120 research outputs found
Positioning of 15,036 Single Nucleotide Polymorphism (SNP) Loci using order algorithms and estimates of pair wise linkage disequilibrium (LD) in Australian dairy cattle
No full textZiel dieser Diplomarbeit war es, mit mathematischen Methoden die chromosomale Position von genetischen Markern basierend auf Schätzwerten des paarweisen Gametenphasenungleichgewichtes (GPU) von Genorten im Rinder-Genom zu bestimmen. Für die Untersuchung standen 15.036 single nuceotide polymorphism (SNP) Marker zur Verfügung, die bei 1.546 australischen Holstein-Friesian Stieren genotypiert wurden. Die Suche einer optimalen Anordnung der SNP-Marker aufgrund von paarweisen Ähnlichkeiten bzw. Distanzen ist eine Version des bekannten "Traveling Salesperson Problems" (TSP). In dieser Arbeit wurden für die optimale Lösung des TSP die Methoden HOPACH (Laan & Pollard 2003), Fast Optimal Leaf Order (Joseph et al. 2001) und Sorting Points into Neighborhood (SPIN) (Tsafrir et al. 2005) angewendet. Ein Vergleich zwischen den Positionen aus der aktuellen Rinder Genom Karte (Btau3.1) und den einzelnen Positionsergebnissen der Algorithmen zeigte, dass nur SPIN für die Positionierung von genetischen Markern basierend auf deren GPU Schätzwerten erfolgreich angewendet werden konnte. Zur Beschreibung des GPU wurden die häufig verwendeten Maße Lewontins's D prime (D') und der quadrierte Korrelationskoeffizient r² verwendet. Die Ergebnisse zeigten, dass D' nützlich ist, eine erste Anordnung von SNPs zu generieren und r² erfolgreich angewendet werden kann, um nicht katalogisierte SNPs auf aktuellen Gen-Karten zu positionieren und in weiterer Folge deren physikalische bzw. genetische Position zu berechnen.The aim of this study was to develop a new procedure for determining locus order solely from pair-wise estimates of linkage disequilibrium (LD) - a so-called LODE map - for a high density single nucleotide polymorphism (SNP) marker panel in dairy cattle. A total of 15,036 SNP were genotyped for 1,546 Australian Holstein Friesian bulls. The proposed formulation of genetic mapping based on LD can be considered as a version of traveling salesperson problem (TSP) - i.e. many solutions need to be optimized to find an optimal outcome. In this study three different ordering algorithms were applied, providing solutions for the TSP: HOPACH (Laan & Pollard 2003), Fast Optimal Leaf order (Joseph et al. 2001) and Sorting Points into Neighbrhood (SPIN) (Tsafrir et al. 2005). The results have been discussed and compared in depth, concluding that the unsupervised novel approach of SPIN was most suitable to create final order of SNPs on single chromosomes and to align unknown SNPs on the current bovine map. Two commonly used measures of LD have been applied: Lewontin's D prime (D') and the squared correlation coefficent, r². The results clearly indicate that Lewontin's D prime (D') is an effective parameter for providing the framework of locus order, and correlation coefficient r² is useful for positioning unaligned loci.vorgelegt von Markus NeuditschkoWien, Univ. für Bodenkultur, Dipl.-Arb., 2008Zsfassung in dt. Sprach
Positioning of 15,036 Single Nucleotide Polymorphism (SNP) Loci using order algorithms and estimates of pair wise linkage disequilibrium (LD) in Australian dairy cattle
No full textZiel dieser Diplomarbeit war es, mit mathematischen Methoden die chromosomale Position von genetischen Markern basierend auf Schätzwerten des paarweisen Gametenphasenungleichgewichtes (GPU) von Genorten im Rinder-Genom zu bestimmen. Für die Untersuchung standen 15.036 single nuceotide polymorphism (SNP) Marker zur Verfügung, die bei 1.546 australischen Holstein-Friesian Stieren genotypiert wurden. Die Suche einer optimalen Anordnung der SNP-Marker aufgrund von paarweisen Ähnlichkeiten bzw. Distanzen ist eine Version des bekannten "Traveling Salesperson Problems" (TSP). In dieser Arbeit wurden für die optimale Lösung des TSP die Methoden HOPACH (Laan & Pollard 2003), Fast Optimal Leaf Order (Joseph et al. 2001) und Sorting Points into Neighborhood (SPIN) (Tsafrir et al. 2005) angewendet. Ein Vergleich zwischen den Positionen aus der aktuellen Rinder Genom Karte (Btau3.1) und den einzelnen Positionsergebnissen der Algorithmen zeigte, dass nur SPIN für die Positionierung von genetischen Markern basierend auf deren GPU Schätzwerten erfolgreich angewendet werden konnte. Zur Beschreibung des GPU wurden die häufig verwendeten Maße Lewontins's D prime (D') und der quadrierte Korrelationskoeffizient r² verwendet. Die Ergebnisse zeigten, dass D' nützlich ist, eine erste Anordnung von SNPs zu generieren und r² erfolgreich angewendet werden kann, um nicht katalogisierte SNPs auf aktuellen Gen-Karten zu positionieren und in weiterer Folge deren physikalische bzw. genetische Position zu berechnen.The aim of this study was to develop a new procedure for determining locus order solely from pair-wise estimates of linkage disequilibrium (LD) - a so-called LODE map - for a high density single nucleotide polymorphism (SNP) marker panel in dairy cattle. A total of 15,036 SNP were genotyped for 