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.

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.

Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea.

Objective: The Jeju native pig (JNP) found on the Jeju Island of Korea is a unique black pig known for high-quality meat. To investigate the genetic uniqueness of JNP, we analyzed the selection signature of the JNP in comparison to commercial pigs such as Berkshire and Yorkshire pigs.

Methods: We surveyed the genetic diversity to identify the genetic stability of the JNP, using the linkage disequilibrium method.

Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs.

The importance of probiotics in swine production is widely acknowledged as crucial. However, gaps still remain in the exact roles played by probiotics in modulation of gut microbiota and immune response. This study determined the roles of probiotic Lactobacillus plantarum strain JDFM LP11in gut microbiota modulation and immune response in weaned piglets.

Extent of linkage disequilibrium and effective population size of Korean Yorkshire swine.

Objective: We aimed to characterize linkage disequilibrium (LD) and effective population size (Ne) in a Korean Yorkshire population using genomic data from thousands of individuals.

Methods: We genotyped 2,470 Yorkshire individuals from four major Grand-Grand-Parent farms in Korea using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 single nucleotide polymorphisms (SNPs) located across all chromosomes and mitochondria. We estimated the expected LD and inferred current Ne as well as ancestral Ne.

Genome analysis of Yucatan miniature pigs to assess their potential as biomedical model animals.

Objective: Pigs share many physiological, anatomical and genomic similarities with humans, which make them suitable models for biomedical researches. Understanding the genetic status of Yucatan miniature pigs (YMPs) and their association with human diseases will help to assess their potential as biomedical model animals. This study was performed to identify non-synonymous single nucleotide polymorphisms (nsSNPs) in selective sweep regions of the genome of YMPs and present the genetic nsSNP distributions that are potentially associated with disease occurrence in humans.

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.

Identification of Gene Expression Signatures in the Chicken Intestinal Intraepithelial Lymphocytes in Response to Herb Additive Supplementations.

Anethole and garlic have an immune modulatory effects on avian coccidiosis, and these effects are correlated with gene expression changes in intestinal epithelial lymphocytes (IELs). In this study, we integrated gene expression datasets from two independent experiments and investigated gene expression profile changes by anethole and garlic respectively, and identified gene expression signatures, which are common targets of these herbs as they might be used for the evaluation of the effect of plant herbs on immunity toward avian coccidiosis. We identified 4,382 and 371 genes, which were differentially expressed in IELs of chickens supplemented with garlic and anethole respectively.