Sofia Mikko
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View article: When large-effect damaging alleles enter small populations
When large-effect damaging alleles enter small populations Open
Large-effect recessive damaging variants found at relatively high frequencies are common enough in domestic animals that they cause problems in breeding programs. There are several potential reasons. Deleterious variants may rise in freque…
View article: Haplotype structure and heterozygosity around the fragile foal syndrome variant in Swedish Warmblod horses
Haplotype structure and heterozygosity around the fragile foal syndrome variant in Swedish Warmblod horses Open
Fragile foal syndrome (FFS) is a disease caused by a recessive lethal missense mutation in the PLOD1 gene located on ECA2. Despite its harmful effect, a relatively high frequency of FFS carriers was observed in Warmblood breeds spanning fr…
View article: Single‐Step Genome‐Wide Association Study of Factors for Evaluated and Linearly Scored Traits in Swedish Warmblood Horses
Single‐Step Genome‐Wide Association Study of Factors for Evaluated and Linearly Scored Traits in Swedish Warmblood Horses Open
Swedish Warmblood horses (SWB) are bred for show jumping and/or dressage with young horse test scores as indicator traits. This study aimed to investigate possible candidate genes and regions of importance for evaluated and linearly scored…
View article: Additional file 3 of Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects
Additional file 3 of Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects Open
Additional file 3: Table S2. Effect of the WFFS genotype on the DEBV for the linear descriptive traits for both NS and SJ SWB horses. Table S2 shows the effect of the WFFS expressed in significance level and in LSM of the DEBV for the line…
View article: Additional file 4 of Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects
Additional file 4 of Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects Open
Additional file 4: Table S3. Descriptive statistics of the traditional evaluating traits in the SJ horses. The following values are reported for each traditional evaluating trait in the SJ horses: number of observations, mean, standard dev…
View article: Additional file 2 of Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects
Additional file 2 of Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects Open
Additional file 2: Table S1. Descriptive statistics of the traditional evaluating traits in the NS horses. The following values are reported for each traditional evaluating trait in the NS horses: number of observations, mean, standard dev…
View article: Using droplet digital PCR for the detection of hco-acr-8b levamisole resistance marker in H. contortus
Using droplet digital PCR for the detection of hco-acr-8b levamisole resistance marker in H. contortus Open
The nematode Haemonchus contortus is one of the most prevalent and pathogenic parasites in small ruminants. Although usually controlled using anthelmintics, the development of drug resistance by the parasite has become a major issue in liv…
View article: Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data
Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data Open
Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity neg…
View article: A genome-wide scan for candidate lethal variants in Thoroughbred horses
A genome-wide scan for candidate lethal variants in Thoroughbred horses Open
Recessive lethal variants often segregate at low frequencies in animal populations, such that two randomly selected individuals are unlikely to carry the same mutation. However, the likelihood of an individual inheriting two copies of a re…
View article: Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines
Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines Open
The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore…
View article: Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds Open
Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds…
View article: Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds Open
Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds…
View article: Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds Open
Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds…
View article: MOESM3 of Signatures of selection in the genome of Swedish warmblood horses selected for sport performance
MOESM3 of Signatures of selection in the genome of Swedish warmblood horses selected for sport performance Open
Additional file 3: Table S1. Genes located within consensus homozygous segments in Exmoor ponies.
View article: MOESM6 of Signatures of selection in the genome of Swedish warmblood horses selected for sport performance
MOESM6 of Signatures of selection in the genome of Swedish warmblood horses selected for sport performance Open
Additional file 6: Table S4. Details on the six overrepresented biological processes and the genes involved in each biological term from the overlapping regions from the XPEHH and Fst tests.
View article: MOESM4 of Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
MOESM4 of Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds Open
Additional file 4: Table S3. Genomic regions validated for CNVs by RT-qPCR. Primer sequences, position, product size, annealing temperature and TaqMan probes are shown. The CNV status in the SNP-array and in the qPCR and the CNV validation…
View article: MOESM5 of Signatures of selection in the genome of Swedish warmblood horses selected for sport performance
MOESM5 of Signatures of selection in the genome of Swedish warmblood horses selected for sport performance Open
Additional file 5: Table S3. SNP markers found to be under potential selection when analysed by the XPEHH test before FDR control.
View article: MOESM3 of Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
MOESM3 of Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds Open
Additional file 3: Table S2. PANTHER gene ontology analysis of significantly over- and underrepresented genes.
View article: MOESM2 of Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
MOESM2 of Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds Open
Additional file 2. List of genes overlapping with the identified CNVRs.
View article: MOESM1 of Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
MOESM1 of Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds Open
Additional file 1: Table S1. CNVRs identified in this study and including information regarding genome position, size, status, segment CNV counts, gene counts, number of individuals for each breed, QTL overlap and novelty.
View article: MOESM4 of Signatures of selection in the genome of Swedish warmblood horses selected for sport performance
MOESM4 of Signatures of selection in the genome of Swedish warmblood horses selected for sport performance Open
Additional file 4: Table S2. Details on the five overrepresented biological processes and the genes involved in each biological term from the ROH analysis.
View article: Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology
Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology Open
The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequenc…
View article: A Nonsense Variant in the <i>ST14</i> Gene in Akhal-Teke Horses with Naked Foal Syndrome
A Nonsense Variant in the <i>ST14</i> Gene in Akhal-Teke Horses with Naked Foal Syndrome Open
Naked foal syndrome (NFS) is a genodermatosis in the Akhal-Teke horse breed. We provide the first scientific description of this phenotype. Affected horses have almost no hair and show a mild ichthyosis. So far, all known NFS affected hors…
View article: Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies Open
Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure and impaired movements, and…