Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout.

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)-array genotyping. The objectives of this study were 2-fold: (1) construct a haplotype reference panel for genotype imputation from lcWGS data in rainbow trout (Oncorhynchus mykiss); and (2) evaluate the concordance between imputed genotypes and SNP-array genotypes in 2 breeding populations. Medium-coverage (12×) whole-genome sequences were obtained from a total of 410 fish representing 5 breeding populations with various spawning dates.

Variance component estimates for growth traits in beef cattle using selected variants from imputed low-pass sequence data.

A beef cattle population (n = 2,343) was used to assess the impact of variants identified from the imputed low-pass sequence (LPS) on the estimation of variance components and genetic parameters of birth weight (BWT) and post-weaning gain (PWG). Variants were selected based on functional impact and were partitioned into four groups (low, modifier, moderate, high) based on predicted functional impact and re-partitioned based on the consequence of mutation, such as missense and untranslated region variants, into six groups (G1-G6). Each subset was used to construct a genomic relationship matrix (GRM) for univariate animal models.

Biological and synthetic surfactant exposure increases antimicrobial gene occurrence in a freshwater mixed microbial biofilm environment.

Aquatic habitats are particularly susceptible to chemical pollution, such as antimicrobials, from domestic, agricultural, and industrial sources. This has led to the rapid increase of antimicrobial resistance (AMR) gene prevalence. Alternate approaches to counteract pathogenic bacteria are in development including synthetic and biological surfactants such as sodium dodecyl sulfate (SDS) and rhamnolipids.

Heritability of beef cow metabolizable energy for maintenance.

Most of the metabolizable energy that a cow uses during a production year is for maintenance; however, less is known about the heritability of maintenance compared to other traits that can be measured directly. Feed intake is a heritable trait in the mature cow and most of the feed consumed is used for maintenance. We hypothesized that maintenance energy was a heritable trait.

gBLUP-GWAS identifies candidate genes, signaling pathways, and putative functional polymorphisms for age at puberty in gilts.

Successful development of replacement gilts determines their reproductive longevity and lifetime productivity. Selection for reproductive longevity is challenging due to low heritability and expression late in life. In pigs, age at puberty is the earliest known indicator for reproductive longevity and gilts that reach puberty earlier have a greater probability of producing more lifetime litters.

Genetic and phenotypic associations of mitochondrial DNA copy number, SNP, and haplogroups with growth and carcass traits in beef cattle.

Mitochondrial DNA copy number (mtDNA CN) is heritable and easily obtained from low-pass sequencing (LPS). This study investigated the genetic correlation of mtDNA CN with growth and carcass traits in a multi-breed and crossbred beef cattle population. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to LPS that resulted in nuclear DNA (nuDNA) and mtDNA sequence reads.

Polymorphism of the follicle stimulating hormone receptor does not impact reproductive performance or in-vitro embryo production in beef heifers.

Assisted reproductive technologies are used to propagate desirable genetics in a shortened timeframe. Selected females undergo ovarian stimulation with the use of follicle stimulating hormone (FSH) to increase embryo recovery for subsequent transfer programs. The FSH receptor (FSHR) c.

Breeding Sustainable Beef Cows: Reducing Weight and Increasing Productivity.

Programs for sustainable beef production are established, but the specific role of beef cows in these systems is not well defined. This work characterized cows for two traits related to sustainability, cow weight (CW) and cumulative weight weaned (WtW). Cow weight indicates nutrient requirements and enteric methane emissions.

Influence of environmental factors and genetic variation on mitochondrial DNA copy number.

Mitochondrial DNA copy number (mtDNA CN) has been shown to be highly heritable and associated with traits of interest in humans. However, studies are lacking in the literature for livestock species such as beef cattle. In this study, 2,371 individuals from a crossbred beef population comprising the Germplasm Evaluation program from the U.

Efficacy of single pass UVC air treatment for the inactivation of coronavirus, MS2 coliphage and bioaerosols.

There is strong evidence that SARS-CoV-2 is spread predominantly by airborne transmission, with high viral loads released into the air as respiratory droplets and aerosols from the infected subject. The spread and persistence of SARS-CoV-2 in diverse indoor environments reinforces the urgent need to supplement distancing and PPE based approaches with effective engineering measures for microbial decontamination - thereby addressing the significant risk posed by aerosols. We hypothesized that a portable, single-pass UVC air treatment device (air flow 1254 L/min) could effectively inactivate bioaerosols containing bacterial and viral indicator organisms, and coronavirus without reliance on filtration technology, at reasonable scale.

Genetic parameters, heterosis, and breed effects for body condition score and mature cow weight in beef cattle.

Understanding the genetic relationship between mature cow weight (MWT) and body condition score (BCS) is useful to implement selection programs focused on cow efficiency. The objectives of this study were to estimate genetic parameters, heterosis, and breed effects for MWT and BCS. In total, 25,035 and 24,522 overlapping records were available for MWT and BCS on 6,138 and 6,131 cows, respectively, from the Germplasm Evaluation program, a crossbred beef population at the U.

Low-Molecular-Weight Seaweed-Derived Polysaccharides Lead to Increased Faecal Bulk but Do Not Alter Human Gut Health Markers.

