Inactivation of mammalian spermatozoa on the exposure of TiO2 nanorods deposited with noble metals.

Titanium dioxide (TiO2) nanorods (NRs) are well-known semiconducting and catalytic material that has been widely applied, but their toxicities have also attracted recent interest. In this study, we investigated and compared the toxic effects of TiO2 NRs and TiO2 NRs loaded with Ag or Au NPs on boar spermatozoa. As a result, sperm incubated with Ag-TiO2 NRs showed lower motility than sperm incubated with controls (with or without TiO2 NRs) or Au-TiO2 NRs. In addition, sperm viability and acrosomal integrity were defective in the presence of Ag-TiO2 NRs, and the generation of intracellular reactive oxygen species (ROS) increased significantly when spermatozoa were incubated with 20 µg/ml Ag-TiO2 NRs. We discussed in depth the charge transfer mechanism between enzymatic NADPH and Ag-TiO2 NRs in the context of ROS generation in spermatozoa. The effects we observed reflected the fertilization competence of sperm incubated with Ag-TiO2 NRs; specifically sperm penetration and embryonic development rates by in vitro fertilization were reduced by Ag-TiO2 NRs. To summarize, our findings indicate that exposure to Ag-TiO2 NRs could affect male fertilization fecundity and caution that care be exercised when using these NRs.

MSENet: Marbling score estimation network for automated assessment of Korean beef.

A novel beef marbling score estimation algorithm is proposed in this work. We develop a marbling score estimation network (MSENet), which simultaneously performs marbling score estimation and eye muscle area segmentation. The proposed MSENet includes a segmentation module, a bridge block, and a marbling scoring module. The segmentation module segments out eye muscle area from input images and the scoring module estimates marbling scores of input beef images. The proposed bridge block conveys the segmentation information for eye muscle area from the segmentation module to the scoring module. MSENet is trained on a new large-scale beef image dataset (more than 10,000), called the Hanwoo dataset. Experimental results demonstrate that the proposed MSENet achieves the reliable score estimation performance on the Hanwoo Dataset and the proposed bridge block effectively improves the estimation accuracy (Pearson's correlation coefficient: 0.952, Mean absolute error: 0.543).

Serial Improvement of Medial Meniscus Extrusion Following Medial Open-Wedge High Tibial Osteotomy Does Not Correlate With Clinical Outcomes and Arthroscopic Articular Cartilage Improvement.

PURPOSE: To assess serial change up to 2 years in medial meniscus extrusion (MME) following medial open-wedge high tibial osteotomy (MOWHTO) and to determine whether postoperative changes in MME correlated with clinical outcomes and arthroscopic articular cartilage status. METHODS: This study included 26 patients from December 2016 to March 2018 who underwent MOWHTO for primary medial osteoarthritis with varus malalignment. Second-look arthroscopy with plate removal was performed at postoperative 2 years. MME was consecutively measured using coronal magnetic resonance imaging at preoperative and postoperative 3 months, 6 months, 1.5 years, and 2 years. We also assessed which preoperative parameters could reflect the postoperative changes in MME and evaluated whether postoperative clinical outcomes and arthroscopic articular cartilage improvement would be influenced by the MME changes. RESULTS: Regarding the postoperative serial changes in MME values, significant improvement in MME was noted from postoperative 6 months (P = .003), and thereafter, mean MME was further improved with time until postoperative 2 years (P < .001). Regarding the correlation between preoperative parameters and MME changes, preoperative medial proximal tibial angle (MPTA) showed significant correlations in univariate and multivariate analysis (P = .004 and P = .004, respectively). Meanwhile, changes in MME were not correlated with postoperative clinical outcomes or arthroscopic articular cartilage improvement. CONCLUSION: After MOWHTO, MME improved with time and was significantly correlated with preoperative MPTA. However, the changes in MME after MOWHTO did not reflect postoperative clinical and arthroscopic articular cartilage improvement. LEVEL OF EVIDENCE: IV, case series.

