Journal of applied genetics.
Publisher:
Institute of Plant Genetics, Polish Academy of Sciences,. Cheshire, United Kingdom : Springer (2011)
Frequency: Four no. a year
Country: England
Language: English
Author(s):
Instytut Genetyki Roślin PAN.
Start Year:1995 -
ISSN:
1234-1983 (Print)
2190-3883 (Electronic)
1234-1983 (Linking)
2190-3883 (Electronic)
1234-1983 (Linking)
Impact Factor
2.4
2022
| NLM ID: | 9514582 |
| (DNLM): | SR0085240(s) |
| (OCoLC): | 32934191 |
| Coden: | JAGEFC |
| LCCN: | sn 95026522 |
| Classification: | W1 GE287K |
A case of non-mosaic X trisomy (65,XXX) in a Thoroughbred mare confirmed by cytogenetic and molecular analysis. A 9-year-old Thoroughbred mare with normal external genitalia and regular oestrus symptoms was gynecologically examined prior to insemination. This primary examination revealed the presence of a hypoplastic uterus and the lack of normal ovaries, and the mare was therefore subjected to more detailed diagnostics, including endocrinological, genetic, and clinical tests. Diagnostic imaging with the use of ultrasonography and endoscopy confirmed the underdevelopment of internal genitalia. Analysis of circulating sex hormones revealed very low concentrations of progesterone and oestradiol. Finally, ...
Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses. In horses, parentage control is currently performed based on an internationally standardized panel of 17 microsatellite (MS) markers comprising 12 mandatory and five optional markers. Unlike MS, single nucleotide polymorphism (SNP) profiles support a wider portfolio of genomic applications, including parentage control. A transition to SNP-based parentage control is favorable, but requires additional efforts for ensuring generation-overlapping availability of marker genotypes of the same type. To avoid double genotyping of either parents or offspring for changing to SNP technology and enable ef...
Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues. In recent years, a vast amount of sequencing data has been generated and large improvements have been made to reference genome sequences. Despite these advances, significant portions of reads still do not map to reference genomes and these reads have been considered as junk or artificial sequences. Recent studies have shown that these reads can be useful, e.g., for refining reference genomes or detecting contaminating microorganisms present in the analyzed biological samples. A special case of this is RNA sequencing (RNA-Seq) reads that come from tissue transcriptomes. Unmapped reads from RNA-...
Genetic and genomic characterization followed by single-step genomic evaluation of withers height in German Warmblood horses. Reliability of genomic predictions is influenced by the size and genetic composition of the reference population. For German Warmblood horses, compilation of a reference population has been enabled through the cooperation of five German breeding associations. In this study, preliminary data from this joint reference population were used to genetically and genomically characterize withers height and to apply single-step methodology for estimating genomic breeding values for withers height. Using data on 2113 mares and their genomic information considering about 62,000 single nucleotide polymorp...
Influence of coat color on genetic parameter estimates in horses. The aim of this study was to verify the effect of the inclusion of coat color on the genetic parameter estimation for linear measurements in Campolina horses. Two models (1 and 2) were applied. For model 1, coat color effect was not included as variable of the contemporary group formation; in model 2, it was included. Model 2 presented the best fitting with a Deviance Information Criterion (DIC) of -979,459.020 compared with -1,818,458.572 DIC from model 1. The average of heritability estimates ranged from low to high magnitude (0.15 to 0.53) for model 1 and from moderate to high magnitude for...
Comparing assignment-based approaches to breed identification within a large set of horses. Considering the extensive data sets and statistical techniques, animal breeding embodies a branch of machine learning that has a constantly increasing impact on breeding. In our study, information regarding the potential of machine learning and data mining within a large set of horses and breeds is presented. The individual assignment methods and factors influencing the success rate of the procedure are compared at the Czech population scale. The fixation index values ranged from 0.057 (HMS1) to 0.144 (HTG6), and the overall genetic differentiation amounted to 8.9% among the breeds. The highes...
Exome sequencing in genomic regions related to racing performance of Quarter Horses. Among horses selected for speed, the racing line of Quarter Horses is characterized by high performance in sprint races, with these animals being considered the fastest horses in the world. However, few studies have investigated in more detail the polymorphisms and genes that act on this trait. The objective of this study was to analyze exomes and UTRs in regions previously associated with this trait by GWAS in Quarter Horse racehorses with contrasting maximum speed index (SImax), prospecting causal gene polymorphisms that are related to or are in strong linkage disequilibrium with racing perf...
