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- Shrestha, Merina
(författare)
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Genetic characterization of the horse breeds from the Netherlands using single nucleotide polymorphisms
- 2016
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Interest on preservation and improvement of performance, fitness and aesthetic traits have created diverse populations in modern horses. This study aims to comprehend genetic diversity status within and across breeds or types of horses sampled in the Netherlands. The genetic diversity is important to maintain survival and adaptive potential of populations and avoid inbreeding in the long term. This study will also identify potential regions of selection. To our knowledge it is the first study to use single nucleotide polymorphism (SNP) information in a diversity study for the horses in the Netherlands. Principal component analysis (PCA) was performed using 203 randomly selected horses (about 20 per breed) and 43,721 autosomal SNPs that remained after pruning for call rate per SNP, per horse and minor allele frequency. The relationships among breeds were visualized by plotting the first two principal components. The Friesian breed seemed genetically distant from the other breeds in the dataset. The relationships among breeds will also be quantified based on FST values. Runs of homozygosity (ROH) using the software PliNK will be determined to identify the regions of selection. Also, diversity indices as heterozygosity (observed and expected) and fixation index (FIS) values will be investigated to understand within breed diversity
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- Shrestha, Merina
(författare)
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Genetics of equine insect bite hypersensitivity and genetic diversity in horses
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Genetic variation contributing to the phenotypic variation was utilized in this thesis to understand the genetic background of a complex trait IBH, and to understand genetic diversity and relationships between various horse populations. IBH is the most common skin allergic disorder in horses, caused by bites of midges, predominantly Culicoides species. It affects various horse breeds worldwide. With no effective treatment, IBH degrades horse health and causes economic loss. In this thesis, we used genome-wide SNPs to identify regions contributing to genetic variance of IBH susceptibility. We also investigated influence of increased number of horses and dense SNPs on identification of genomic regions associated to IBH susceptibility. Multiple genomic regions with small effects were observed in Studies I-III. Interesting genomic regions in the Icelandic horse population across the studies I and II, was observed on chromosomes 1, 7, 10, 15 and 17. The percentage of the genetic variance explained by top ten windows increased from 3.07% (Study I) to 6.56% (Study II). Novel genomic regions were identified when number of Icelandic horses was increased in Study II. Using dense SNPs on the Exmoor pony population we identified novel genomic regions, on chr 8, associated to IBH susceptibility, though with borderline significance. In Study IV, pre-conceived understanding about evolutionary history of horse populations matched obtained results from investigation of genetic relationships within Dutch warmblood populations (pairwise mean FST ≤ 0.070), and within pony-like populations (pairwise mean FST ≤ 0.078). Horse populations with similar genetic background might share similar genetic components for IBH susceptibility. The Friesian horse population had lowest diversity (mean inbreeding coefficients: fi: 30.4%, fiROH= 22.2%) in Study IV and was genetically distinct (FST ranged from 0.13 to 0.17). This might be a result of a history of several population bottlenecks and selection on a closed breeding scheme. Low diversity in immunity related genes, observed in the Friesian horse population, might have led to increased prevalence of IBH. Similarly, low susceptibility of IBH in a warmblood population, KWPN sport horse population might be due to high genetic diversity ( fi =-6.9%). High genetic diversity in KWPN sport horse population might be a result of an open breeding scheme and interbreeding with other warmblood populations.
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- Shrestha, Merina, et al.
(författare)
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Genome-wide association study for insect bite hypersensitivity susceptibility in horses revealed novel associated loci on chromosome 1
- 2020
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 137, s. 223-233
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Tidskriftsartikel (refereegranskat)abstract
- Equine insect bite hypersensitivity (IBH) is a pruritic skin allergy caused primarily by biting midges, Culicoides spp. IBH susceptibility has polygenic inheritance and occurs at high frequencies in several horse breeds worldwide, causing increased costs and reduced welfare of affected horses. The aim of this study was to identify and validate single nucleotide polymorphisms (SNPs) associated with equine IBH susceptibility. After quality control, 33,523 SNPs were included in a Bayesian genome-wide association study on 177 affected and 178 unaffected Icelandic horses. We report associated regions in E. caballus (ECA) 1, 3, 15 and 18, overlapping with known IBH QTLs in horses, and novel regions containing several genes, together explaining 11.46% of the total genetic variance. For validation, three SNPs on ECA 1 and ECA X (explaining the largest percentage of genetic variance) within 1-mb genomic windows for IBH were genotyped in an independent population of 280 Exmoor ponies. The associated genomic region (152-153 mb) on ECA 1 was confirmed in Exmoor ponies and contains the AQR gene involved in splicing processes and a long non-coding RNA. This study confirms the polygenic nature of IBH susceptibility and suggests a role of transcriptional regulatory mechanisms (e.g., alternative splicing) for IBH predisposition in these horse breeds.
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