Genome-wide identification of major genes and genomic prediction using high-density and text-mined gene-based SNP panels in Hanwoo (Korean cattle).

It was hypothesized that single-nucleotide polymorphisms (SNPs) extracted from text-mined genes could be more tightly related to causal variant for each trait and that differentially weighting of this SNP panel in the GBLUP model could improve the performance of genomic prediction in cattle. Fitting two GRMs constructed by text-mined SNPs and SNPs except text-mined SNPs from 777k SNPs set (exp_777K) as different random effects showed better accuracy than fitting one GRM (Im_777K) for six traits (e.g. backfat thickness: + 0.002, eye muscle area: + 0.014, Warner-Bratzler Shear Force of semimembranosus and longissimus dorsi: + 0.024 and + 0.068, intramuscular fat content of semimembranosus and longissimus dorsi: + 0.008 and + 0.018). These results can suggest that attempts to incorporate text mining into genomic predictions seem valuable, and further study using text mining can be expected to present the significant results.

Analysis of Risk Factors for Ramp Lesions Associated With Anterior Cruciate Ligament Injury.

BACKGROUND: The incidence of meniscocapsular junction tears of the medial meniscus posterior horn, known as ramp lesions, is reported to be 9.3% to 23.9%. However, these lesions are not consistently diagnosed with routine arthroscopic exploration and magnetic resonance imaging (MRI). PURPOSE: To determine risk factors associated with ramp lesions in anterior cruciate ligament-injured knees. STUDY DESIGN: Cross-sectional study; Level of evidence, 3. METHODS: A total of 275 patients undergoing anterior cruciate ligament reconstruction between June 2011 and March 2019 were included in this study. Exclusion criteria were revisions, fracture histories, and multiple-ligament injuries other than medial collateral ligament injury. Patients were divided into 2 groups, those with and without ramp lesions according to arthroscopic diagnosis. Binary logistic regression was used to analyze risk factors: age, sex, body mass index, time from injury to surgery (<3 or ≥3 months), mechanism of injury (contact/noncontact), Segond fracture, side-to-side laxity, location of bone contusion, medial and lateral tibial/meniscal slope, and mechanical axis angle. Receiver operating characteristic curves and area under the curve were evaluated. A prediction model was developed by multivariable regression with generalized estimating equations. RESULTS: Overall, 95 patients (34.5%) were confirmed as having a ramp lesion. The sensitivity of MRI for ramp lesions was 85.3%, and specificity was 78.3%. Significant risk factors for ramp lesion were as follows: posterior medial tibial plateau bone contusion on MRI (odds ratio [OR], 4.201; 95% CI, 2.081-8.482; P < .001), ≥3 months from injury (OR, 4.818; 95% CI, 2.158-10.757; P < .001), varus knee >3° (OR, 2.339; 95% CI, 1.048-5.217; P = .038), steeper medial tibial slope (OR, 1.289; 95% CI, 1.002-1.66; P = .049) and meniscal slope (OR, 1.464; 95% CI, 1.137-1.884; P = .003), and gradual lateral tibial slope (OR, 0.775; 95% CI, 0.657-0.914; P = .002). The area under the curve for the prediction model developed by logistic regression was 0.779 (sensitivity, 75.8%; specificity, 71.7%; P < .001) for ramp lesions. CONCLUSION: Care should be taken with patients who have significant risk factors for ramp lesions, including bone contusion at the posterior medial tibial plateau, chronic injury, steeper medial tibial and meniscal slope, gradual lateral tibial slope, and varus knee >3°.

Genetic Diversity and Ancestral Study for Korean Native Pigs Using 60K SNP Chip.

