The Pig Genome Database (PiGenome): an integrated database for pig genome research

Lim, Dajeong,Cho, Yong-Min,Lee, Kyung-Tai,Kang, Yeonkyung,Sung, Samsun,Nam, Jungrye,Park, Eung-Woo,Oh, Sung-Jong,Im, Seok-Ki,Kim, Heebal Springer-Verlag 2009 Mammalian genome Vol.20 No.1

Analysis of gene expression profiles from subcutaneous adipose tissue of two pig breeds

Dajeong Lim,이경태,Jong Eun Park,김희발,Tae-Hun Kim,Bong-Hwan Choi,Myung Jick Kim,Hye-Sun Park,장길원 한국유전학회 2011 Genes & Genomics Vol.33 No.6

Lipid deposition, especially in subcutaneous (backfat) adipose tissues, is directly related to the meat yield and quality in pork. We hypothesized that differentially expressed genes and their transcription factors play a role in the regulation of adipogenesis in porcine backfat. We identified 136 differentially expressed genes (DEGs) in subcutaneous adipose tissue between two pig breeds, the Korean native pig (KNP) and Yorkshire,using a cDNA microarray. Gene ontology analysis demonstrated that some DEGs are involved in fat metabolism processes such as adipogenesis, adipocyte differentiation, and lipolysis. In addition, we identified the regulatory relationship between DEGs and their transcription factors using in silico and qRT-PCR analysis. Two transcription factors (TEF-1,IRF-7) have positively regulated DEGs in KNP backfat. Three other transcription factors (STAT3, OCT1 and HNF4) are negatively correlated with the DEGs in KNP backfat. Our findings suggest that DEGs and their transcription factors may have a potential role in adipogenesis and/or lipid deposition in backfat tissues between pig breeds.

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle

Lim, Dajeong,Lee, Seung-Hwan,Kim, Nam-Kuk,Cho, Yong-Min,Chai, Han-Ha,Seong, Hwan-Hoo,Kim, Heebal Asian Australasian Association of Animal Productio 2013 Animal Bioscience Vol.26 No.1

Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

Association of Heat Shock Protein Beta 1 (HSPB1) Gene Expression with Tenderness in Loin Muscle of Korean Cattle (Hanwoo)

Dajeong Lim(임다정),Seung-Hwan Lee(이승환),Yong-Min Cho(조용민),Bong-Hwan Choi(최봉환),Han-Ha Choi(최한하),Hwan-Hoo Seong(성환후),Seong-Koo Hong(홍성구),Nam-Kuk Kim(김남국) 한국생명과학회 2012 생명과학회지 Vol.22 No.11

육질 등급에 차이를 보이는(3등급과 1++등급) 한우 등심육을 대상으로 한 단백체 연구를 통해 heat shock protein beta 1 (HSPB1)의 발현 차이가 관찰되었다. 따라서 본 연구는 HSPB1의 유전자와 단백질 수준에서의 발현이 육질에 중요한 요인으로 작용하는 연도(전단력)에 미치는 영향을 규명하기 위하여 수행하였다. 전단력 값의 차이를 보이는 동기우 집단 20두를 대상으로 유전자 및 단백질의 발현량을 분석하였고, 통계분석을 수행하였다. 유전자 및 단백질 수준에서의 발현량을 분석한 결과 HSPB1은 전단력이 낮은 그룹에서 전단력이 높은 그룹보다 2배 발현이 높은 것으로 확인되었으며(p<0.05), 전단력과의 관련성 분석 결과에서도 유전자와 단백질 발현량 모두에서 통계적 유의성이 확인하였다(p<0.05). 이러한 결과로 볼 때 HSPB1 유전자는 한우 등심육의 연도와 밀접히 관련되어있다고 판단되며, 지속적으로 유전자구조 변이연구 등을 통해 유전자 마커로의 개발이 필요할 것으로 생각된다. In a previous proteomic study, heat shock protein beta 1 (HSPB1) was detected as differentially expressed protein in longissimus thoracis between low (grade 3) and high (grade 1++) meat quality groups by 2DE gel electrophoresis. The present study investigated an association of HSPB1 expression at the level of gene and protein with Warner-Bratzler shear force (WBS) measured in 20 Hanwoo steers. An analysis of variance (ANOVA) between expression values and WBS showed that WBS was affected by HSPB1 expression (p<0.05). The expression (at both gene and protein level) of the HSPB1 was 2 times higher in the low WBS group than that in the high WBS group (p<0.01). This result suggests that the HSPB1 gene may be a candidate gene associated with tenderness in longissimus thoracis of Korean cattle.

