Kyle E. Martin
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Development and application of an updated haplotype reference panel for association analysis of spontaneous sex reversal in XX rainbow trout Open
With the rapid cost reduction of next-generation sequencing, low-coverage whole-genome sequencing (lcWGS) followed by genotype imputation is becoming a cost-effective alternative to SNP (single nucleotide polymorphism) array genotyping. Pr…
View article: Genome-wide association analysis of resistance to bacterial cold-water disease in an important rainbow trout aquaculture breeding population
Genome-wide association analysis of resistance to bacterial cold-water disease in an important rainbow trout aquaculture breeding population Open
Bacterial cold-water disease (BCWD) outbreaks in salmonid aquaculture have resulted in significant losses in commercial populations. Currently, there is no commercially available vaccine for the disease caused by Flavobacterium psychrophil…
View article: Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout
Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout Open
With the rapid and significant cost reduction of next-generation sequencing, low-coverage whole-genome sequencing (lcWGS), followed by genotype imputation, is becoming a cost-effective alternative to single-nucleotide polymorphism (SNP)-ar…
View article: Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci
Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci Open
Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV), which can cause substantial mortality and economic losses in rainbow trout aquaculture and fisheries enhancement hatchery program…
Effects of fertilizing eggs from a summer-spawning line with cryopreserved milt from a winter-spawning line on spawning date and egg production traits in rainbow trout Open
Rainbow trout lines have been selected to produce gametes at different times of the year to insure a year-round supply of seedstock. Protocols for cryopreservation of milt have also been established and cryopreservation services are curren…
View article: Identification of Haplotypes Associated With Resistance to Bacterial Cold Water Disease in Rainbow Trout Using Whole-Genome Resequencing
Identification of Haplotypes Associated With Resistance to Bacterial Cold Water Disease in Rainbow Trout Using Whole-Genome Resequencing Open
Bacterial cold water disease (BCWD) is an important disease in rainbow trout aquaculture. Previously, we have identified and validated two major QTL (quantitative trait loci) for BCWD resistance, located on chromosomes Omy08 and Omy25, in …
Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing Open
Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout ( Oncorhynchus mykiss ), an important aquaculture species of cold freshwater. The objec…
Additional file 1 of Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability Open
Additional file 1: Table S1. Gene abbreviations and sequence of gene coding regions targeted for Nanostring nCounter CodeSet. Table S2. Assessment of early embryo development in each Group B selected family. Table S3A. Regression analysis …
Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability Open
Background: Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage of the embryo. The …
Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss Open
Our results indicate that differences in egg quality may be derived from differences in maternal nuclear transcript activation and cytoplasmic polyadenylation before ovulation, as opposed to accumulation and storage of maternal nuclear tra…
Additional file 1: of Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss Open
Table S1. Differentially expressed transcripts among low-, medium- and high-quality eggs identified by DESeq2. Table S2. Mean and log2FC of normalized mitochondrial DET reads. Table S3. Quality analyses for RNAs treated with DNase and subm…
MOESM4 of Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations Open
Additional file 4: Table S1. Annotated protein coding genes in RefSeq (NCBI genome annotation of predicted protein coding genes; Accession GCA_002163495.1) found within the QTL region with the largest effect on resistance to CD in the NCCC…
Variance and covariance estimates for resistance to bacterial cold water disease and columnaris disease in two rainbow trout breeding populations1 Open
Family-based selective breeding can be an effective strategy for controlling diseases in aquaculture. This study aimed to estimate (co)variance components for resistance to bacterial cold water disease (BCWD) and columnaris disease (CD) in…
Retrospective Evaluation of Marker-Assisted Selection for Resistance to Bacterial Cold Water Disease in Three Generations of a Commercial Rainbow Trout Breeding Population Open
Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is an endemic and problematic disease in rainbow trout (Oncorhynchus mykiss) aquaculture. Previously, we have identified SNPs (single nucleotide polymorphisms) as…
Similar Genetic Architecture with Shared and Unique Quantitative Trait Loci for Bacterial Cold Water Disease Resistance in Two Rainbow Trout Breeding Populations Open
Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect quantitative trait loci (QTL) for BCWD resistance in rainbow trout (Onco…
209 Prospecting genomic regions associated with columnaris disease in two rainbow trout breeding populations Open
Flavobacterium Columnare, the causative agent of columnaris disease (CD), is distributed around the world in fresh water sources, infecting freshwater finfish species. Recently, it has been identified as an emerging problem for the rainbow…
Genome-wide Association Studies Reveal Similar Genetic Architecture with Shared and Unique QTL for Bacterial Cold Water Disease Resistance in Two Rainbow Trout Breeding Populations Open
Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect QTL for BCWD resistance in rainbow trout ( Oncorhynchus mykiss ). Howeve…
Erratum to: Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research Open
In the version of this article that was originally published [1] there was an error with the author name "Karim Khalil" as it was incorrectly put as "Karim Kahlil". The original article was corrected.
MOESM4 of Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture Open
Additional file 4: Table S2. Mean progeny phenotype (MPP) and genomic predictions for BCWD resistance estimated with BayesB method using five genomic selection (GS) schemes in progeny testing families (PTF) of rainbow trout. The data provi…
MOESM1 of Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture Open
Additional file 1: Table S1. Mean progeny phenotype (MPP) and predictions for BCWD resistance estimated with pedigree-based BLUP (P-BLUP) and genomic selection (GS) models in progeny testing families (PTF) of rainbow trout. The data provid…