The Korean native pig (KNP; Sus scrofa coreanus) is an indigenous porcine breed in South Korea considered as a valuable but dwindling genetic resource. Studies using diverse methodologies and genetic markers suggest that this population originated from the Manchu province of Northeastern China and migrated approximately 3000 years ago into the Korean peninsula. This study aimed to verify those findings by performing diversity and ancestral analyses using the 60K single-nucleotide polymorphism (SNP) BeadChip on 891 pigs of 47 breeds worldwide. We also performed principal component analysis (PCA), ancestry analyses, phylogenetic tree analysis using SNPhylo, and linkage disequilibrium analysis. Furthermore, we generated heatmap, obtained Nei's genetic distance and FST values, and explored the heterozygosity of commercial and native Korean pigs. The results demonstrated that KNP pigs are more closely related to European breeds than to Chinese breeds. In addition, as previous studies have suggested, our admixture analyses indicated that KNP pigs showed distinguishable genetic structure.

Association of the thyroid hormone responsive spot 14 alpha gene with growth-related traits in Korean native chicken.

OBJECTIVE: Thyroid hormone responsive spot 14 alpha (THRSP) has been used to investigate the regulation of de novo lipogenesis because the variation of THRSP mRNA content in the tissue affects directly the ability of that tissue to synthetize lipids. Also, this gene responds to thyroid hormone stimulation and high level of carbohydrate feeding or insulin-injection. This study was carried out to investigate variations within THRSP and their effects on body and carcass weights in Korean native chicken (KNC). METHODS: A total of 585 chickens which represent the five lines of KNC (Black, Gray-Brown, Red-Brown, White, and Yellow-Brown) were reared and body weight data were recorded every two weeks from hatch until 20 weeks of age. Polymerase chain reaction- restriction fragment length polymorphism, DNA chips for Agilent 2100 Bioanalyzer, and Fluidigm Genotyping Technology, were applied to genotype selected markers. A linear mixed-effect model was used to access association between these single nucleotide polymorphism (SNP) markers and growth-related traits. RESULTS: A total of 30 polymorphisms were investigated in THRSP. Of these, nine SNPs for loci were selected to perform association analyses. Significant associations were detected between g.-49G>T SNP with body weight at 20 weeks of age (BW20), g.451T>C SNP with growth at 10 to 12 weeks of age (GR10-12), and g.1432A>C SNP with growth at 14 to 16 weeks trait (GR14-16) and body weight at 18 weeks of age (BW18). Moreover, diplotype of the THRSP gene significantly affected body weight at 12 weeks of age (BW12) and GR10-12 traits. Diplotype of ht1/ht2 was favorable for BW12 and GR10-12 traits. CONCLUSION: These results suggest that THRSP can be regarded as a candidate gene for growth traits in KNC.

Suspension culture of Vero cells for the production of adenovirus type 5.

PURPOSE: Most cell culture processes for viral vaccine production are mainly based on adherent cell culture systems using serum, which are associated with expensive and labor-intensive processes to produce large amounts of viral vaccine strains. In this study, we investigated whether Vero cells could be grown in serum-free and shaking suspension conditions. Furthermore, we assessed the ability of the Vero cell suspension culture system to produce adenovirus type 5 (Ad5), compared to that of the adhesive Vero cell culture system. MATERIALS AND METHODS: We tested the feasibility of commercial serum-free media for Vero cell culture. For the adaptation of Vero cells in suspension culture, adhesive Vero cells were added in the early phase of shaking suspension culture, and 50 days after shaking suspension culture, suspension-adapted Vero cells were subcultured continuously. To assess the virus production ability of Vero cells in suspension, the cells were infected with Ad5-green fluorescent protein and evaluated based on their fluorescence intensity. RESULTS: The Vero cells grown in OptiPRO serum-free medium showed no changes in morphology and growth rate, but MRC-5 and FRhk-4 cells showed morphological changes and decreased growth rate, respectively. The Vero cells were well adapted to the suspension culture system. The Vero cells in suspension showed a better Ad5 production ability than the adherent Vero cells. CONCLUSION: Vero cells can be grown in OptiPRO serum-free medium. Further, our suspension culture-adapted Vero cells may be suitable to produce viral vaccine strains due to their high ability to produce viruses such as Ad5.

Heterologous prime-boost vaccination with adenoviral vector and protein nanoparticles induces both Th1 and Th2 responses against Middle East respiratory syndrome coronavirus.