Gene Expression Patterns Associated with Peroxisome Proliferator-activated Receptor (PPAR) Signaling in the Longissimus dorsi of Hanwoo (Korean Cattle)

Lim, Dajeong,Chai, Han-Ha,Lee, Seung-Hwan,Cho, Yong-Min,Choi, Jung-Woo,Kim, Nam-Kuk Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.8

Adipose tissue deposited within muscle fibers, known as intramuscular fat (IMF or marbling), is a major determinant of meat quality and thereby affects its economic value. The biological mechanisms that determine IMF content are therefore of interest. In this study, 48 genes involved in the bovine peroxisome proliferator-activated receptor signaling pathway, which is involved in lipid metabolism, were investigated to identify candidate genes associated with IMF in the longissimus dorsi of Hanwoo (Korean cattle). Ten genes, retinoid X receptor alpha, peroxisome proliferator-activated receptor gamma (PPARG), phospholipid transfer protein, stearoyl-CoA desaturase, nuclear receptor subfamily 1 group H member 3, fatty acid binding protein 3 (FABP3), carnitine palmitoyltransferase II, acyl-Coenzyme A dehydrogenase long chain (ACADL), acyl-Coenzyme A oxidase 2 branched chain, and fatty acid binding protein 4, showed significant effects with regard to IMF and were differentially expressed between the low- and high-marbled groups (p<0.05). Analysis of the gene co-expression network based on Pearson's correlation coefficients identified 10 up-regulated genes in the high-marbled group that formed a major cluster. Among these genes, the PPARG-FABP4 gene pair exhibited the strongest correlation in the network. Glycerol kinase was found to play a role in mediating activation of the differentially expressed genes. We categorized the 10 significantly differentially expressed genes into the corresponding downstream pathways and investigated the direct interactive relationships among these genes. We suggest that fatty acid oxidation is the major downstream pathway affecting IMF content. The PPARG/RXRA complex triggers activation of target genes involved in fatty acid oxidation resulting in increased triglyceride formation by ATP production. Our findings highlight candidate genes associated with the IMF content of the loin muscle of Korean cattle and provide insight into the biological mechanisms that determine adipose deposition within muscle.

Analysis of extended haplotype in Korean cattle (Hanwoo) population

( Dajeong Lim ),( Bong Hwan Choi ),( Yong Min Cho ),( Han Ha Chai ),( Gul Won Jang ),( Cedric Gondro ),( Yeoung Ho Jeoung ),( Seung Hwan Lee ) 생화학분자생물학회(구 한국생화학분자생물학회) 2016 BMB Reports Vol.49 No.9

Korean cattle (Hanwoo) are categorized into three breeds based on color: brown, brindle, and black. Among these breeds, brown Hanwoo has been subjected to intensive selection to improve meat traits. To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip. We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 individuals each of brown and brindle Hanwoo. In particular, non-synonymous SNPs in the ADSL gene (K88M, L189H, and R302Q) might have had mutational effects on protein structure as a result of altering the purine pathway during nucleotide breakdown. The ADSL gene was previously reported to affect meat quality and yield in livestock. Meat quality and yield are main breeding goals for brown Hanwoo, and our results support a potential causal influence of non-synonymous SNPs in the ADSL gene. [BMB Reports 2016; 49(9): 514-519]