5′-flanking variants of equine casein genes (CSN1S1, CSN1S2, CSN2, CSN3) and their relationship with gene expression and milk composition. Genes encoding casein proteins are important candidates for milk composition traits in mammals. In the case of the domestic horse, our knowledge of casein genes is limited mainly to coding sequence variants. This study involved screening for polymorphism in 5'-flanking regions of four genes encoding equine caseins (CSN1S1, CSN1S2, CSN2, and CSN3) and making a preliminary assessment of their effect on the gene expression (on the mRNA and protein levels) and milk composition traits in selected horse breeds. Altogether, 23 polymorphisms (21 described previously SNPs and two novel InDels) were fou...
Differences between horse selection based on two forms of osteochondrosis in fetlock. Horses lose potential opportunities because of health problems. Available breeding strategies are not effective enough, probably also because of the different definition used and its genetic usefulness. The aim of the study was to compare the genetic background estimated by the genome-wide association study (GWAS) for osteochondrosis using two different scaling osteochondrosis (OC)/healthy and osteochondrosis dissecans (OCD)/healthy systems for evaluating the disease status of investigated fetlock joints. Two hundred one Warmblood horses trained for performance tests (87 stallions and 114 mare...
Diversity of mitochondrial DNA in three Arabian horse strains. Arabian horse registries classify Arabian horses based on their dam lineages into five main strains. To test the maternal origin of Syrian Arabian horses, 192 horses representing the three major strains Saglawi, Kahlawi, and Hamdani were sequenced for 353 bp of their mitochondrial displacement loop (D-loop) region. Sequencing revealed 28 haplotypes comprising 38 sequence variations. The haplotype diversity values were 0.95, 0.91, and 0.90 in Kahlawi, Hamdani, and Saglawi strains, respectively. The pair-wise population differentiation estimates (Fst) between strains were low, ranging between 0...
Polymorphisms in ten candidate genes are associated with conformational and locomotive traits in Spanish Purebred horses. The Spanish Purebred horses, also known as Andalusian horses, compete to the highest standards in international dressage events. Gait and conformation could be used as early selection criteria to detect young horses with promising dressage ability. Although the genetic background of equine size variation has been recently uncovered, the genetic basis of horse conformational and locomotive traits is not known, hampered by the complex genetic architecture underlying quantitative traits and the lack of phenotypic data. The aim of this study was to validate the loci associated with size in 144 Spa...
Distribution of coat-color-associated alleles in the domestic horse population and Przewalski’s horse. Considering the hidden mode of inheritance of some coat-color-associated alleles, we investigated the presence/absence of coat-color-associated alleles in 1093 domestic horses of 55 breeds and 20 specimens of Przewalski's horse. For coat-color genotyping, allele specific PCR, pyrosequencing and Li-Cor analyses were conducted on 12 coat-color-associated alleles of five genes. Our data provide deep insight into the distribution of coat-color-associated alleles within breeds. We found that the alleles for the basic colorations (bay, black, and chestnut) are widely distributed and occur in nearly ...
Age-related methylation profiles of equine blood leukocytes in the RNASEL locus. Methylation profiles across three CpG islands of the RNASEL gene were determined in blood leukocyte samples of Anglo-Arabian and Hucul horses. Bisulfite sequencing revealed hypomethylated state of the RNASEL promoter coinciding with methylated CpG island placed inside the gene. Several CpG sites were identified for which the methylation state was influenced by DNA polymorphism. Two of them showed monoallelic methylation. One of the CpG sites revealed functional polymorphism. A number of partially methylated CpG sites have been observed in the promoter area of RNASEL, which were used for the co...
RNA sequencing as a powerful tool in searching for genes influencing health and performance traits of horses. RNA sequencing (RNA-seq) by next-generation technology is a powerful tool which creates new possibilities in whole-transcriptome analysis. In recent years, with the use of the RNA-seq method, several studies expanded transcriptional gene profiles to understand interactions between genotype and phenotype, supremely contributing to the field of equine biology. To date, in horses, massive parallel sequencing of cDNA has been successfully used to identify and quantify mRNA levels in several normal tissues, as well as to annotate genes. Moreover, the RNA-seq method has been applied to identify the ...
Epigenetic structure and the role of polymorphism in the shaping of DNA methylation patterns of equine OAS1 locus. DNA methylation patterns and their relation with genetic polymorphisms were determined in the equine OAS1 locus. Genetic variants of OAS1 were previously found to be associated with susceptibility to West Nile virus infections in horses. The subject of the study were white blood cells of 13 juvenile and 13 old horses from AA and HC breed and a set of solid tissues from a single adult horse. The aim was to determine the degree of variation of CpG methylation profiles with concern for tissue type, horse breed and age. Results of direct BSPCR and cloned BSPCR sequencing revealed that all of deter...
