A genomic estimated breeding value-assisted reduction method of single nucleotide polymorphism sets: a novel approach for determining the cutoff thresholds in genome-wide association studies and best linear unbiased prediction.

Traditionally, the -value is the criterion for the cutoff threshold to determine significant markers in genome-wide association studies (GWASs). Choosing the best subset of markers for the best linear unbiased prediction (BLUP) for improved prediction ability (PA) has become an interesting issue. However, when dealing with many traits having the same marker information, the -values' themselves cannot be used as an obvious solution for having a confidence in GWAS and BLUP.

Antitumorigenic effect of insect-derived peptide poecilocorisin-1 in human skin cancer cells through regulation of Sp1 transcription factor.

Malignant melanoma is highly resistant to conventional treatments and is one of the most aggressive types of skin cancers. Conventional cancer treatments are limited due to drug resistance, tumor selectivity, and solubility. Therefore, new treatments with fewer side effects and excellent effects should be developed.

Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle.

Whole-genome sequence (WGS) data are increasingly being applied into genomic predictions, offering a higher predictive ability by including causal mutations or single-nucleotide polymorphisms (SNPs) putatively in strong linkage disequilibrium with causal mutations affecting the trait. This study aimed to improve the predictive performance of the customized Hanwoo 50 k SNP panel for four carcass traits in commercial Hanwoo population by adding highly predictive variants from sequence data. A total of 16,892 Hanwoo cattle with phenotypes (i.

Risk prediction and marker selection in nonsynonymous single nucleotide polymorphisms using whole genome sequencing data.

Despite the various existing studies about nonsynonymous single nucleotide polymorphisms (nsSNPs), genome-wide studies based on nsSNPs are rare. NsSNPs alter amino acid sequences, affect protein structure and function, and have deleterious effects. By predicting the deleterious effect of nsSNPs, we determined the total risk score per individual.

Molecular modeling and dynamic simulation of chicken Mx protein with the S631N polymorphism.

Myxovirus resistance (Mx) proteins are antiviral GTPases induced by type I interferons (IFNs). In chickens, a single Mx protein variant, S631N, has been suggested to possess antiviral activity. However, the impact of this variant on chicken Mx (chMx) protein structure and conformation has not been investigated.

Correction: Weighted Genomic Best Linear Unbiased Prediction for Carcass Traits in Hanwoo Cattle. 2019, , 1019.

The authors wish to make the following corrections to this paper [...

Comparative genomics of canine Lactobacillus reuteri reveals adaptation to a shared environment with humans.

Background: Lactobacillus reuteri is a gram-positive, non-motile bacterial species that has been used as a representative microorganism model to describe the ecology and evolution of vertebrate gut symbionts.

Objective: Because the genetic features and evolutionary strategies of L. reuteri from the gastrointestinal tract of canines remain unknown, we tried to construct draft genome canine L.

Conformational Changes Induced by S34Y and R98C Variants in the Death Domain of Myd88.

Myeloid differentiating factor 88 (Myd88) is a universal adaptor protein that plays a critical role in innate immunity by mediating TLR downstream signaling. Myd88 death domain (DD) forms an oligomeric complex by association with other DD-containing proteins such as IRAK4. Despite its universal role, polymorphisms in Myd88 can result in several diseases.

Comparison of characteristics of long noncoding RNA in Hanwoo according to sex.

Objective: Cattle were some of the first animals domesticated by humans for the production of milk, meat, etc. Long noncoding RNA (lncRNA) is defined as longer than 200 bp in non-protein coding transcripts. lncRNA is known to function in regulating gene expression and is currently being studied in a variety of livestock including cattle.

Weighted Genomic Best Linear Unbiased Prediction for Carcass Traits in Hanwoo Cattle.

The genomic best linear unbiased prediction (GBLUP) method has been widely used in routine genomic evaluation as it assumes a common variance for all single nucleotide polymorphism (SNP). However, this is unlikely in the case of traits influenced by major SNP. Hence, the present study aimed to improve the accuracy of GBLUP by using the weighted GBLUP (WGBLUP), which gives more weight to important markers for various carcass traits of Hanwoo cattle, such as backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS).

In silico approach to calculate the transcript capacity.