Gene Co-Expression Network Analysis of Reproductive Traits in Bovine Genome

Lim, Dajeong,Cho, Yong-Min,Lee, Seung-Hwan,Chai, Han-Ha,Kim, Tae-Hun The Korean Society of Animal Reproduction 2013 Reproductive & developmental biology Vol.37 No.4

Many countries have implemented genetic evaluation for fertility traits in recent years. In particular, reproductive trait is a complex trait and need to require a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with reproductive trait, we applied a weighted gene co-expression network analysis from expression value of bovine genes. We identified three co-expressed modules associated with reproductive trait from bovine microarray data. Hub genes (ZP4, FHL2 and EGR4) were determined in each module; they were topologically centered with statistically significant value in the gene co-expression network. We were able to find the highly co-expressed gene pairs with a correlation coefficient. Finally, the crucial functions of co-expressed modules were reported from functional enrichment analysis. We suggest that the network-based approach in livestock may an important method for analyzing the complex effects of candidate genes associated with economic traits like reproduction.

Characterization of Genes for Beef Marbling Based on Applying Gene Coexpression Network

Lim, Dajeong,Kim, Nam-Kuk,Lee, Seung-Hwan,Park, Hye-Sun,Cho, Yong-Min,Chai, Han-Ha,Kim, Heebal Hindawi Publishing Corporation 2014 International journal of genomics Vol.2014 No.-

<P>Marbling is an important trait in characterization beef quality and a major factor for determining the price of beef in the Korean beef market. In particular, marbling is a complex trait and needs a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with marbling, we used a weighted gene coexpression network analysis from the expression value of bovine genes. Hub genes were identified; they were topologically centered with large degree and BC values in the global network. We performed gene expression analysis to detect candidate genes in <I>M. longissimus</I> with divergent marbling phenotype (marbling scores 2 to 7) using qRT-PCR. The results demonstrate that transmembrane protein 60 (TMEM60) and dihydropyrimidine dehydrogenase (DPYD) are associated with increasing marbling fat. We suggest that the network-based approach in livestock may be an important method for analyzing the complex effects of candidate genes associated with complex traits like marbling or tenderness.</P>

Gene Co-Expression Network Analysis of Reproductive Traits in Bovine Genome

Dajeong Lim,Yong-Min Cho,Seung-Hwan Lee,Han-Ha Chai,Tae-Hun Kim 한국동물번식학회 2013 Reproductive & developmental biology Vol.37 No.4

Global trends in regulatory frameworks for animal genome editing in agriculture

Dajeong Lim,Inchul Choi 한국동물생명공학회(구 한국수정란이식학회) 2023 한국동물생명공학회지 Vol.38 No.4

Revolutionary advancements, such as the reduction in DNA sequencing costs and genome editing, have transformed biotechnology, fostering progress in manipulating biomolecules, engineering cells, and computational biology. Agriculture and food production have significantly benefited from tools like high-throughput microarrays, accelerating the selection of desired traits. Genetic engineering, especially utilizing genome editing, facilitates precise alterations in plants and animals, harnessing microbiomes and fostering lab-grown meat production to alleviate environmental pressures. The emergence of new biotechnologies, notably genome editing, underscores the necessity for regulatory frameworks governing LM (living modified) organisms. Global regulations overseeing genetically engineered or genome-edited (GE) organisms, encompassing animals, exhibit considerable diversity. Nonetheless, prevailing international regulatory trends typically exclude genomeedited plants and animals, employing novel biotechnological techniques, from GMO/ LMO classification if they lack foreign genes and originate through natural mutations or traditional breeding programs. This comprehensive review scrutinizes ongoing risk and safety assessment cases, such as genome-edited beef cattle and fish in the USA and Japan. Furthermore, it investigates the limitations of existing regulations related to genome editing in Korea and evaluates newly proposed legislation, offering insights into the future trajectory of regulatory frameworks.