• Journal of Microbiology and Biotechnology
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• v.27 no.10
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• pp.1753-1762
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• 2017

Sea cucumber (Apostichopus japonicus) is a popular seafood source in Asia, including South Korea, and its consumption has recently increased with recognition of its medicinal properties. However, because raw sea cucumber contains various microbes, its ingestion can cause foodborne illness. Therefore, analysis of the microbiota in the whole body of sea cucumber can extend our understanding of foodborne illness caused by microorganisms and help to better manage products. We collected 40 sea cucumbers from four different sites in August and November, which are known as the maximum production areas in Korea. The microbiota was analyzed by an Illumina MiSeq system, and bacterial amounts were quantified by real-time PCR. The diversity and bacterial amounts in sea cucumber were higher in August than in November. Alpha-, Beta-, and Gammaproteobacteria were common dominant classes in all samples. However, the microbiota composition differed according to sampling time and site. Staphylococcus warneri and Propionibacterium acnes were commonly detected potential pathogens in August and November samples, respectively. The effect of experimental Vibrio parahaemolyticus infection on the indigenous microbiota of sea cucumber was analyzed at different temperatures, revealing clear alterations of Psychrobacter and Moraxella; thus, these shifts can be used as indicators for monitoring infection of sea cucumber. Although further studies are needed to clarify and understand the virulence and mechanisms of the identified pathogens of sea cucumber, our study provides a valuable reference for determining the potential of foodborne illness caused by sea cucumber ingestion and to develop monitoring strategies of products using microbiota information.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.8
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• pp.1066-1073
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• 2017

Objective: Growth-related traits are important economic traits in the swine industry. However, the genetic mechanism of growth-related traits is little known. The aim of this study was to screen the candidate genes and molecular markers associated with body dimension and body weight traits in pigs. Methods: A genome-wide association study (GWAS) on body dimension and body weight traits was performed in a White $Duroc{\times}Erhualian$ $F_2$ intercross by the illumina PorcineSNP60K Beadchip. A mixed linear model was used to assess the association between single nucleotide polymorphisms (SNPs) and the phenotypes. Results: In total, 611 and 79 SNPs were identified significantly associated with body dimension traits and body weight respectively. All SNPs but 62 were located into 23 genomic regions (quantitative trait loci, QTLs) on 14 autosomal and X chromosomes in Sus scrofa Build 10.2 assembly. Out of the 23 QTLs with the suggestive significance level ($5{\times}10^{-4}$), three QTLs exceeded the genome-wide significance threshold ($1.15{\times}10^{-6}$). Except the one on Sus scrofa chromosome (SSC) 7 which was reported previously all the QTLs are novel. In addition, we identified 5 promising candidate genes, including cell division cycle 7 for abdominal circumference, pleiomorphic adenoma gene 1 and neuropeptides B/W receptor 1 for both body weight and cannon bone circumference on SSC4, phosphoenolpyruvate carboxykinase 1, and bone morphogenetic protein 7 for hip circumference on SSC17. Conclusion: The results have not only demonstrated a number of potential genes/loci associated with the growth-related traits in pigs, but also laid a foundation for studying the genes' role and further identifying causative variants underlying these loci.

• Genomics & Informatics
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• v.14 no.4
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• pp.230-233
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• 2016

Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ~29,000 single nucleotide polymorphisms (SNPs) for which $r^2$ value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average $r^2$ between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on $r^2$ varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.12
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• pp.1674-1680
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• 2012

The purpose of this study was to detect significant SNPs for blood components that were related to immunity using high single nucleotide polymorphism (SNP) density panels in a Korean native pig (KNP)${\times}$Yorkshire (YK) cross population. A reciprocal design of KNP${\times}$YK produced 249 $F_2$ individuals that were genotyped for a total of 46,865 available SNPs in the Illumina porcine 60K beadchip. To perform whole genome association analysis (WGA), phenotypes were regressed on each SNP under a simple linear regression model after adjustment for sex and slaughter age. To set up a significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were determined using a stepwise regression procedure with the rates of inclusion and exclusion of each SNP out of the model at 0.001 level. A total of 54 SNPs were detected; 10, 6, 4, 4, 5, 4, 5, 10, and 6 SNPs for neutrophil, lymphocyte, monocyte, eosinophil, basophil, atypical lymph, immuno-globulin, insulin, and insulin-like growth factor-I, respectively. Each set of significant SNPs per trait explained 24 to 42% of phenotypic variance. Several pleiotropic SNPs were detected on SSCs 4, 13, 14 and 15.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.5
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• pp.696-703
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• 2020

