Biology subjects

Hoff, J. L.

Publications and source records attributed to Hoff, J. L..

3 recordsLinked to original sources

bioRxiv2023

Variance component estimates, phenotypic characterization, and genetic evaluation of bovine congestive heart failure in commercial feeder cattle

1. Introduction Abstract 1. Introduction 2. Methods 3. Results and Discussion 4. Conclusions 5. Conflict of Interest 6. Author Contributions 7. Funding 9. Availability of Data... 10 References Bovine congestive heart failure (BCHF) observed in feedlot cattle is responsible for significant and increasing economic loss to the feedlot industry, with the largest losses occurring during the latter part of the finishing period (Neary et al., 2015a; Johnson et al., 2021). This condition has been characterized in a variety of studies and is commonly referred to as congestive heart failure, right-sided heart failure, cor pulmonale, or noninfectious heart disease. These conditions generally describe morb ...

genetics↗

bioRxiv2019

A Multi-Breed Reference Panel and Additional Rare Variation Maximizes Imputation Accuracy in Cattle

BackgroundThe use of array-based SNP genotyping in the beef and dairy industries has produced an astounding amount of medium-to-low density genomic data in the last decade. While low-density assays work exceptionally well in the context of genomic prediction, they are less useful in mapping and causal variant discovery. This project focuses on maximizing imputation accuracies to the marker set of two high-density research assays, the Illumina Bovine HD, and the GGP-F250 which contains a large proportion of rare and potentially functional variants (~850,000 total SNPs). This 850K SNP set is well-suited for both imputation to sequence-level genotypes and direct downstream analysis.\n\nResultsWe find that a large multi-breed composite imputation reference comprised of 36,131 samples with either HD and/or F250 genotypes significantly increases imputation accuracy compared to a standard within-breed reference panel, particularly at low minor allele frequencies. Imputation accuracies were maximized when an individuals ancestry was adequately represented in the composite reference, particularly with complete 850K genotypes. The addition of rare content from the F250 to our composite reference panel significantly increased the imputation accuracy of rare variants found exclusively on the HD. Additionally, we identify 50,000 variants as an ideal starting density for 850K imputation.\n\nConclusionUsing high-density genotypes on all available individuals in a multi-breed reference panel maximizes imputation accuracy for all cattle populations. Admixed breeds or those sparsely represented in the composite reference are still imputed at high accuracy which will increase further as the reference panel grows. We expect that the addition of rare variation from the F250 will increase the accuracy of imputation at the sequence level.

genomics↗

bioRxiv2017

Lethal Haplotypes And Candidate Casual Mutations In Angus Cattle

BackgroundIf unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, developmentally lethal recessive loci can be localized. This analysis comes without the need for observation of the loss-associated phenotype (e.g., failure to implant, first trimester abortion, deformity at birth). In this study, haplotypes were estimated for 3,961 registered Angus individuals using 52,545 SNP loci using findhap v2, which exploited the complex pedigree among the individuals in this population.\n\nResultsSeven loci were detected to possess haplotypes that were not observed in homozygous form despite a sufficiently high frequency and pedigree-based expectation of homozygote occurrence. These haplotypes were identified as candidates for harboring autosomal recessive lethal alleles. Of the genotyped individuals, 109 were resequenced to an average 27X depth of coverage to identify putative loss-of-function alleles genome-wide and had variants called using a custom in-house developed pipeline. For the candidate lethal-harboring haplotypes present in these bulls, sequence-called genotypes were used to identify concordant variants. In addition, whole-genome sequence imputation of variants was performed into the set of 3,961 genotyped animals using the 109 resequenced animals to identify candidate lethal recessive variants at the seven loci.\n\nConclusionsSelective breeding programs could utilize the predicted lethal haplotypes associated with SNP genotypes. Sequencing and other methods for identifying the causal variants underlying these haplotypes can allow for more efficient methods of management such as gene editing. These two methods in total will reduce the negative impacts of inbreeding on fertility and maximize overall genetic gains.

genomics↗