-value breeding horses that are potentially infertile could be substantial. As horse genotyping for parentage verification and discovery is transitioning to medium-density single nucleotide polymorphism panels, routine genomic screening for autosomal aneuploidy could be readily undertaken and potentially should form a standard screening prerequisite along with other genetic defects at horse sales. Currently, thoroughbred horses registered for racing are not genotyped, and only a limited number of sport horse studbooks are using SNP genotyping. This highlights an opportunity for those already genotyping to expand their support for breeders through low-cost, high-value chromosomal screening at the time of registration rather than incurring additional costs over the horse’s life cycle to determine the root cause of certain phenotypes owing to the undiagnosed trisomy. Full article

Microsatellite markers are widely used in aquaculture for genetic analysis and breeding programs, but challenges such as segregation distortion and allelic instability can impact their effectiveness in parentage verification and inheritance studies. This study evaluated 15 microsatellite loci in seven experimental olive flounder (Paralichthys olivaceus) families bred through 1:1 full-sibling crosses, assessing their utility for accurate parentage and inheritance stability. Parentage assignments were conducted within an expanded pool of 647 candidate parents (including the actual 14 parents), encompassing both closely related and moderately distant individuals. Despite increased genetic diversity, assignments maintained a high accuracy rate (99.6%), demonstrating marker robustness. Differences in delta values highlighted the influence of genetic backgrounds on assignment clarity, with some groups showing reduced distinctiveness in the expanded pool. Segregation distortion was observed at certain loci, deviating from Mendelian inheritance, likely due to meiotic drive and post-zygotic selection. These findings underscore the need for empirical validation of microsatellite loci for stable inheritance and reliable parentage in diverse breeding programs, especially with genetically similar spawners. Full article

Swine DNA profiling is highly important for animal identification and parentage verification and also increasingly important for meat traceability. This work aimed to analyze the genetic structure and genetic diversity in selected Polish pig breeds. The study used a set of 14 microsatellite (STR) markers recommended by ISAG for parentage verification in the native Puławska pig (PUL, n = 85) and three commercial pig breeds: Polish Large White (PLW, n = 74), Polish Landrace (PL, n = 85) and foreign breed Duroc (DUR, n = 84). Genetic differentiation among breeds accounted for 18% of the total genetic variability (AMOVA). Bayesian structure analysis (STRUCTURE) indicated that the four distinct genetic clusters obtained corresponded to the four breeds studied. The genetic Reynolds distances (Ɵw) showed a close relationship between PL and PLW breeds and the most distant for DUR and PUL pigs. The genetic differentiation values (F_ST) were lower between PL and PLW and higher between PUL and DUR. The principal coordinate analysis (PCoA) supported the classification of the populations into four clusters. Full article

The genus Narcissus belongs to the family Amaryllidaceae. This genus has been the subject of numerous cytological and cytometric studies and have shown enormous variation in terms of genome size, ploidy level, and even the basic chromosome number. The basic chromosome numbers are 5 or 7, but 10, 11, and 12 have been recorded as well. Most narcissus cultivars are euploid tetraploids. There are also numerous triploids. Some cultivars are aneuploid such as tetraploids or triploids, with missing chromosomes or possessing additional chromosomes. Due to their very complex parentage, cultivars have various numbers of chromosomes not found in the species. In this publication, we present a study on the genome size and assessment of the likely ploidy level of 38 cultivars and breeding clones of Narcissus in relation to their selected morphological traits and information on their parental forms. For the first time, 12 Polish cultivars and breeding clones of narcissus were the subject of such an evaluation. Perianth diameter, leaf length, and width were evaluated and rated with notes according to the descriptor of the International Union for the Protection of New Varieties of Plants. Stomatal density and stomata length were measured using light microscopy. Analysis of genome size was carried out using flow cytometry. For three selected genotypes, the chromosome number was counted. Our results lead to the general conclusion that the morphological traits studied and nuclear DNA content can be useful for determining the possible ploidy level of narcissi. The information on the origin and parental forms of narcissi can be helpful in determining the ploidy level of narcissi. However, clear confirmation of ploidy level requires verification of chromosome number and preferably karyotyping. The results obtained are a prelude to further studies. Full article

