우리나라 8개의 배추 생산지에서 배추좀나방을 채집하여 아세틸콜린에스테라제 유전자 AceI 의 SNP를 조사하여, 집단 간 유사도를 비교하였다. 또한 10개의 채집 지역 배추좀나방 계통에 대해 8종의 방제 약제로 생물 검정을 실시한 후 추천 농도에 대한 상대적 저항성 비로 군집 분석을 실시, SNP의 군집 분석 결과와 비교하였다. SNP 비율에 의한 군집 분석으로 배추좀나방은 크게 태백산맥 고지대에서 서식하는 배추좀나방과 태백산맥 서쪽 저지대에서 서식하 는 배추좀나방 군으로 분류되었는데, 이는 배추좀나방의 지역 정착, 발달 패턴이 두 지역 간 서로 달랐음을 암시한다. 그러나 약제반응에 의한 군집 분류는 지역 간 어떤 공통점을 보이지 않아 약제 저항성은 배추좀나방의 지역 정착 후 짧은 시간에 약제저항성이 발달한 것으로 추정된다.

The HNF4α (hepatocyte nuclear factor 4, alpha) is a hepatic transcription factor related to the lipid metabolism and regulation of insulin secretion in humans. The current study about commercial broiler reported that the A543G single nucleotide polymorphism (SNP) within HNF4α gene has an effect on fat deposition and wing yield in the chicken. This study was performed to investigate the association between the SNP within HNF4α gene and growth trait and to verify the applicability as a molecular marker for the improving the performance in Korean native chickens (KNCs). A total of 764 KNCs was collected from the livestock farm of Gyeongnam National University of Science and Technology in Korea and genotyped by PCR-RFLP. The body weight measured at birth, 2, 4, 6, 8, 10, 12, 14, 15, 16, 18, 20, 24, 28, 32, 36, and 40 weeks of age for the association analysis between chicken growth and the SNP genotype. Statistical analysis of the SNP with phenotypic traits was performed using SAS program. The KNC strain was classified by the genotypes of the A543G SNP. The frequencies of three genotypes were 0.47 (AA), 0.43 (AG) and 0.10 (GG), respectively. The SNP of HNF4α has highly significant association (p<0.001) with all-round growth in KNCs. These results suggest that the A543G SNP within HNF4α gene could be a genetic marker for the breeding in Korean native chickens.

Growth traits, such as body weight, directly influence productivity and economic efficiency in the swine industry. In this study, we estimate heritability for body weight traits usinginformation from pedigree and genome-wide single nucleotide polymorphism (SNP) chip data. Four body weight phenotypes were measured in 1,105 F2 progeny from an intercross between Landrace and Jeju native black pigs. All experimental animals were subjected to genotypic analysis using PorcineSNP60K BeadChip platform, and 39,992 autosomal SNP markers filtered by quality control criteria were used to construct genomic relationship matrix for heritability estimation. Restricted maximum likelihood estimates of heritability were obtained using both genomic- and pedigree- relationship matrix in a linear mixed model. The heritability estimates using SNP information were smaller (0.36-0.55) than those which were estimated using pedigree information (0.62-0.97). To investigate effect of common environment, such as maternal effect, on heritability estimation, we included maternal effect as an additional random effect term in the linear mixed model analysis. We detected substantial proportions of phenotypic variance components were explained by maternal effect. And the heritability estimates using both pedigree and SNP information were decreased. Therefore, heritability estimates must be interpreted cautiously when there are obvious common environmental variance components.