The Middle East respiratory syndrome coronavirus (MERS-CoV) is a highly pathogenic and zoonotic virus with a fatality rate in humans of over 35%. Although several vaccine candidates have been developed, there is still no clinically available vaccine for MERS-CoV. In this study, we developed two types of MERS-CoV vaccines: a recombinant adenovirus serotype 5 encoding the MERS-CoV spike gene (Ad5/MERS) and spike protein nanoparticles formulated with aluminum (alum) adjuvant. Next, we tested a heterologous prime-boost vaccine strategy, which compared priming with Ad5/MERS and boosting with spike protein nanoparticles and vice versa, with homologous prime-boost vaccination comprising priming and boosting with either spike protein nanoparticles or Ad5/MERS. Although both types of vaccine could induce specific immunoglobulin G against MERS-CoV, neutralizing antibodies against MERS-CoV were induced only by heterologous prime-boost immunization and homologous immunization with spike protein nanoparticles. Interestingly, Th1 cell activation was induced by immunization schedules including Ad5/MERS, but not by those including only spike protein nanoparticles. Heterologous prime-boost vaccination regimens including Ad5/MERS elicited simultaneous Th1 and Th2 responses, but homologous prime-boost regimens did not. Thus, heterologous prime-boost may induce longer-lasting immune responses against MERS-CoV because of an appropriate balance of Th1/Th2 responses. However, both heterologous prime-boost and homologous spike protein nanoparticles vaccinations could provide protection from MERS-CoV challenge in mice. Our results demonstrate that heterologous immunization by priming with Ad5/MERS and boosting with spike protein nanoparticles could be an efficient prophylactic strategy against MERS-CoV infection.

A hot-water extract of Sanguisorba officinalis ameliorates endotoxin-induced septic shock by inhibiting inflammasome activation.

The inflammasome is a multiprotein signaling complex that mediates inflammatory innate immune responses through caspase 1 activation and subsequent IL-1ß secretion. However, because its aberrant activation often leads to inflammatory diseases, targeting the inflammasome holds promise for the treatment of inflammation-related diseases. In this study, it was found that a hot-water extract of Sanguisorba officinalis (HSO) suppresses inflammasome activation triggered by adenosine 5'-triphosphate, nigericin, microbial pathogens, and double stranded DNA in bone marrow-derived macrophages. HSO was found to significantly suppress IL-1ß production in a dose-dependent manner; this effect correlated well with small amounts of caspase 1 and little ASC pyroptosome formation in HSO-treated cells. The anti-inflammatory activity of HSO was further confirmed in a mouse model of endotoxin-induced septic shock. Oral administration of HSO reduced IL-1ß titers in the serum and peritoneal cavity, increasing the survival rate. Taken together, our results suggest that HSO is an inhibits inflammasome activation through nucleotide-binding domain and leucine-rich repeat pyrin domain 3, nucleotide-binding domain and leucine-rich repeat caspase recruitment domain 4 and absent in melanoma 2 pathways, and may be useful for treatment of inflammasome-mediated diseases.

Identification of MC1R SNPs and their Association with Plumage Colors in Asian Duck.

The melanocortin 1 receptor (MC1R) gene is a candidate functional gene that controls the pigment production in melanocytes. The aim of this study was to identify polymorphisms and investigate the effect of the MC1R gene on plumage coloration in duck breeds, including Korean native ducks. Initially, 34 individuals from seven duck breeds were sequenced, obtaining 12 polymorphisms. Five single nucleotide polymorphisms (SNPs) in the coding region were non-synonymous, with mutations corresponding to amino acid changes. Among these, four SNPs were genotyped using polymerase chain reaction-restriction fragment length polymorphism method in 264 individuals from same seven duck breeds. Fisher's exact test was conducted to identify possible relationships between the MC1R gene polymorphisms and plumage color variations. Four non-synonymous SNPs, c.52A>G (p.Lys18Glu), and c.376 A>G (p.Ile126Val), c.409G>A (p.Ala137Thr) and c.649C>T (p.Arg217Cys), were associated with the two deduced genotypes (i.e., E/E and e+ /e+) based on plumage color phenotypes. In addition, we reconstructed MC1R gene haplotypes, where the haplotype AAGC showed its highest frequency in Nageswari duck breed, which presents an extended black phenotype. Our results indicate that the identified polymorphisms by this study can be used to explore associations with plumage color variations in Asian duck breeds.