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 nonprotein coding transcripts. lncRNA is known to function in regulating gene expression and is currently being studied in a variety of livestock including cattle. The purpose of this study is to analyze the characteristics of lncRNA according to sex in Hanwoo cattle. Methods: This study was conducted using the skeletal muscles of 9 Hanwoo cattle include bulls, steers and cows. RNA was extracted from skeletal muscle of Hanwoo. Sequencing was conducted using Illumina HiSeq2000 and mapped to the Bovine Taurus genome. The expression levels of lncRNAs were measured by DEGseq and quantitative trait loci (QTL) data base was used to identify QTLs associated with lncRNA. The python script was used to match the nearby genes Results: In this study, the expression patterns of transcripts of bulls, steers and cows were identified. And we identified significantly differentially expressed lncRNAs in bulls, steers and cows. In addition, characteristics of lncRNA which express differentially in muscles according to the sex of Hanwoo were identified. As a result, we found differentially expressed lncRNAs according to sex were related to shear force and body weight. Conclusion: This study was classified and characterized lncRNA which differentially expressed by sex in Hanwoo cattle. We believe that the characterization of lncRNA by sex of Hanwoo will be helpful for future studies of the physiological mechanisms of Hanwoo cattle.

• Food Science of Animal Resources
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• v.38 no.5
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• pp.936-949
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• 2018

Changes in microbial community and physicochemical traits of chicken summer sausage made from spent layer thigh added with different level (0%, 0.1%, 0.3%, and 0.5% w/w) of ground chopi (Zanthoxylum piperitum) during manufacture were analyzed. The microbial community was profiled and analyzed by sequencing 16S rRNA gene using Illumina MiSeq. Samples were taken from raw sausage batter, after 15 h of fermentation, 8 h of cooking including cooling down, and 7 d of drying. The final pH of the sausage was reduced by the addition of ground chopi. However, no clear effect on water activity was observed. Ground chopi inhibited the development of red curing color after fermentation as it exhibited antimicrobial effect. However, the effect on species richness and microbial composition after cooking was unclear. Ground chopi delayed lipid oxidation during manufacture and the effect was dependent on the addition level. Fermentation reduced the species richness with a dominancy of lactic acid bacteria. The profile of microbiota in the raw batter was different from other stages, while the closest relationship was observed after cooking and drying. Proteobacteria was predominant, followed by Firmicutes and Bacteroidetes in raw samples. Firmicutes became dominating after fermentation and so forth, whereas other predominant phylum decreased. At genus level, unclassified Lactobacillales was the most abundant group found after fermentation and so forth. Therefore, the overall microbial composition aspects were mainly controlled during fermentation by the abundance of lactic acid bacteria, while bacterial counts and lipid oxidation were controlled by cooking and the addition of ground chopi.

• Journal of Plant Biotechnology
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• v.39 no.1
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• pp.49-61
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• 2012

This review summarises the biology, discovery and applications of single nucleotide polymorphisms in complex polyploid crop genomes, with a focus on the important oilseed crop $Brassica$ $napus$. $Brassica$ $napus$ is an allotetraploid species, and along with soybean and oil palm is one of the top three most important oilseed crops globally. Current efforts are well underway to $de$ $novo$ assemble the $B.$ $napus$ genome, following the release of the related $B.$ $rapa$ 'A' genome last year. The next generation of genome sequencing, SNP discovery and analysis pipelines, and the associated challenges for this work in $B.$ $napus$, will be addressed. The biological applications of SNP technology for both evolutionary and molecular geneticists as well as plant breeders and industry are far-reaching, and will be invaluable to our understanding and advancement of the $Brassica$ crop species.