NGS data was yielded by using Illumina Hiseq platform. The short reads were filtered by quality score and read length were mapped against the reference genome (KACC42780). Genome-wide reanalyzed data of Flammulina strains were compared against the reference genome to establish a genome-wide single nucleotide polymorphism (SNP). The rate of mapping differences between the strains reflected in the strain variation in its result. The genome-wide SNPs distribution divided into types of homozygous SNP and heterozygous SNP moreover all of the strains demonstrated a wide variation in all of the regions. In the further study of topological relationship between the collected strains, phylogenetic tree was separated into 3 major groups. Group I contained F. velutipes var. related strains of ASI 4062, 4148, 4195. Group Ⅱ contained strains that were different species of ASI 4188 F. elastica, ASI 4190 F. fennae, and ASI 4194 F. rossica. The other 19 strains F. velutipes were classified as a single group. Polymorphic SNPs of F. velutipes strains representing the phylogenetic segregation of whiteand brown-fruiting body forming groups were compared. As previously reported, white gene expression is recessive to brown in fruiting body color gene expression. The white strains produced 131,874 SNPs to be aa type and homozygous from of SNP. 407,947 SNPs were detected as AA, Aa type from the brown-fruiting body of SNP. We constructed a SNP matrix with 8 white strains and 12 brown strains. To develop the molecular marker related in to fruiting body color and geographical origin, we isolated 240 SNPs from the white-and brown-fruiting body forming. To determine the chromosome relationship on polymorphic SNP between Korea and Japan strains producing white-fruiting body, we analyzed that the Korea white strains detected 185,695 SNPs and the Japan white strains produced 263,811 SNPs. Using the constructed SNP matrix with 3 Korea white strains and 3 Japan white strains, the experiment generated 475 SNPs of phylogenetic SNPs fromKorea and Japan white-fruiting body. As a result, we regarded as they are potentially related to the white color. White and brown color and origin specific SNPs could be used as an identification marker for selection of F. veluipes strains in the breeding program.

The ANK1 (Ankyrin-1) gene, located on the bovine chromosome 27, encodes a structural protein which forms an important component of the cytoskeleton. Ankyrin belongs to a protein family that links membrane proteins to the underlying spectrin-actin cytoskeleton. Many studies on gene expression regulation have revealed that RNA polymerase binds to the ANK1 gene promoter region. The purpose of the present study was to investigate the relationship between the SNP of the ANK1 promoter region and economic traits in Hanwoo cattle. A total of seven SNPs (C-944T, C-733T, C-687G, A-672G, C-307T, A-104G, C-24T), found in 119 animals, were correlated to economic traits. One of these SNPs, A-104G, was reported for the first time in the present study. Three newly discovered haplotypes were not associated with economic traits. Significant (p<0.05) relationships were found between C-944T and carcass weight, backfat thickeness, loin muscle area and between C-733T, A-672G and intramuscular fat. These results suggest that the SNPs of ANK1 gene may be useful molecular markers for selection of meat yield and quality traits in Hanwoo

Cryopreservation of boar semen is continually researched in reproductive technologies and genetic resource banking in breed conservation. For evaluating the boar semen quality, sperm motility (MOT) is an important parameter because the movement of spermatozoa indicates active metabolism, membrane integrity and fertilizing capacity. Various researches have been trying to improve the quality of semen Post-thawed in boar. Recently, polymorphism (g. 35756 T>C) of Estrogen Receptor 1 (ESR1) gene reported to be significant association with MOT. This study was conducted to evaluate the ESR1 gene as a positional controlling for motility and kinematic characteristics of post-thawed boar semen. To results, The g.35756 T>C SNP of ESR1 was significantly associated with frozen semen motility and kinematic characteristics. The g.35756 T>C SNP was high significantly associated with MOT, VCL, VSL and VAP (p<0.001). The SNP was also significantly associated with ALH (P<0.05). Therefore, we suggest that the g. 35756 T>C polymorphism in the intron 1 region of the porcine ESR1 gene could potentially be applied in frozen semen programs to improve MOT trait, but only after validation in other populations.

The insulin-like growth factor binding proteins (IGFBPs) is involved in the regulating effects and the biological activities of the insulin-like growth factors (IGFs). Recently, It has been reported that the IGFBP2 gene polymorphism was associated growth and skeletal development in chicken. This study was designed to investigate the association of the C1032T SNP of IGFBP2 gene with growth and egg production traits in Korean native chicken (KNC) population as well as other chicken breeds. A total of 225 chickens from the three breeds (Rhode Island Red, Cornish, Leghorn) and 245 chickens from the six strains of Korean native chickens including Black, Gray, Ogol, Red, White, and Yellow, were genotyped by PCR-RFLP (polymerase chain reaction-restricted fragment length polymorphism) and analyzed the association between their genotypes and economic traits by SAS program. The results showed that the SNP (single nucleotide polymorphism) was significantly associated with multiple traits, including body weight of 150 days (p<0.001 and p<0.05) in the Rhode Island Red and the KNC (White) and egg production number (p<0.05) in the KNC (Black) breed. These results suggest that IGFBP2 C1032T SNP could be used as a DNA marker for the improvement of economic traits in Korean native chicken breeding.

