Browsing by Subject "Candidate gene"

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    Genetic exploration of exercise associated sudden death in racehorses
    (2024) Stock, Joy
    Background: Exercise-associated sudden death (EASD) is a fatal collapse occurring during or within 2 hours of racing or training in an otherwise healthy individual. It represents a significant cause of mortality in racehorses, accounting for 25% of the approximately 500 annual racehorse fatalities in the United States. Beyond its negative impact on equine welfare, EASD poses risks to jockey safety and challenges the public perception of horse racing. Cardiac-related issues are the cause of approximately 50% of EASD cases. Cardiac arrhythmias are also thought to be an important contributor to the EASD cases without a diagnosis at necropsy. In human patients without a diagnosis at necropsy, ion channelopathies are found to be an important underlying cause. The genetics underlying EASD have been largely unexplored in horses.Hypothesis: Thoroughbred racehorses with variants in ion channels and other arrhythmogenic genes are predisposed to a higher risk of EASD. Specific Aim1: This study aimed to identify causative positional candidate regions for EASD in Thoroughbred racehorses. Methods: Whole-genome sequencing (target: 12X coverage) and a Genome-wide Efficient Mixed Model Association (GEMMA) univariate linear mixed model genome-wide association study (GWAS) were performed on 50 EASD cases and 48 controls. Results: We identified 8 significant regions linked to EASD. Although genes in these regions were not directly analogous to known human ion channelopathy genes, aquaporin 4 (AQP4) and potassium channel tetramerization domain containing 1 (KCTD1) on the region in chromosome 8, showed potential relevance to dysrhythmia development. Specific Aim 2: This study aimed to identify causative variants in arrhythmogenic candidate genes for EASD in Thoroughbred racehorses. Methods: Candidate genes were identified using a keyword-based query of four databases: Phenolyzer, ClinVar, Online Mendelian Inheritance of Man, and OpenTargets. From these, a narrow (genes identified in all four programs) and a broad (genes identified in two or three programs) candidate gene set were established. SnpSift CaseControl was used to identify significant differences between EASD cases and controls. Results: We identified a significant modifier variant in troponin T2-cardiac type (TNNT2) from the narrow gene set. The broad gene set analysis identified 39 significant variants across 21 genes, with notable findings in triadin (TRDN) and calcium voltage-gated channel subunit alpha1 D (CACNA1D), both of which are linked to cardiac arrhythmias in people and may contribute to equine EASD. Conclusions: We identified variants and genes that may be contributing to EASD in Thoroughbred racehorses. These variants and genes warrant further investigation for their roles in exercise-induced arrhythmias, sudden death, and EASD in Thoroughbred racehorses.
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    Trichome density phenotypic data, image data, candidate genes Nanopore sequencing data
    (2020-08-13) Yin, Lu; Clark, Matthew; yinxx134@umn.edu; Yin, Lu
    Two experiments of phenotypic data on trichome density scores and sequencing data in a hybrid grape population (GE1025 family and GE1783 family). The excel file contains this data. Experiment 1 was conducted on greenhouse-maintained GE1025 cuttings in 2018 and 2019 and on field-grown leaves of GE1025 in 2019 (3 environments). Experiment 2 was conducted on GE1783 field-grown leaves in 2019 (1 environment). Experiment 1 was conducted under a dissecting scope. The images were where the trichome scores were obtained in Experiment 2. Nanopore sequencing data was part of Experiment 2. It is released now because it is under review for publication and it is needed to derive the conclusion for the fine mapped trichome region on chromosome 1 of hybrid grapes (Lu Yin's Ph.D. thesis in 2020 Chapter 4). This study on trichome offers information for hybrid grape breeding programs for a minor role in foliar phylloxera resistance.