We sought the novel concept, transcript capacity (TC) and analyzed TC. Our approach to estimate TC was through an in silico method. TC refers to the capacity that a transcript exerts in a cell as enzyme or protein function after translation.

Comparison of long noncoding RNA between muscles and adipose tissues in beef cattle.

Long noncoding RNAs (lncRNAs) regulate the expression of mRNA and can affect various biological processes and phenotypes. Currently, studies of lncRNAs in cattle are under way, but their exact function for several tissues has not yet been established. cattle () have inhabited the Korean peninsula for about 6000 years and are one of the representative domesticated animals in Korea.

Analysis of genetic characteristics of pig breeds using information on single nucleotide polymorphisms.

Objective: This study was undertaken to investigate the genetic characteristics of Berkshire (BS), Landrace (LR), and Yorkshire (YS) pig breeds raised in the Great Grandparents pig farms using the single nucleotide polymorphisms (SNP) information.

Methods: A total of 25,921 common SNP genotype markers in three pig breeds were used to estimate the expected heterozygosity (HE), polymorphism information content, F-statistics (FST), linkage disequilibrium (LD) and effective population size (Ne).

Results: The chromosome-wise distribution of FST in BS, LR, and YS populations were within the range of 0-0.

In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome.

Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs.

Methods: nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs.

Characterization of gene expression and genetic variation of horse ERBB receptor feedback inhibitor 1 in Thoroughbreds.

Objective: This study aimed to test the expression patterns of ERBB receptor feedback inhibitor 1 () before and after exercise and the association of non-synonymous single-nucleotide polymorphisms (nsSNPs) of horse with racing traits in Thoroughbreds.

Methods: We performed bioinformatics and gene expression analyses for horse . Transcription factor (TF) binding sites in the 5'-regulatory region of this gene were identified through a tool for prediction of TF-binding site (PROMO).

Validation of selection accuracy for the total number of piglets born in Landrace pigs using genomic selection.

Objective: This study was to determine the relationship between estimated breeding value and phenotype information after farrowing when juvenile selection was made in candidate pigs without phenotype information.

Methods: After collecting phenotypic and genomic information for the total number of piglets born by Landrace pigs, selection accuracy between genomic breeding value estimates using genomic information and breeding value estimates of best linear unbiased prediction (BLUP) using conventional pedigree information were compared.

Results: Genetic standard deviation ( ) for the total number of piglets born was 0.

Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (Coturnix coturnix japonica).

Japanese quail (Coturnix coturnix japonica) reach sexual maturity earlier, breed rapidly and successfully, and cost less and require less space than other birds raised commercially. Given the value of this species for food production and experimental use, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeding lines of Japanese quail (random bred control, heavy weight, low weight).

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing.

Background: Natural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand.

Exploring the genetic signature of body size in Yucatan miniature pig.

Since being domesticated about 10,000-12,000 years ago, domestic pigs (Sus scrofa domesticus) have been selected for traits of economic importance, in particular large body size. However, Yucatan miniature pigs have been selected for small body size to withstand high temperature environment and for laboratory use. This renders the Yucatan miniature pig a valuable model for understanding the evolution of body size.

Genome Wide Association Studies Using Multiple-lactation Breeding Value in Holsteins.

A genome wide association study was conducted using estimated breeding value (EBV) for milk production traits from 1st to 4th lactation. Significant single nucleotide polymorphism (SNP) markers were selected for each trait and the differences were compared by lactation. DNA samples were taken from 456 animals with EBV which are Holstein proven bulls whose semen is being sold or the daughters of old proven bulls whose semen is no longer being sold in Korea.

Uncovering genomic features and maternal origin of korean native chicken by whole genome sequencing.

The Korean Native Chicken (KNC) is an important endemic biological resource in Korea. While numerous studies have been conducted exploring this breed, none have used next-generation sequencing to identify its specific genomic features. We sequenced five strains of KNC and identified 10.

Single nucleotide polymorphism analysis of Korean native chickens using next generation sequencing data.

There are five native chicken lines in Korea, which are mainly classified by plumage colors (black, white, red, yellow, gray). These five lines are very important genetic resources in the Korean poultry industry. Based on a next generation sequencing technology, whole genome sequence and reference assemblies were performed using Gallus_gallus_4.