Identification of biological pathways and putative candidate genes for residual feed intake in a tropically adapted beef cattle breed by plasma proteome analysis.

This study identified potential biomarkers for feed efficiency by blood plasma proteome analysis of a tropically adapted beef cattle breed. Two experimental groups were selected based on residual feed intake (RFI). The proteome was investigated by LC-MS/MS in a data-dependent acquisition mode.

Proteomic identification of potential biomarkers for heat tolerance in Caracu beef cattle using high and low thermotolerant groups.

Background: Heat stress has deleterious effects on physiological and performance traits in livestock. Within this context, using tropically adapted cattle breeds in pure herds or terminal crossbreeding schemes to explore heterosis is attractive for increasing animal production in warmer climate regions. This study aimed to identify biological processes, pathways, and potential biomarkers related to thermotolerance in Caracu, a tropically adapted beef cattle breed, by proteomic analysis of blood plasma.

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.

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 programs. In a previous study on a commercial rainbow trout breeding line that has undergone selection, we found that genetic resistance to IHNV is controlled by the oligogenic inheritance of several moderate and many small effect quantitative trait loci (QTL). Here we used genome wide association analyses in two different commercial aquaculture lines that were naïve to previous exposure to IHNV to determine whether QTL were shared across lines, and to investigate whether there were major effect loci that were still segregating in the naïve lines.

Weighted single-step genome-wide association study and functional enrichment analyses for gastrointestinal nematode resistance traits in Santa Ines sheep.

This study aimed to identify genomic regions, pathways, and putative candidate genes associated with resistance to gastrointestinal nematode in Santa Ines sheep. The phenotypic information comprised 5529 records from 1703 naturally infected animals. After genomic data quality control, 37,511 SNPs from 589 animals were available.

Alternative SNP weighting for multi-step and single-step genomic BLUP in the presence of causative variants.

The accuracy of genetic selection in dairy can be increased by the adoption of new technologies, such as the inclusion of sequence data. In simulation studies, assigning different weights to causative single-nucleotide polymorphism (SNP) markers led to better predictions depending on the genomic prediction method used. However, it is still not clear how the weights should be calculated.

Effect of Thermal Stress on Thermoregulation, Hematological and Hormonal Characteristics of Caracu Beef Cattle.

This study evaluated the influence of environmental temperature on thermoregulation, hormonal, and hematological characteristics in Caracu cattle. Blood samples, hair length, coat and muzzle colors, rectal (RT), and surface temperatures were collected from 48 males and 43 females before (morning) and after sun exposure for eight hours (afternoon). Infrared thermography (IRT) was used to identify superficial temperature that exhibits a high correlation with RT.

Effects of Feeding and Drinking Behavior on Performance and Carcass Traits in Beef Cattle.

Feed and water efficiency are important traits to improve beef cattle production’s economic and environmental sustainability. This study evaluated residual feed intake (RFI) and residual water intake (RWI) and their relationship with performance, ingestive behavior, and carcass traits in Caracu beef cattle. The data were analyzed using a generalized linear model with least squares means.

Single-Step GBLUP and GWAS Analyses Suggests Implementation of Unweighted Two Trait Approach for Heat Stress in Swine.

The purpose of this study was to perform a genome-wide association study to determine the genomic regions associated with heat stress tolerance in swine. Phenotypic information on carcass weight was available for 227,043 individuals from commercial farms in North Carolina and Missouri, U.S.

Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford.

The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent.

Protective Effect of Baicalin against Infection in Mice.

This study investigated the prophylactic and therapeutic efficacies of baicalin (BC), a plant-derived flavone glycoside, in reducing the severity of infection (CDI) in a mouse model. In the prophylactic trial, C57BL/6 mice were provided with BC (0, 11, and 22 mg/L in drinking water) from 12 days before challenge through the end of the experiment, whereas BC administration started day 1 post challenge in the therapeutic trial. Both challenge and control groups were infected with 10 CFU/mL of hypervirulent BAA 1803 spores or sterile PBS, and the clinical and diarrheal scores were recorded for 10 days post challenge.

A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive.

Background: In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs.

Results: A total of 3892 samples were genotyped with the Porcine SNP80 BeadChip. After quality control, a total of 57,962 high-quality SNPs from 3520 Duroc pigs were retained.

Bias in heritability estimates from genomic restricted maximum likelihood methods under different genotyping strategies.