• Journal of Microbiology and Biotechnology
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• v.26 no.10
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• pp.1736-1745
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• 2016

The interactions of microbiota in the gut play an important role in promoting or maintaining the health of hosts. In this study, in order to investigate and compare the effects of dietary supplementation with Lactobacillus pentosus HC-2 (HC-2), Enterococcus faecium NRW-2, or the bacteria-free supernatant of a HC-2 culture on the bacterial composition of Litopenaeus vannamei, Illumina sequencing of the V1-V2 region of the 16S rRNA gene was used. The results showed that unique species exclusively existed in specific dietary groups, and the abundance of Actinobacteria was significantly increased in the intestinal bacterial community of shrimp fed with the bacteria-free supernatant of an HC-2 culture compared with the control. In addition, the histology of intestines of the shrimp from the four dietary groups was also described, but no obvious improvements in the intestinal histology were observed. The findings in this work will help to promote the understanding of the roles of intestinal bacteria in shrimps when fed with probiotics or probiotic supernatant.

• Journal of Applied Biological Chemistry
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• v.58 no.4
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• pp.369-375
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• 2015

Meat from black pigs (BP) is in high demand compared with that from modern white pig (WP) breeds such as Landrace pigs owing to its high quality. However, the growth rate of black pigs is slower than that of white pig breeds. We investigated differences in the fecal microbial composition between white and black pigs to explore whether these breeds differed in the composition of their gut microbial communities. The swine gut microbiota was investigated using Illumina's MiSeq-based sequencing technology by targeting the V4 region of the 16S rRNA gene. Our results showed that the composition of the gut microbiota was significantly different between the two pig breeds. While the composition of the WP microbiota shifted according to the growth stage, fewer shifts in composition were observed for the BP gut microbiota. In addition, the WP gut microbiota showed a higher Firmicutes/Bacteroidetes ratio compared with that of BP. A high ratio between these phyla was previously reported as an obesity-linked microbiota composition. Moreover, the WP microbiota contained a significantly higher abundance of cellulolytic bacteria, suggesting a possibility of higher fiber digestion efficiency in WP compared to BP. These findings may be important factors affecting growth performance and energy-harvesting capacities in pigs. Our findings of differences in the gut microbiota composition between the two breeds may provide new leads to understand growth rate variation across pig breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.7
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• pp.936-942
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• 2015

The purpose of this study was to characterize genetic architecture of behavior patterns in Sapsaree dogs. The breed population (n=8,256) has been constructed since 1990 over 12 generations and managed at the Sapsaree Breeding Research Institute, Gyeongsan, Korea. Seven behavioral traits were investigated for 882 individuals. The traits were classified as a quantitative or a categorical group, and heritabilities ($h^2$) and variance components were estimated under the Animal model using ASREML 2.0 software program. In general, the $h^2$ estimates of the traits ranged between 0.00 and 0.16. Strong genetic ($r_G$) and phenotypic ($r_P$) correlations were observed between nerve stability, affability and adaptability, i.e. 0.9 to 0.94 and 0.46 to 0.68, respectively. To detect significant single nucleotide polymorphism (SNP) for the behavioral traits, a total of 134 and 60 samples were genotyped using the Illumina 22K CanineSNP20 and 170K CanineHD bead chips, respectively. Two datasets comprising 60 (Sap60) and 183 (Sap183) samples were analyzed, respectively, of which the latter was based on the SNPs that were embedded on both the 22K and 170K chips. To perform genome-wide association analysis, each SNP was considered with the residuals of each phenotype that were adjusted for sex and year of birth as fixed effects. A least squares based single marker regression analysis was followed by a stepwise regression procedure for the significant SNPs (p<0.01), to determine a best set of SNPs for each trait. A total of 41 SNPs were detected with the Sap183 samples for the behavior traits. The significant SNPs need to be verified using other samples, so as to be utilized to improve behavior traits via marker-assisted selection in the Sapsaree population.