Kang-k Seo

Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines

This study examined the fecal bacterial diversity of 15-weekold pigs from three purebred lines: Duroc, Landrace, and Yorkshire. Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. Among the breeds evaluated, Landrace had the most diverse bacterial community composition. Prevotella, Blautia, Oscillibacter, and Clostridium were detected in all samples regardless of breed. On the other hand, Catenibacterium, Blautia, Dialister, and Sphaerochaeta were differentially detected among breeds, as demonstrated by the canonical loading plot. The discriminant analysis of principal components plot also showed clear separation of the three purebred pig lines, with a certain degree of similarity between Landrace and Yorkshire pigs and a distinct separation between Duroc pigs and the other two breeds. Other factors not related to breed, such as season or time of sampling and pen effects, may contribute to shaping the gut microbiota of pigs.

Differentially expressed proteins during fat accumulation in bovine skeletal muscle.

The objective of this study was to identify the proteins involved in bovine intramuscular fat (IMF) development. Global proteins were monitored in bovine skeletal muscle at muscle-developing versus IMF-increasing stages and with higher versus lower IMF scores, respectively. We identified two differentially expressed (two-fold or more) proteins at the IMF-increasing stage, up-regulated heat shock protein beta 1 (HSPB1) and down-regulated ATP synthase D chain (ATP5H), and two down-regulated proteins with higher IMF scores, carbonic anhydrase 2 (CA2) and myosin light chain 3 (MYL3). In vitro, after adipogenic differentiation, the mRNA expression of HSPB1 and ATP5H did not be changed, but that of CA2 and MYL3 decreased significantly (P<0.05). After myogenic differentiation, the mRNA expression of HSPB1 increased significantly (P<0.05), but expression of other genes did not vary. We suggested that CA2 and MYL3, which expressed down during adipogenic differentiation, could be indicative markers for negative regulation of IMF development.

Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing

This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level). Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

Genetic Traceability of Black Pig Meats Using Microsatellite Markers

Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and −0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10−14 in population J, 3.17×10−9 in population B, and 1.03×10−12 in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers.

Association of CAST gene polymorphisms with carcass and meat quality traits in Yanbian cattle of China

Bovine calpastatin (CAST) gene polymorphisms have been associated with meat tenderness traits; however, little is known about how the CAST gene affects beef quality traits. In this study, 25 single nucleotide polymorphisms were detected in the CAST gene using polymerase chain reaction with single-strand conformation polymorphism and gene sequencing. Different preponderant genotypes were found at the corresponding gene locus. The E1-1, E1-2, and C3-1 loci were correlated with meat tenderness height and highly correlated with the fatty acid content and the amino acid content. The E4-2 locus was not correlated with meat tenderness, but it was correlated with cooking loss, brightness, and yellowness, among others. The CAST gene is a potential marker for these meat quality traits, but further research is required.

Genome-wide Association Study of Integrated Meat Quality-related Traits of the Duroc Pig Breed

The increasing importance of meat quality has implications for animal breeding programs. Research has revealed much about the genetic background of pigs, and many studies have revealed the importance of various genetic factors. Since meat quality is a complex trait which is affected by many factors, consideration of the overall phenotype is very useful to study meat quality. For integrating the phenotypes, we used principle component analysis (PCA). The significant SNPs refer to results of the GRAMMAR method against PC1, PC2 and PC3 of 14 meat quality traits of 181 Duroc pigs. The Genome-wide association study (GWAS) found 26 potential SNPs affecting various meat quality traits. The loci identified are located in or near 23 genes. The SNPs associated with meat quality are in or near five genes (ANK1, BMP6, SHH, PIP4K2A, and FOXN2) and have been reported previously. Twenty-five of the significant SNPs also located in meat quality-related QTL regions, these result supported the QTL effect indirectly. Each single gene typically affects multiple traits. Therefore, it is a useful approach to use integrated traits for the various traits at the same time. This innovative approach using integrated traits could be applied on other GWAS of complex-traits including meat-quality, and the results will contribute to improving meat-quality of pork.