1,546 Australian Holstein Friesian bulls. The proposed formulation of genetic mapping based on LD can be considered as a version of traveling salesperson problem (TSP) - i.e. many solutions need to be optimized to find an optimal outcome. In this study three different ordering algorithms were applied, providing solutions for the TSP: HOPACH (Laan & Pollard 2003), Fast Optimal Leaf order (Joseph et al. 2001) and Sorting Points into Neighbrhood (SPIN) (Tsafrir et al. 2005). The results have been discussed and compared in depth, concluding that the unsupervised novel approach of SPIN was most suitable to create final order of SNPs on single chromosomes and to align unknown SNPs on the current bovine map. Two commonly used measures of LD have been applied: Lewontin's D prime (D') and the squared correlation coefficent, r². The results clearly indicate that Lewontin's D prime (D') is an effective parameter for providing the framework of locus order, and correlation coefficient r² is useful for positioning unaligned loci.vorgelegt von Markus NeuditschkoWien, Univ. für Bodenkultur, Dipl.-Arb., 2008Zsfassung in dt. Sprach
A Novel QTL and a Candidate Gene Are Associated with the Progressive Motility of Franches-Montagnes Stallion Spermatozoa after Thaw
No full textThe use of frozen-thawed semen is an important reproduction tool to preserve the biodiversity of small, native horse breeds such as the Franches-Montagnes (FM). However, not all stallions produce cryotolerant semen with a progressive motility after thaw ≥ 35%. To improve our understanding of the genetic background of male fertility traits in both fresh and frozen-thawed semen, we performed genome-wide association studies (GWAS) on gel-free volume, sperm cell concentration, total sperm count, and progressive motility in fresh and frozen-thawed semen from 109 FM stallions using 335,494 genome-wide single nucleotide polymorphisms (SNPs). We identified one significant (p < 1.69 × 10−7) quantitative trait locus (QTL) on ECA6 within the SCN8A gene for progressive motility after thaw, which was previously associated with progressive motility in boars. Homozygous stallions showed a substantial drop in progressive motility after thaw. This QTL could be used to identify cryointolerant stallions, avoiding the costly cryopreservation process. Further studies are needed to confirm whether this QTL is also present in other horse breeds
Increased heterozygosity in low‐pass sequencing data allows identification of blood chimeras in cattle
No full textIn about 90% of multiple pregnancies in cattle, shared blood circulation between fetuses leads to genetic chimerism in peripheral blood and can reduce reproductive performance in heterosexual co-twins. However, the early detection of heterosexual chimeras requires specialized tests. Here, we used low-pass sequencing data with a median coverage of 0.64× generated from blood samples of 322 F1 crosses between beef and dairy cattle and identified 20 putative blood chimeras through increased levels of genome-wide heterozygosity. In contrast, for 77 samples with routine SNP microarray data generated from hair bulbs of the same F1s, we found no evidence of chimerism, simultaneously observing high levels of genotype discordance with sequencing data. Fifteen out of 18 reported twins showed signs of blood chimerism, in line with previous reports, whereas the presence of five alleged singletons with strong signs of chimerism suggests that the in-utero death rate of co-twins is at the upper limit of former estimates. Together, our results show that low-pass sequencing data allow reliable screening for blood chimeras. They further affirm that blood is not recommended as a source of DNA for the detection of germline variants
A Nonsense Variant in the ST14 Gene in Akhal-Teke Horses with Naked Foal Syndrome
No full textNaked 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 horses died between a few weeks and 3 yr of age. It is not clear whether a specific pathology caused the premature deaths. NFS is inherited as a monogenic autosomal recessive trait. We mapped the disease causing genetic variant to two segments on chromosomes 7 and 27 in the equine genome. Whole genome sequencing of two affected horses, two obligate carriers, and 75 control horses from other breeds revealed a single nonsynonymous genetic variant on the chromosome 7 segment that was perfectly associated with NFS. The affected horses were homozygous for ST14:c.388G>T, a nonsense variant that truncates >80% of the open reading frame of the ST14 gene (p.Glu130*). The variant leads to partial nonsense-mediated decay of the mutant transcript. Genetic variants in the ST14 gene are responsible for autosomal recessive congenital ichthyosis 11 in humans. Thus, the identified equine ST14:c.388G>T variant is an excellent candidate causative variant for NFS, and the affected horses represent a large animal model for a known human genodermatosis. Our findings will enable genetic testing to avoid the nonintentional breeding of NFS-affected foals
Population structure and genomic diversity of the Einsiedler horse.