Seaweeds are potentially sustainable crops and are receiving significant interest because of their rich bioactive compound content; including fatty acids, polyphenols, carotenoids, and complex polysaccharides. However, there is little information on the in vivo effects on gut health of the polysaccharides and their low-molecular-weight derivatives. Herein, we describe the first investigation into the prebiotic potential of low-molecular-weight polysaccharides (LMWPs) derived from alginate and agar in order to validate their in vivo efficacy.

Biofilm regulation in Clostridioides difficile: Novel systems linked to hypervirulence.

Clostridiodes difficile (C. difficile) was ranked an "urgent threat" by the Centers for Disease Control and Prevention (CDC) in 2019. C.

Breed and heterotic effects for mature weight in beef cattle.

Cow mature weight (MWT) is heritable and affects the costs and efficiency of a breeding operation. Cow weight is also influenced by the environment, and the relationship between the size and profitability of a cow varies depending on production system. Producers, therefore, need tools to incorporate MWT in their selection of cattle breeds and herd replacements.

Does each bead count? A reduced-cost approach for recovering waterborne protozoa from challenge water using immunomagnetic separation.

Giardia duodenalis and Cryptosporidium spp. are two of the most prominent aetiological agents of waterborne diseases. Therefore, efficient and affordable methodologies for identifying and quantifying these parasites in water are increasingly necessary.

Genetic changes in beef cow traits following selection for calving ease.

One approach to reducing calving difficulty is to select heifers with higher breeding value for calving ease. Calving ease is often associated with lower birth weight and that may result in other possible effects on lifetime productivity. Females from experimental select and control calving ease lines within each of the seven populations were compared.

Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers.

Decreasing costs are making low coverage sequencing with imputation to a comprehensive reference panel an attractive alternative to obtain functional variant genotypes that can increase the accuracy of genomic prediction. To assess the potential of low-pass sequencing, genomic sequence of 77 steers sequenced to >10X coverage was downsampled to 1X and imputed to a reference of 946 cattle representing multiple and -influenced breeds. Genotypes for nearly 60 million variants detected in the reference were imputed from the downsampled sequence.

Competent but complex communication: The phenomena of pheromone-responsive plasmids.

Enterococci are robust gram-positive bacteria that are found in a variety of surroundings and that cause a significant number of healthcare-associated infections. The genus possesses a high-efficiency pheromone-responsive plasmid (PRP) transfer system for genetic exchange that allows antimicrobial-resistance determinants to spread within bacterial populations. The pCF10 plasmid system is the best characterised, and although other PRP systems are structurally similar, they lack exact functional homologues of pCF10-encoded genes.

De novo assembly of the cattle reference genome with single-molecule sequencing.

Background: Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.

Using SNP Weights Derived From Gene Expression Modules to Improve GWAS Power for Feed Efficiency in Pigs.

The "large small " problem has posed a significant challenge in the analysis and interpretation of genome-wide association studies (GWAS). The use of prior information to rank genomic regions and perform SNP selection could increase the power of GWAS. In this study, we propose the use of gene expression data from RNA-Seq of multiple tissues as prior information to assign weights to SNP, select SNP based on a weight threshold, and utilize weighted hypothesis testing to conduct a GWAS.

Heritability and genetic correlations of feed intake, body weight gain, residual gain, and residual feed intake of beef cattle as heifers and cows.

The cow herd consumes approximately 70% of the annual feed resources. To date, most genetic evaluations of feed intake in beef cattle have been made in growing animals and little information is available for mature cows. Genetic evaluations in mature cows have predominately been confined to lactating dairy cows and the relationship between feed intake as growing heifers and mature cows has not been addressed.

Electroanalytical properties of chlorophenol red at disposable carbon electrodes: Implications for Escherichia coli detection.

The use of coliforms and Escherichia coli as indicator species for assessing the quality of water is well established and a large variety of methods based on β-galactosidase (B-GAL) activity, inherent to the microbes within this classification, have arisen to enable their detection and enumeration. Chlorophenol red (CPR) is widely used as a chromogenic label, but its capacity for translation to electroanalytical devices has yet to be fully explored. The CPR moiety is capable of undergoing oxidation at carbon substrates (+0.

Comparison of different functions to describe growth from weaning to maturity in crossbred beef cattle1.

Cow mature weight (MWT) has increased in the past 30 yr. Larger cows cost more to maintain, but their efficiency-and thus profitability-depends on the production environment. Incorporating MWT effectively into selection and mating decisions requires understanding of growth to maturity.

A rapid and sensitive system for recovery of nucleic acids from Mycobacteria sp. on archived glass slides.

Background: The field of diagnostics continues to advance rapidly with a variety of novel approaches, mainly dependent upon high technology platforms. Nonetheless much diagnosis, particularly in developing countries, still relies upon traditional methods such as microscopy. Biological material, particularly nucleic acids, on archived glass slides is a potential source of useful information both for diagnostic and epidemiological purposes.

Genetic correlations among weight and cumulative productivity of crossbred beef cows.

Mature weight of beef cows in the United States has been increasing as a correlated response to selection for calf growth. Unfavorable genetic correlations between cow weight and various measures of female fertility, stayability, and lifetime production suggest declining cow productivity might also be expected as a correlated response to growth selection. National cattle evaluations, however, show increasing trends for stayability and sustained fertility.