영지버섯은 두 가지 형태인 녹각형과 편각형이 알려져 있다. 최근 녹각형 영지버섯이 편각형 영지버섯보다 더 많은 양의 β-glucans 및 triterpenoids 가 함유되어있어 편각형 영지버섯보다 더 강한 생리활성이 있다고 제안되었으며, 실제로 녹각형 영지버섯의 추출물을 이용한 항종양활성 연구에서 종양억제의 탁월한 효과가 있다는 것이 보고되었다. 따라서 본 연구에서는 영지버섯(Ganoderma lucidum) 종내 24균주(녹각형 5균주, 편각형 19균주)를 대상으로 미토콘드아 SSU rDNA의 염기서열을 비교 하였고 녹각형과 편각형 영지버섯을 판별할 수 있는 SNP 부위에 대해 분석을 수행하였다. 그 결과, SNP를 포함한 미토콘드리아 SSU rDNA 부위의 단편(499bp)을 증폭하여 HinfI 제한효소를 처리하였을 때 녹각형 영지버섯에서만 369bp와 130bp 크기를 가진 두 개의 제한 단편이 확인되었고 편각형 영지버섯에서는 499bp의 증폭산물이 유지되는 것을 확인하였다. 이에 따라 녹각 형태의 영지버섯의 자실체 발생은 CO2 농도 및 광량뿐만 아니라 유전적인 관련성이 어느 정도 있을 것으로 사료된다.

본 연구는 R을 기반으로 하여 벌점화 축소추정 기법을 활용한 유전체 선발 방법론들을 소개하고 이를 활용하여 요크셔 돼지의 산자수를 추정하고 비교 분석하고자 하였다. 비교하고자 하는 7가지의 벌점화 축소추정 기법은 다음과 같다: 능형회귀, 능형회귀 BLUP, LASSO, adaptive LASSO, fused LASSO, elastic net 그리고 SCAD. 농촌진흥청에서 제공한 519마리 암퇘지의 2,000개 유전자형 자료와 종속변수로 사용된 산자수가 연구에 사용되었다. 연구 결과의 비교 평가를 위해서 사용된 예측오차와 Pearson 상관계수에 따르면, 예측오차는 LASSO와 elastic net이 각각 0.6884과 0.6876으로 가장 작은 값을 가졌으며, 상관계수는 0.7466과 0.7388로 7가지 방법론 중에서 가장 좋은 예측력을 나타내었다. R을 활용한 이러한 연구 결과를 토대로 LASSO와 elastic net이 유전체 선발 기법 중 좋은 방법론임을 알 수 있었다.

소의 14번 염색체에 위치한 2,4-Dienoyl CoA reductase1(DECR1) 유전자는 polyunsaturated fatty enoyl-CoA의 β-oxidation과 연관된 호르몬으로 지질대사조절에 영향을 미치는 유전자로 알려져 있다. 따라서 본 연구는 한우의 경제형질 관련 DNA 마커 개발을 목적으로 DECR1 유전자 내의 single nucleotide polymorphisms(SNPs)를 탐색하고, 경제형질간의 연관성을 분석하고자 수행하였다. 먼저 부모가 서로 다른 한우 종모우에서 DECR1 유전자 내의 SNP를 탐색한 결과 총 13개의 SNPs를 확인하였고, 이 중 G20788A는 valine(Val)에서 methionine(Met)으로, A23262G는 isoleucine(Ile)에서 valine(Val)으로 바뀌는 missense mutation으로 확인되었다. 그리고 도체 성적을 보유한 200두의 한우를 대상으로 missense mutation으로 확인된 G20788A와 A23262G의 유전자형과 경제형질간의 연관성을 분석하였다. 그 결과 G20788A는 근내지방도와 도체중에서 A23262G는 등지방두께, 배최장근단면적, 근내지방도와 도체중에서 통계적 유의성을 확인 할 수 있었고(P<0.05), 이를 통해 missence mutation인 G20788A와 A23262G는 각 경제형질에 영향을 미치는 것을 알 수 있었다. 따라서 본 연구에서 탐색된 한우 DECR1 유전자의 SNP 유전자형은 한우 선발 및 개량을 위한 DNA 마커로 활용 가능할 것으로 기대된다.