Armenia is an important country of origin of cultivated Vitis vinifera subsp. vinifera and wild Vitis vinifera subsp. sylvestris and has played a key role in the long history of grape cultivation in the Southern Caucasus. The existence of immense grapevine biodiversity in a small territory is strongly linked with unique relief and diverse climate conditions assembled with millennium-lasting cultural and historical context. In the present in-depth study using 25 nSSR markers, 492 samples collected in old vineyards, home gardens, and private collections were genotyped. For verification of cultivar identity, the symbiotic approach combining genotypic and phenotypic characterization for each genotype was carried out. The study provided 221 unique varieties, including 5 mutants, from which 66 were widely grown, neglected or minor autochthonous grapevine varieties, 49 turned out to be new bred cultivars created within the national breeding programs mainly during Soviet Era and 34 were non-Armenian varieties with different countries of origin. No references and corresponding genetic profiles existed for 67 genotypes. Parentage analysis was performed inferring 62 trios with 53 out of them having not been previously reported and 185 half-kinships. Instability of grapevine cultivars was detected, showing allelic variants, with three and in rare cases four alleles at one loci. Obtained results have great importance and revealed that Armenia conserved an extensive grape genetic diversity despite geographical isolation and low material exchange. This gene pool richness represents a huge reservoir of under-explored genetic diversity. Full article

Chinese jujube (Ziziphus jujuba Mill.) is an economically important fruit tree with outstanding adaptability to marginal lands and a broad range of climate conditions. There are over 800 cultivars, mostly landraces from China. However, a high rate of mislabeling in Chinese jujube germplasm restricts the sharing of information and materials among jujube researchers and hampers the use of jujube germplasm in breeding. In the present study, we developed a large panel of single nucleotide polymorphism (SNP) markers and validated 288 SNPs by genotyping 114 accessions of Chinese jujube germplasm. The validation resulted in the designation of a set of 192 polymorphic SNP markers that revealed a high rate of synonymous mislabeling in the jujube germplasm collection in Ningxia, China. A total of 17 groups of duplicates were detected, encompassing 49 of the 114 Chinese jujube cultivars. Model-based population stratification revealed two germplasm groups, and the core members of the two groups showed a significant genetic differentiation (Fst = 0.16). The results supported the hypothesis that the cultivated Chinese jujube had multiple origins and multiple regions of domestication. The Neighbor-Joining dendrogram further revealed that this collection is comprised of multiple sub-groups, each including 1-13 closely related cultivars. Parentage analysis of cultivars with known pedigree information proved the efficacy of using these SNP markers for parentage verification. A subset of 96 SNPs with high information index was selected for future downstream application including gene bank management, verification of pedigrees in breeding programs, quality control for propagation of planting materials and support of the traceability and authentication of jujube products. Full article

Parrots are considered the third most popular pet species, after dogs and cats, in the United States of America. Popular birds include budgerigars, lovebirds and cockatiels and are known for their plumage and vocal learning abilities. Plumage colour variation remains the main driving force behind breeder selection. Despite the birds’ popularity, only two molecular genetic tests—bird sexing and pathogen screening—are commercially available to breeders. For a limited number of species, parentage verification tests are available, but are mainly used in conservation and not for breeding purposes. No plumage colour genotyping test is available for any of the species. Due to the fact that there isn’t any commercial plumage genotype screening or parentage verification tests available, breeders mate close relatives to ensure recessive colour alleles are passed to the next generation. This, in turn, leads to inbreeding depression and decreased fertility, lower hatchability and smaller clutch sizes, all important traits in commercial breeding systems. This review highlights the research carried out in the field of pet parrot genomics and points out the areas where future research can make a vital contribution to understanding how parrot breeding can be improved to breed healthy, genetically diverse birds. Full article