Family of melanocortin receptor (MCR) genes in mammals-mutations, polymorphisms and phenotypic effects. The melanocortin receptor gene family consists of five single-exon members, which are located on autosomes. Three genes (MC2R, MC4R and MC5R) are syntenic in the human, mouse, cattle and dog genomes, while in the pig, the syntenic group comprises MC1R, MC2R and MC5R. Two genes (MC1R and MC4R) have been extensively studied due to their function in melanogenesis (MC1R) and energy control (MC4R). Conservative organisation of these genes in five mammalian species (human, mouse, cattle, pig and dog), in terms of the encoded amino acid sequence, is higher in the case of MC4R compared to MC1R. Polymo...
Genetic diversity and conservation in a small endangered horse population. The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes an...
Chromosomal assignment of R-spondin genes in the donkey (Equus asinus, 2n = 62). R-spondins constitute a recently discovered small family of growth factors, and the evidence of their role in several developmental pathways is growing fast. In this work we describe the chromosomal location of the four RSPO genes in the donkey. Using horse BACs, we localized RSPO1 on EAS 5q23, RSPO2 on EAS 12q13, RSPO3 on EAS 24q26, and RSPO4 on EAS 15p13. Moreover, RSPO2, RSPO3, and RSPO4 are the first genes mapped on donkey chromosomes 12, 24, and 15, respectively.
Horse breed discrimination using machine learning methods. Genetic relationships and population structure of 8 horse breeds in the Czech and Slovak Republics were investigated using classification methods for breed discrimination. To demonstrate genetic differences among these breeds, we used genetic information - genotype data of microsatellite markers and classification algorithms - to perform a probabilistic prediction of an individual's breed. In total, 932 unrelated animals were genotyped for 17 microsatellite markers recommended by the ISAG for parentage testing (AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20, HTG6, HMS2, HTG7, ASB17, AS...
Combining microsatellite and pedigree data to estimate relationships among Skyros ponies. Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data, but in case of incomplete or inexistent pedigrees they are replaced by coefficients calculated from molecular data. The main objective of this study was to develop a new method to estimate relationship coefficients by combining molecular with pedigree data, which is useful for specific situations where neither pedigree nor molecular data are complete. The developed method was applied to contribute to the conservation of the Skyr...
Genetic evaluation of performance traits in Brazilian Quarter Horse. The aim of this study was to estimate genetic parameters for racing performance traits in Quarter Horses in Brazil. The data (provided by the Sorocaba Jockey Club) came from 3 Brazilian hippodromes in 1994-2003, with 11 875 observations of race time and 7775 of the speed index (SI), distributed in 2403 and 2169 races, respectively. The variance components were estimated by the MTGSAM program, under animal models including the random additive genetic effect, random permanent environmental effect, and the fixed effects of sex, age and race. Heritabilities for race time and the SI, for the 3 dist...
Genetic structure and phylogenetic relationships of the Polish Heavy horse. In this study a wide range of genetic markers (12 microsatellites, 7 blood-group loci, 10 blood-protein loci) and mitochondrial DNA (mtDNA) were used to assess genetic diversity in Polish Heavy horses. Three random samples were sequenced for 421 bp of the mitochondrial D-loop region, but no clear phylogenetic patterns were seen in mtDNA variation. Both heterozygosity and diversity levels are fairly high in Polish Heavy horses. In phylogenetic analysis the draught horses form a distinct cluster that pairs with the true pony breeds. Within this 'cold-blooded' group, the Polish Heavy Horse cluste...
Genetic variation of Polish endangered Biłgoraj horses and two common horse breeds in microsatellite loci. Genetic variation of endangered Biłgoraj horses and two common Polish horse breeds was compared with the use of 12 microsatellite loci (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, VHL20). Lower allelic diversity was detected in all investigated populations in comparison to other studies. Large differences in the frequencies of microsatellite alleles between Biłgoraj horses and two other horse breeds were discovered. In all polymorphic loci all investigated breeds were in the Hardy-Weinberg equilibrium. Mean Fis values and the results of a test for the presence of a rec...
A low-level X chromosome mosaicism in mares, detected by chromosome painting. Fluorescence in situ hybridization with the use of the equine X whole chromosome painting probe was carried out on chromosome spreads originating from three mares with poor reproductive performance (infertility, miscarriage or stillbirth). The numbers of analysed spreads were high (105, 300 and 480) and in all three mares a low frequency of mosaicism was identified. The mares had the following karyotypes: 64,XX/63,X/65,XXX (93.6%/5.7%/0.7%), 64,XX/63,X (98.9%/1.1%) and 64,XX/63,X (94.3%/5.7%). The incidence and importance of the low percentage X chromosome mosaicism are discussed.