Genome scan linkage analysis identifies quantitative trait loci affecting serum clinical-chemical traits in Korean native chicken.

Alterations in robustness- and health-related traits lead to physiological changes, such as changes in the serum clinical chemical parameters in individuals. Therefore, clinical-chemical traits can be used as biomarkers to examine the health status of chickens. The aim of the present study was to detect the quantitative trait loci (QTLs) influencing eight clinical-chemical traits (glucose, total protein, creatinine, high-density lipoprotein cholesterol, total cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and α-amylase) in an F1 nuclear families comprising 83 F0 founders and 585 F1 progeny of Korean native chickens. Genotypic data on 135 DNA markers representing 26 autosomes have been generated for this resource pedigree. The total length of the map was 2729.4 cM. We used a multipoint variance component linkage approach to identify QTLs for the traits. A significant QTL affecting serum α-amylase levels was identified on chicken chromosome (GGA) 7 [logarithm of odds (LOD) = 3.02, P value = 1.92 × 10(-4)]. Additionally, we detected several suggestive linkage signals for the levels of total cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and creatinine on GGA 4, 12, 13, and 15. In this study, serum α-amylase levels related significant QTL was mapped on GGA7 and cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and creatinine traits related suggestive QTLs were detected on GGA4, 12, 13 and 15, respectively. Further verification and fine mapping of these identified QTLs can provide valuable information for understanding the variations of clinical chemical trait in chickens.

A hot water extract of Aralia cordata activates bone marrow-derived macrophages via a myeloid differentiation protein 88-dependent pathway and protects mice from bacterial infection.

In traditional Asian medicine, Aralia cordata (AC) is a known as a pain reliever and anti-inflammatory drug. Although several of its biological activities have been reported, the immunomodulatory effects of a hot water extract of AC (HAC) have not yet been described. The aim of this study was to investigate whether HAC modulates the activation of macrophages, which play important roles in innate immune responses against microbial pathogens, and if so, to determine the molecular mechanisms by which HAC mediates this process. It was found that HAC activates bone marrow-derived macrophages (BMDM) and increases amounts of nitric oxide and proinflammatory cytokines in a dose-dependent manner. In addition, HAC was found to induce phosphorylation of NF-κB and mitogen-activated protein kinases (MAPKs), including c-Jun N-terminal kinases, extracellular signal-regulated kinases and p38. Interestingly, these effects were absent in BMDM prepared from myeloid differentiation protein 88-knockout mice. Polysaccharides from HAC exerted stronger immunostimulatory effects than HAC itself. Furthermore, orally administered HAC clearly enhanced clearance of the intracellular pathogen Listeria monocytogenes by boosting innate immune responses. These results demonstrate that HAC exerts immunostimulatory effects through the TLR/MyD88 and NF-κB/MAPK signal transduction pathways.

Analysis of Swine Leukocyte Antigen Haplotypes in Yucatan Miniature Pigs Used as Biomedical Model Animal.