MYC (v-myelocytomatosis viral oncogene homologue) is a regulator gene that encodes for a nuclear phosphoprotein. Porcine MYC gene was mapped on chromosome SSC 4p13 and is associated with a variety of functions such as cell proliferation and cell growth. MYC expression is coupled to a multitude of physiological processes and is regulated by hormones, growth factors, cytokines, lymphokines, nutritional status, development and differentiation. MYC is also involved in myogenesis, muscle hyperplasia and adipogenesis. In this study, we investigated SNPs in MYC gene and their association with economic traits in Duroc, Landrace and Yorkshire populations. We detected a single point mutation in exon 3 of porcine MYC gene as a change of T to C at 906 base (amino acid position 302, nonsynomous mutation of alanine) in MYC-N domain. MYC mutation (T906C) was significantly associated with age at 90 kg in these breeds, signifying that this mutation can serve as a selection marker for growth traits in pigs.

Single nucleotide polymorphisms (SNPs), that usually occurs with a modification in single nucleotide among the population of 1000 nucleotides. Such changes in nucleotides have been investigated and been associated by meat scientist for economically important traits and to increase economical profits in stock breeding. Pluralities in the study have correlated SNPs of potential candidate gene with economically important traits in domestic animals have been put forward. In chickens, INS, IGF1, IGF1R, IGFBP, CAPN1, CAPN3, GHSR, FATP1, FGFBP1, FGFBP2, apoVlDL-Ⅱ, PB1, miR-1614-3p, DAAM1, Wnt3A, LRP5, CHP, RHOA, MAPK9, SFRP1, ATGL, PGC-1α, NPY, GnRHR, PRL, TGFβ2, CASR. UCP, ADSL, STAT5b, LRP2 and CTSD genes have been found to have significant effects on body weight, breast muscle weight, carcass weight and egg number. For the similar reasons, SNPs of these genes have been considered useful DNA markers for the improvement economic value of poultry. Although further studies on different breeds of chickens would be required to segregate such dataset for different breeds of chickens.

The purpose of the livestock industry is to pursuit economic profits by increasing the economic productivity of livestock. Single nucleotide polymorphisms (SNPs), that is characterized by one variation out of every 1000 polymorphisms, to increase economical benefits in stock breeding has been extensively studied. Particularly, replete number of investigations have been put forward that has associated SNPs of candidate genes with economically important traits such as carcass weight (CW), longissimus muscle area (LMA), backfat thickness (BFT) and marbling score (MS) in beef cattle. Bovine genome sequencing and HapMap projects have provided, millions of SNPs in the cattle genome. However, till date studies related to the association of the SNPs with economic traits in beef cattles are meager. Discovering of SNPs bovine whole genome would certainly be useful genetic assets for the development of SNP marker for economically important traits in beef cattle.

The role of Fatty acid binding protein 4 (FABP4) gene is critical for lipid metabolism and for maintaining homeostasis in adipocytes. Association between Hanwoo carcass traits and FABP4 gene g.7516G>C SNP has been reported previously, however, its association and how does it influence Korean brindle and black cattle has not been demonstrated and established till date. For this purpose, the study was planned to analyze the SNP association (Single Nucleotide Polymorphism) (g.7516G>C) in FABP4 gene and gather genetic information on economic traits of Korean brindle cattle and black cattle. As per sequence of bovine FABP4 gene available (Genbank accession No. NC_007312.4), one pair of primers (5’-ATA TAG TCC ATA GGG TGG CAA AGA-3’ and 5’-AAC CTC TCT TTG AAT TCT CCA TTC T-3’) was designed to amplify a 452bp product of the FABP4 gene including the region of 7417–7868. The SNP, detected by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) methods using restriction enzyme MspA1I, was genotyped in 117 animals of brindle cattle and 24 animals of black cattle population. Statistical analysis revealed that the FABP4 genotype significantly (p<0.05) affect with carcass weight, but there was no significant association with any other economic traits was observed in brindle as well as in black cattle. In conclusion, these results suggested that SNP (g.7516G>C), located in FABP4 gene, could be used as important DNA marker of economic traits in Korean brindle cattle. Furthermore, we suggest that additional samples needs to further analysed to make related data exclusively authentic.