No full textThe breeding history of the Einsiedler horse is closely connected with the Benedictine cloister Einsiedeln. In the mid-nineteenth century, it was decided to use European Warmblood stallions for cross-breeding and to abandon the selection of stallions. Since that time, it has only been possible to trace back the origin of Einsiedler horses using maternal ancestry information. Here, we collected high-density genotype data for European Warmblood horses (Selle Français, Swiss Warmblood and Einsiedler) and Franches-Montagnes horses, the last native Swiss horse breed, to unravel the current population structure of the Einsiedler horse. Using commonly applied methods to ascertain fine-scale population structures, it was not possible to clearly differentiate the Einsiedler from other European Warmblood horses. However, by means of runs of homozygosity (ROH) we were able to detect breed-specific ROH islands for the Einsiedler horse, including genes involved in domestication and adaptation to high altitude. Therefore, future breeding activities should involve the screening of these breed-specific ROH segments, the revival of cryopreserved sperm and the selection of Einsiedler stallions
Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses.
No full textThe evaluation of conformation traits is an important part of selection for breeding stallions and mares. Some of these judged conformation traits involve joint angles that are associated with performance, health, and longevity. To improve our understanding of the genetic background of joint angles in horses, we have objectively measured the angles of the poll, elbow, carpal, fetlock (front and hind), hip, stifle, and hock joints based on one photograph of each of the 300 Franches-Montagnes (FM) and 224 Lipizzan (LIP) horses. After quality control, genome-wide association studies (GWASs) for these traits were performed on 495 horses, using 374,070 genome-wide single nucleotide polymorphisms (SNPs) in a mixed-effect model. We identified two significant quantitative trait loci (QTL) for the poll angle on ECA28 (p = 1.36 × 10-7), 50 kb downstream of the gene, involved in cranial morphology, and for the elbow joint on ECA29 (p = 1.69 × 10-7), 49 kb downstream of the gene, and 75 kb upstream of the gene. Both genes are associated with bone mineral density in humans. Furthermore, we identified other suggestive QTL associated with the stifle joint on ECA8 (p = 3.10 × 10-7); the poll on ECA1 (p = 6.83 × 10-7); the fetlock joint of the hind limb on ECA27 (p = 5.42 × 10-7); and the carpal joint angle on ECA3 (p = 6.24 × 10-7), ECA4 (p = 6.07 × 10-7), and ECA7 (p = 8.83 × 10-7). The application of angular measurements in genetic studies may increase our understanding of the underlying genetic effects of important traits in equine breeding
Using Whole-Genome Sequence Information to Foster Conservation Efforts for the European Dark Honey Bee, Apis mellifera mellifera
No full textPas de Clé UTInternational audiencePollination is a key ecosystem service for agricultural systems and Western honey bees, Apis mellifera, are the most important managed pollinators. Major losses of managed honey bee colonies reinforced the need to take advantage of locally adapted subspecies and ecotypes to buffer populations against various stressors. However, introductions of non-native honey bees from distant lineages are likely to undermine respective conservation efforts unless reliable and cost effective tools can be used to identify hybridization. The purpose of this study is to characterize current population structure and genetic diversity, and to assess the degree of admixture between native and introduced honey bees. Moreover, we aim to select a reduced number of genetic markers to improve conservation management strategies. We take advantage of recent developments in next-generation sequencing and network-based clustering to investigate conservation efforts for the native European Dark honey bee, A. m. mellifera, which is threatened by introgression in most of its range. We collected whole-genome sequence information from haploid drones of A. m. mellifera, A. m. carnica, and Buckfast sampled throughout Switzerland (N = 81), as well as from four Swiss A. m. mellifera conservation areas (N = 39) and from one conservatory in the French Alps (N = 31). Population structure analyses based upon 3.375 M genome-wide SNPs discerned samples by subspecies and geographic origin (Switzerland or France). Ancestry inference indicated admixed individuals in all of the protected areas, calling for improved management efforts. After testing different subsets of ancestry informative SNPs using three different selection strategies (FST, PCA-based or at random), as few as 50 SNPs are found to be sufficient to differentiate native from introduced honey bees. Therefore, our data suggests that a low-density SNP panel can be a precise and cost-effective tool to support conservation management efforts for managed pollinators
Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions.
No full textThe Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern European haplotypes, all modern horse breeds clustered together in a roughly 700-year-old haplogroup that was transmitted to Europe by the import of Oriental stallions. The Oriental horse group consisted of two major subclades: the Original Arabian lineage and the Turkoman horse lineage. We show that the English Thoroughbred MSY was derived from the Turkoman lineage and that English Thoroughbred sires are largely responsible for the predominance of this haplotype in modern horses
- …