The porcine major histocompatibility complex (MHC) is called swine leukocyte antigen (SLA), which controls immune responses and transplantation reactions. The SLA is mapped on pig chromosome 7 (SSC7) near the centromere. In this study, 3 class I (SLA-1, SLA-3, and SLA-2) and 3 class II (DRB1, DQB1, and DQA) genes were used for investigation of SLA haplotypes in Yucatan miniature pigs in Korea. This pig breed is a well-known model organism for biomedical research worldwide. The current study indicated that Korean Yucatan pig population had 3 Class I haplotypes (Lr-4.0, Lr-6.0, and Lr-25.0) and 3 class II haplotypes (Lr-0.5, Lr-0.7, and Lr-0.25). The combinations of SLA class I and II haplotype together, 2 homozygous (Lr-4.5/4.5 and Lr-6.7/6.7) and 3 heterozygous (Lr-4.5/6.7, Lr-4.5/25.25, and Lr-6.7/25.25) haplotypes were identified, including previously unidentified new heterozygous haplotypes (Lr-4.5/4.7). In addition, a new SLA allele typing method using Agilent 2100 bioanalyzer was developed that permitted more rapid identification of SLA haplotypes. These results will facilitate the breeding of SLA homozygous Yucatan pigs and will expedite the possible use of these pigs for the biomedical research, especially xenotransplantation research.

Variance Component Quantitative Trait Locus Analysis for Body Weight Traits in Purebred Korean Native Chicken.

Quantitative trait locus (QTL) is a particular region of the genome containing one or more genes associated with economically important quantitative traits. This study was conducted to identify QTL regions for body weight and growth traits in purebred Korean native chicken (KNC). F1 samples (n = 595) were genotyped using 127 microsatellite markers and 8 single nucleotide polymorphisms that covered 2,616.1 centi Morgan (cM) of map length for 26 autosomal linkage groups. Body weight traits were measured every 2 weeks from hatch to 20 weeks of age. Weight of half carcass was also collected together with growth rate. A multipoint variance component linkage approach was used to identify QTLs for the body weight traits. Two significant QTLs for growth were identified on chicken chromosome 3 (GGA3) for growth 16 to18 weeks (logarithm of the odds [LOD] = 3.24, Nominal p value = 0.0001) and GGA4 for growth 6 to 8 weeks (LOD = 2.88, Nominal p value = 0.0003). Additionally, one significant QTL and three suggestive QTLs were detected for body weight traits in KNC; significant QTL for body weight at 4 weeks (LOD = 2.52, nominal p value = 0.0007) and suggestive QTL for 8 weeks (LOD = 1.96, Nominal p value = 0.0027) were detected on GGA4; QTLs were also detected for two different body weight traits: body weight at 16 weeks on GGA3 and body weight at 18 weeks on GGA19. Additionally, two suggestive QTLs for carcass weight were detected at 0 and 70 cM on GGA19. In conclusion, the current study identified several significant and suggestive QTLs that affect growth related traits in a unique resource pedigree in purebred KNC. This information will contribute to improving the body weight traits in native chicken breeds, especially for the Asian native chicken breeds.

Methyl 9-Oxo-(10E,12E)-octadecadienoate Isolated from Fomes fomentarius Attenuates Lipopolysaccharide-Induced Inflammatory Response by Blocking Phosphorylation of STAT3 in Murine Macrophages.

Fomes fomentarius is a fungus of the Polyporaceae family and is used in traditional oriental therapies. Although the anti-inflammatory activities of this species have been previously reported, the identity of the bioactive compounds responsible for this activity remains unknown. Here, we investigated whether methyl 9-oxo-(10E,12E)-octadecadienoate (FF-8) purified from F. fomentarius exerts anti-inflammatory activity in murine macrophages stimulated with lipopolysaccharide (LPS). FF-8 suppressed secretion of nitric oxide (NO) and prostaglandin E2 through downregulation of inducible NO synthase and cyclooxygenase-2 expression induced by LPS. In addition, pretreatment of cells with FF-8 led to a reduction in levels of secreted inflammatory cytokines such as tumor necrosis factor-α and interleukin-6 in macrophages stimulated with LPS. Conversely, FF-8 did not affect nuclear factor κB, p38, c-Jun NH2-terminal kinase, and extracellular signal-regulated kinase pathways. Instead, FF-8 specifically interfered with signal transducer and activator of transcription 3 (STAT3) phosphorylation induced by LPS. Collectively, this study demonstrated that FF-8 purified from F. fomentarius suppresses inflammatory responses in macrophages stimulated with LPS by inhibiting STAT3 activation. Further studies will be required to elucidate the anti-inflammatory effect of FF-8 in vivo.