The aim of this study is to investigate the genetic interrelationships between economic or meat quality traits (birth weight, weaning weight, average daily gain, market weight, carcass weight, backfat thickness, water, ash, fat, protein, water holding capacity and pH) and 6 SNPs located on six selected candidate genes (MC4R, PGK2, TNNI1, TNNI2, PIK3C3, and CTSK) in Korean native pigs. The genotypes were identified in the 6 SNPs by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) procedure, and association of the genotype on economically important traits was analyzed by general liner model. According to the analyzed results, the MC4R c.1426A>G was correlated with birth weight (p=0.032) and the PGK2 g.122T>G was associated with pH (p=0.026). These findings obtained in the present revealed that the each SNPs of MC4R and PGK2 could be useful as potential genetic markers for birth weight and pH in Korean native pigs, respectively.

The melanocortin receptor type 4 (MC4R) gene is expressed in the hypothalamus and regulates energy intake and body weight. Recently, it has been reported that obesity and energy balance in human were also regulated by the MC4R gene. Therefore the objective of this study was to identify the polymorphism on the MC4R gene SNP C1786T and its association with economic traits in Korean native cattle (brindle and black cattle) by PCR-RFLP. A total of 125 cattle from the two breeds were tested for economic traits (meat quality index, backfat, thickness, carcass weight, longissimus muscle area and marbling score) and data was analyzed using SAS program. In the results, C allele had highest frequency than G allele frequency in the both breeds and the gene was significantly associated with meat quantity index and backfat thickness in brindle cattle breed. However, in black cattle, the gene was significantly associated with longissimus muscle area (p<0.05). These results suggest that C1786T SNP of the MC4R gene may be useful as a genetic marker for economic traits in the brindle and black cattle.

Stearoyl-CoA desaturase (SCD1) gene plays important role in fatty acid composition. In order to find marker-assisted selection (MAS) for improving the economic trait, this study was performed to identify the 878T>C single nucleotide polymorphism (SNP) on SCD1 gene. Three genotypes (CC, CT, and TT) were detected in 878T>C SNP of SCD1 gene from 103 Hanwoo population by polymorphism chain reaction-restriction fragment length polymorphism (PCR-RFLP) and economic traits were analyzed by general linear model. The frequency of allele C and T was 0.534 and 0.466, also the genotype frequency of CC, CT and TT was 0.252, 0.563, and 0.184, respectively in the Hanwoo population. The TT genotype of SCD1 gene showed a significantly higher measures (p<0.05) of carcass weight (CW) than CT, CC genotype. No significant association was detected between genotype and other economic trait (marbling, backfat thickness, and longissimus muscle area) in this study. The results revealed that SCD1 gene 878T>C SNP could be useful for effective MAS to increase the economic quality in Hanwoo population.

Myopalladin (MYPN) is an important expression gene associated with regulation of Z-line structure in muscle and maintains sarcomeric integrity. In this study, we investigated the association between MYPN A1795G SNP (single nucleotide polymorphism) and carcass traits (LMA, longissimus muscle area; CW, carcass weight; BF, backfat thickness; MS, marbling score) in Korean cattle. The MYPN A1795G SNP was genotyped in 212 steers and analyzed the associations with carcass traits by PCR-RFLP (Restriction fragment length polymorphism) method. The allele frequencies were 0.566 for G allele and 0.434 for A allele. And the genotype frequencies of GG, GA, and AA genotype were 32.1%, 49%, and 18.9%, respectively. Association analysis indicated that the A1795G SNP of MYPN gene showed a significant association with LMA (p<0.05). The steers with GG genotype had higher LMA than those with the genotypes AA. But no significant associations were observed in other carcass traits (CW, BF, MS). The steers with the GG genotype showed higher CW and BF than those with the genotypes AA and GA. These results suggest that the A1795G SNP of the MYPN gene is associated with LMA and may be useful for candidate marker-assisted selection to increase the levels of LMA in Korean cattle.