Application of LogitBoost Classifier for Traceability Using SNP Chip Data

Consumer attention to food safety has increased rapidly due to animal-related diseases; therefore, it is important to identify their places of origin (POO) for safety purposes. However, only a few studies have addressed this issue and focused on machine learning-based approaches. In the present study, classification analyses were performed using a customized SNP chip for POO prediction. To accomplish this, 4,122 pigs originating from 104 farms were genotyped using the SNP chip. Several factors were considered to establish the best prediction model based on these data. We also assessed the applicability of the suggested model using a kinship coefficient-filtering approach. Our results showed that the LogitBoost-based prediction model outperformed other classifiers in terms of classification performance under most conditions. Specifically, a greater level of accuracy was observed when a higher kinship-based cutoff was employed. These results demonstrated the applicability of a machine learning-based approach using SNP chip data for practical traceability.

Estimation of Genetic Parameters for Economic Traits in Swine

This study was conducted to estimate genetic parameter of Duroc, Landrace and Yorkshire breeds based on the on-farm performance tested records of 57,316 pigs under the supervision of Korean Animal Improvement Association from 1992 to 1999. Genetic parameters were estimated with a multiple trait animal model by using DF - REML. The result obtained in this study was summarized as follow ; The estimated heritabilities of Duroc, Landrace and Yorkshire were 0.460.65 for the average backfat thickness, 0.280.31 for loin depth, 0.50～0.60 for percent lean, 0.450.55 for the average daily gain, 0.380.50 for age at 90kg, respectively. Phenotypic correlation of average backfat thickness with loin depth, percent lean, average daily gain and age at 90㎏ for the three breeds were -0.12-0.01, -0.81-0.76, 0.340.46, and -0.41-0.33, respectively. Phenotypic correlation of loin depth with percent lean, average daily gain and age at 90kg were 0.120.23, 0.030.21, and -0.17-0.03, respectively. Phenotypic correlation of percent lean with average daily gain and age at 90kg were -0.37-0.26 and 0.26～0.35, respectively. Phenotypic correlation of average daily gain with age at 90kg was -0.97-0.95. The estimated genetic correlation coefficients of average backfat thickness with loin depth, percent lean, average daily gain and age at 90kg estimated for the three breeds were -0.170.03, -0.79-0.69, 0.240.45 and -0.41-0.19, respectively. The estimated genetic correlation coefficients of loin depth with percent lean, average daily gain and age at 90kg were 0.11～0.19, 0.23 and -0.30～-0.20, respectively. The estimated correlation coefficients of percent lean with average daily gain and age at 90kg were -0.36-0.13 and 0.10～0.34, respectively. The estimated genetic correlation coefficients of average daily gain with age at 90㎏ was -0.96-0.95.

The Influence of Feed Energy Density and a Formulated Additive on Rumen and Rectal Temperature in Hanwoo Steers

The present study investigated the optimum blending condition of protected fat, choline and yeast culture for lowering of rumen temperature. The Box Benken experimental design, a fractional factorial arrangement, and response surface methodology were employed. The optimum blending condition was determined using the rumen simulated in vitro fermentation. An additive formulated on the optimum condition contained 50% of protected fat, 25% of yeast culture, 5% of choline, 7% of organic zinc, 6.5% of cinnamon, and 6.5% of stevioside. The feed additive was supplemented at a rate of 0.1% of diet (orchard grass:concentrate, 3:7) and compared with a control which had no additive. The treatment resulted in lower volatile fatty acid (VFA) concentration and biogas than the control. To investigate the effect of the optimized additive and feed energy levels on rumen and rectal temperatures, four rumen cannulated Hanwoo (Korean native beef breed) steers were in a 4×4 Latin square design. Energy levels were varied to low and high by altering the ratio of forage to concentrate in diet: low energy (6:4) and high energy (4:6). The additive was added at a rate of 0.1% of the diet. The following parameters were measured; feed intake, rumen and rectal temperatures, ruminal pH and VFA concentration. This study was conducted in an environmentally controlled house with temperature set at 30°C and relative humidity levels of 70%. Steers were housed individually in raised crates to facilitate collection of urine and feces. The adaptation period was for 14 days, 2 days for sampling and 7 days for resting the animals. The additive significantly reduced both rumen (p<0.01) and rectal temperatures (p<0.001) without depressed feed intake. There were interactions (p<0.01) between energy level and additive on ruminal temperature. Neither additive nor energy level had an effect on total VFA concentration. The additive however, significantly increased (p<0.01) propionate and subsequently had lower acetate:propionate (A/P) ratios than non-additive supplementation. High concentrate diets had significantly lower pH. Interactions between energy and additive were observed (p<0.01) in ammonia nitrogen production. Supplementation of diets with the additive resulted in lower rumen and rectal temperatures, hence the additive showed promise in alleviating undesirable effects of heat stress in cattle.