Proximate Composition, and l-Carnitine and Betaine Contents in Meat from Korean Indigenous Chicken.

This study investigated the proximate composition and l-carnitine and betaine content of meats from 5 lines of Korean indigenous chicken (KIC) for developing highly nutritious meat breeds with health benefits from the bioactive compounds such as l-carnitine and betaine in meat. In addition, the relevance of gender (male and female) and meat type (breast and thigh meat) was examined. A total of 595 F1 progeny (black [B], grey-brown [G], red-brown [R], white [W], and yellow-brown [Y]) from 70 full-sib families were used. The moisture, protein, fat, and ash contents of the meats were significantly affected by line, gender, and meat type (p<0.05). The males in line G and females in line B showed the highest protein and the lowest fat content of the meats. l-carnitine and betaine content showed effects of meat type, line, and gender (p<0.05). The highest l-carnitine content was found in breast and thigh meats from line Y in both genders. The breast meat from line G and the thigh meat from line R had the highest betaine content in males. The female breast and thigh meats showed the highest betaine content in line R. These data could be valuable for establishing selection strategies for developing highly nutritious chicken meat breeds in Korea.

Discrimination of the commercial Korean native chicken population using microsatellite markers.

BACKGROUND: Korean native chicken (KNC) is a well-known breed due to its superior meat taste. This breed, however, owing to a low growth rate, has a high market price. In order to overcome this disadvantage, the National Institute of Animal Science (NIAS) in Korea developed a commercial KNC breed, named Woorimatdag version 2 (WM2), an upgraded version of the Woorimatdag (WM1) breed and the WM2 was created by crossing the KNC with meat type breeds. This study aims to discriminate between WM2 and other chicken breeds using microsatellite (MS) markers. METHODS: A total of 302 individuals from eight Korean chicken populations were examined. The genetic diversity and population structure analysis were investigated using Cervus, API-CALC, STRUCTURE, PowerMarker programs. RESULTS: Based on heterozygosity and polymorphic information content (PIC) values, 30 MS markers were initially selected from 150 markers. The identified average number of alleles (Na), expected heterozygosity, and PIC values for the WM2 samples were 7.17, 0.741, and 0.682, respectively. Additionally, the paternity of individuals was assigned with a success rate of greater than 99% using 12 markers, the best minimum number of markers. The 12 selected markers contained heterozygosity and PIC values above 0.7 and probability of identity values around zero. Using these markers, the determined probability of identity (PI), PI half-sibs , and PI sibs values were 3.23E-33, 5.03E-22, and 8.61E-08, respectively. CONCLUSIONS: WM2 is well differentiated with respect to other chicken breeds based on estimated genetic distances. The results presented here will contribute to the identification of commercial WM2 chicken in the market.

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_4.0 (NCBI) with whole genome sequences from these lines to identify common and novel single nucleotide polymorphisms (SNPs). We obtained 36,660,731,136 ± 1,257,159,120 bp of raw sequence and average 26.6-fold of 25-29 billion reference assembly sequences representing 97.288 % coverage. Also, 4,006,068 ± 97,534 SNPs were observed from 29 autosomes and the Z chromosome and, of these, 752,309 SNPs are the common SNPs across lines. Among the identified SNPs, the number of novel- and known-location assigned SNPs was 1,047,951 ± 14,956 and 2,948,648 ± 81,414, respectively. The number of unassigned known SNPs was 1,181 ± 150 and unassigned novel SNPs was 8,238 ± 1,019. Synonymous SNPs, non-synonymous SNPs, and SNPs having character changes were 26,266 ± 1,456, 11,467 ± 604, 8,180 ± 458, respectively. Overall, 443,048 ± 26,389 SNPs in each bird were identified by comparing with dbSNP in NCBI. The presently obtained genome sequence and SNP information in Korean native chickens have wide applications for further genome studies such as genetic diversity studies to detect causative mutations for economic and disease related traits.