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean H_o = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation. Full article

Swine DNA profiling is of high importance for animal identification and parentage verification. The aim of this study was to test a set of 14 microsatellite (STR) markers recommended by ISAG for parentage verification in Polish Landrace (PL, n = 900), Polish Large White (PLW, n = 482), Pulawska (PUL, n = 127), and Duroc pigs (DU n = 108). The studied breeds showed a medium level of genetic differentiation. The average value of heterozygosity and degree of polymorphism (PIC) were above 0.5 for the studied breeds, except for the DU breed (PIC = 0.477). The population inbreeding coefficient indicates an absence of inbreeding in the studied breeds (an average value of F_IS = 0.007). The cumulative power of discrimination for all breeds reached high values close to 1.0, while the probability of identity (P_ID) was low, with P_ID values ranging between 10⁻⁹ (for DU) and 10⁻¹² (for PLW). The cumulative exclusion probability for PE₁ and PE₂ showed that the parentage can be confirmed with a probability of from 92.75% to 99.01% and from 99.49% to 99.97%, respectively. Full article

There is growing concern that extreme breed standardization contributes to a reduction of the effective population size and high levels of inbreeding, resulting in the loss of genetic diversity in many breeds. This study examined genetic diversity among eight popular dog breeds in Poland and evaluated the effectiveness of a 21-microsatellite (STR) panel recommended by the International Society for Animal Genetics (ISAG) for parent verification. The following breeds were characterized: German Shepherd, Maltese, Irish Wolfhound, Yorkshire Terrier, Biewer Yorkshire Terrier, Golden Retriever, Labrador Retriever, and French Bulldog. STRUCTURE analysis showed breed distinctiveness among all the dog breeds under study. Reynold’s distance ranged between θ_w = 0.634 and θ_w = 0.260. The studied breeds showed a medium level of genetic differentiation; the mean number of alleles per locus ranged from 3.4 to 6.6, and the effective number of alleles from 2.1 to 3.5. The mean degree of heterozygosity varied from 49% to 69% and from 47% to 68% for H_O and H_E, respectively. The population inbreeding coefficient (FIS) indicated an absence of inbreeding in the studied breeds. The average polymorphism information content (PIC) values for most of the breeds were higher than 0.5. The cumulative power of discrimination (PD) for all the markers in all breeds reached high values (close to 1.0), while the probability of identity (P_ID) was low, ranging between 10⁻¹¹ and 10⁻¹⁹. The cumulative exclusion probability when the genotypes of one (PE₁) and both parents (PE₂) are known and showed that the parentage can be confirmed with a probability of 94.92% to 99.95% and 99.78% to 99.9999%, respectively. Full article

Transitioning from traditional to new genotyping technologies requires the development of bridging methodologies to avoid extra genotyping costs. This study aims to identify the optimum number of single nucleotide polymorphisms (SNPs) necessary to accurately impute microsatellite markers to develop a low-density SNP chip for parentage verification in the Assaf sheep breed. The accuracy of microsatellite marker imputation was assessed with three metrics: genotype concordance (C), genotype dosage (length r²), and allelic dosage (allelic r²), for all imputation scenarios tested (0.5–10 Mb microsatellite flanking SNP windows). The imputation accuracy for the three metrics analyzed for all haplotype lengths tested was higher than 0.90 (C), 0.80 (length r²), and 0.75 (allelic r²), indicating strong genotype concordance. The window with 2 Mb length provides the best accuracy for the imputation procedure and the design of an affordable low-density SNP chip for parentage testing. We additionally evaluated imputation performance under two null models, naive (imputing the most common allele) and random (imputing by randomly selecting the allele), which in comparison showed weak genotype concordances (0.41 and 0.15, respectively). Therefore, we describe a precise methodology in the present article to impute multiallelic microsatellite genotypes from a low-density SNP chip in sheep and solve the problem of parentage verification when different genotyping platforms have been used across generations. Full article