We investigated the effects of different strategies for genotyping populations on variance components and heritabilities estimated with an animal model under restricted maximum likelihood (REML), genomic REML (GREML), and single-step GREML (ssGREML). A population with 10 generations was simulated. Animals from the last one, two or three generations were genotyped with 45,116 SNP evenly distributed on 27 chromosomes.

Animal factors associated with core body temperature of nonlactating dairy cows during summer.

The primary objectives of the current study were to investigate animal factors associated with core body temperature (CBT) and to determine the time of the day in which CBT assessment best describes the magnitude of hyperthermia throughout the day of heat-stressed dry cows. The secondary objective was to develop a predictive model for CBT of dry cows. Nonlactating Holstein cows (n = 105) with 250 to 260 d of gestation from 2 commercial dairies were enrolled in the study during summer.

Similar Genetic Architecture with Shared and Unique Quantitative Trait Loci for Bacterial Cold Water Disease Resistance in Two Rainbow Trout Breeding Populations.

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 (). However, the recent availability of a 57 K SNP array and a reference genome assembly have enabled us to conduct genome-wide association studies (GWAS) that overcome several experimental limitations from our previous work.

Incorporation of causative quantitative trait nucleotides in single-step GBLUP.

Background: Much effort is put into identifying causative quantitative trait nucleotides (QTN) in animal breeding, empowered by the availability of dense single nucleotide polymorphism (SNP) information. Genomic selection using traditional SNP information is easily implemented for any number of genotyped individuals using single-step genomic best linear unbiased predictor (ssGBLUP) with the algorithm for proven and young (APY). Our aim was to investigate whether ssGBLUP is useful for genomic prediction when some or all QTN are known.

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.

Background: Previously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative that enables exploitation of within-family genetic variation.

Methods: We compared three GS models [single-step genomic best linear unbiased prediction (ssGBLUP), weighted ssGBLUP (wssGBLUP), and BayesB] to predict genomic-enabled breeding values (GEBV) for BCWD resistance in a commercial rainbow trout population, and compared the accuracy of GEBV to traditional estimates of breeding values (EBV) from a pedigree-based BLUP (P-BLUP) model.

Evaluation of Genome-Enabled Selection for Bacterial Cold Water Disease Resistance Using Progeny Performance Data in Rainbow Trout: Insights on Genotyping Methods and Genomic Prediction Models.

Bacterial cold water disease (BCWD) causes significant economic losses in salmonid aquaculture, and traditional family-based breeding programs aimed at improving BCWD resistance have been limited to exploiting only between-family variation. We used genomic selection (GS) models to predict genomic breeding values (GEBVs) for BCWD resistance in 10 families from the first generation of the NCCCWA BCWD resistance breeding line, compared the predictive ability (PA) of GEBVs to pedigree-based estimated breeding values (EBVs), and compared the impact of two SNP genotyping methods on the accuracy of GEBV predictions. The BCWD phenotypes survival days (DAYS) and survival status (STATUS) had been recorded in training fish (n = 583) subjected to experimental BCWD challenge.

Accuracy of estimated breeding values with genomic information on males, females, or both: an example on broiler chicken.

Background: As more and more genotypes become available, accuracy of genomic evaluations can potentially increase. However, the impact of genotype data on accuracy depends on the structure of the genotyped cohort. For populations such as dairy cattle, the greatest benefit has come from genotyping sires with high accuracy, whereas the benefit due to adding genotypes from cows was smaller.

Changes in variance explained by top SNP windows over generations for three traits in broiler chicken.

The purpose of this study was to determine if the set of genomic regions inferred as accounting for the majority of genetic variation in quantitative traits remain stable over multiple generations of selection. The data set contained phenotypes for five generations of broiler chicken for body weight, breast meat, and leg score. The population consisted of 294,632 animals over five generations and also included genotypes of 41,036 single nucleotide polymorphism (SNP) for 4,866 animals, after quality control.

Assessment of neurotoxicity of monocrotaline, an alkaloid extracted from Crotalaria retusa in astrocyte/neuron co-culture system.

Studies have shown cases of poisoning with plants from the genus Crotalaria (Leguminosae) mainly in animals. They induce damages in the central nervous system (CNS), which has been attributed to toxic effects of the pyrrolizidine alkaloid (PA) monocrotaline (MCT). Previously we demonstrated that both MCT and dehydromonocrotaline (DHMC), its main active metabolite, induce changes in the levels and patterns of expression of the main protein from astrocyte cytoskeleton, glial fibrillary acidic protein (GFAP).