Estimation of Genetic Parameters and Genetic Trends for Major Economic Traits in Swine

본 연구에서는 18,668두의 농장 검정된 종돈 자료를 이용하여 유전모수 및 육종가를 추정하였다. 2007년부터 5월부터 2011년 4월까지 영광 소재 N종돈장에서 검정된 Duroc, Berkshire, Landrace 및 Yorkshire종 18,668두에 대한 자료를 근거로 하여 돼지의 주요 경제형질인 90 kg 도달일령, 등지방두께 및 등심단면적에 대한 유전력, 유전상관, 표현형상관 및 육종가를 다형질 Animal model을 이용하여 추정하였다. 본 연구에서 추정된 Duroc종에 대한 90kg 도달일령, 등지방두께 및 등심단면적에 대한 유전력은 0.22, 0.62, 0.37로 추정되었으며 Berkshire종의 유전력은 0.52, 0.57 및 0.32로 나타났고 Landrace종의 각 형질의 유전력은 0.26, 0.51 및 0.23이었으며 Yorkshire종의 유전력은 0.29, 0.47 및 0.26을 나타내었다. 본 연구에서 추정된 Duroc의 주요 경제 형질간의 유전 상관 및 표현형 상관은 90 kg 도달일령과, 등지방두께, 등심단면적, 등지방와 등심단면적간에 각각 유전, 표현형상관 0.24, -0.25과 0.11, -0.21 그리고 -0.41 및 -0.19로 추정되었으며 Berkshire종 유전 상관 및 표현형 상관은 -0.01, -0.35 및 0.01, -0.28 그리고 등지방두께에 대한 등심단면적은 -0.68 및 -0.22를 나타내었다. Landrace종의 경우 유전 상관 및 표현형 상관이 90 kg 도달일령과, 등지방두께, 등심단면적, 등지방두께와 등심단면적간에 각각 유전, 표현형 상관 0.01,.-0.23과 0.03, -0.37 그리고 -0.17 및 -0.24로 추정 되었으며 Yorkshire종은 0.01, -0.23 및 0.03, -0.37 그리고 -0.17, -0.24로 추정 되었다. 연도별 유전적 개량 추세를 살펴보면 90 kg 도달일령의 경우 매년도달일령이 짧아지는 것을 나타냈으며 등지방두께의 경우 모든 품종에서 매년 두꺼워지는 것을 보였고 등심단면적은 각 품종이 매년 증감을 반복하는 것을 나타냈다. 【The objective of this study was to estimate the genetic parameters and breeding value of swine using their economic traits. The traits considered were age at 90 kilograms body weight (D90 kg), backfat thickness (BF) and eye muscle area (EMA). Estimation of genetic parameters and breeding value from 18,668 heads considering the economic traits were based on farm performance data from May 2007 to April 2011. Estimation of genetic parameters based on economic traits revealed that the single best model was fitted after finding source of variance on fixed and random effects and estimated by a multiple trait model using DF-REML (Derivative-FREE Restricted Maximum Likelihood). In this study, the estimated heritabilities of Duroc, Berkshire, Landrace and Yorkshire were about 0.22-0.59 for the D90 kg, 0.47-0.62 for the BF and 0.23-0.37 for the EMA. Genetic correlation of D90 kg with BF and EMA of the four breeds were -0.01-0.24 and -0.35--0.23, respectively. Moreover, the genetic correlation of BF with EMA was -0.68--0.17. On the other hand, the phenotypic correlation of D90 kg with BF and EMA of the four breeds were about 0.01-0.11 and -0.37--0.21, respectively, while the phenotypic correlation of BF with EMA was -0.68--0.17. Results showed that the genetic trends of breeding value every year were decreasing for D90 kg, increasing for BF while for EMA inconsistent values were obtained.】