본 연구는 Yorkshire종, Landrace종 및 Duroc종에 대한 유전체자료를 이용하여 수퇘지의 웅취를 유발하는 세 가지 호르몬인 androstenone, indole 및 skatole 호르몬에 대한 유의적인 유전자영역, SNP 마커 및 후보유전자를 발굴하여 최종적으로 저웅취 종돈을 육종하는데 그 목적이 있다. Genomoe-Wide Association Study를 수행하기 위한 참조집단으로 수집한 유전체 정보는 Yorkshire, Landrace 및 Duroc종에서 각각 3,858 두, 472두 및 1,029두로 총 5,359두에 대한 유전체자료를 분석에 이용하였다. 추정되는 육종가의 정확도를 평가하기 위하여 REML방법을 ASREML 4.1 소프트웨어를 이용하여 분석하였고 세 가지 호르몬에 대하여 다형질 개체모형을 적용하였으며 추정된 육종가로부터 산출한 deregreessed DEBVincPA를 반응변수로 이용하여 연구를 수행하였다. 세 가지 호르몬에 대하여 BayesB와 C의 방법론을 통하여 분석한 결과 BayesB에서 세 가지 호르몬과 연관될 것으로 예상되는 SNP marker 9개, 즉 androstenone에서 3개, indole에서 1개 및 skatole에서 5개가 발굴되었다. BayesC에 서는 이보다 적은 SNP marker 3개가 발굴되었다. 수퇘지의 웅취 호르몬에 영향을 미칠 것으로 예상되는 후보유전자는 총 6개로 각각 LMAN2L, ABLI, NRG3, CDH12, TRAPPC9, MAN1A2로 나타났다

본 연구는 제주지역에서 사육되고 있는 제주 재래돼지기반의 제주흑돈(제주재래돼지 합성돈)에 대하여 산육형질인 등지방 두께, 일당증체량, 90 kg 도달일령에 대한 후보유전자 탐색을 위해 전장유전체 분석을 실시하였고, 유전체 육종가의 정확도 비교를 위해 베이지안 방법(BayesB, BayesC), π(0.00, 0.50, 0.90, 0.99)값과 개체 자신과 후대의 정보만 포함하고 조상의 정보에 대해 정보를 보정한 DEBVexcPA (Deregressed EBV exlude parents average)와 부모 평균을 포함한 DEBVincPA (Deregressed EBV include parents average)의 반응변수를 이용하였다. 산육형질에 대한 전장유전체 분석을 실시한 결과 등지방두께는 KIAA1549 유전자(SSC18 at 11Mb region), 일당증체량과 90 kg 도달일령에서 POLD3(SSC9 at 9Mb region), STX6(SSC9 at 134Mb region) 유전자가 공통적으로 탐색되었다. 유전체의 정확도 범위는 일당증체량 BayesB의 경우 DEBVexcPA와 DEBVincPA에서 각각 0.285~0.305와 0.497~0.510과 BayesC에서 0.287~0.296와 0.499~0.511으로 추정되었다. 90 kg 도달일령은 BayesB에서 DEBVexcPA와 DEBVincPA는 각각 0.284~0.305와 0.497~0.510, BayesC에서는 0.284~0.296와 0.498-0.511로 추정되었다. 특히, 등지방두께의 유전체 정확도가 BayesB방법론의 DEBVincPA에서 0.625로 가장 높게 추정되었다. 제주흑돈의 산육형질에 대한 유전적인 개량 속도를 가속화하기 위해 유전체 선발법을 적용하는데 있어 부모 평균을 포함한 DEBVincPA (Deregressed EBV include parents average)의 반응변수를 이용하는 것이 바람직하다고 판단된다.

Some behaviors of pigs that are not expressed in the wild state or are observed in a small minority of individuals after groups of pigs are mixed have been reported to indicate poor welfare. A GWAS analysis was performed by measuring the frequency and duration of the four ethological traits and using the mlma command provided by the genome-wide complex trait analysis (GCTA). The positional candidate genes on significantly identified single nucleotide polymorphism (SNP) markers were identified by using the dbSNP provided by the National Center for Biotechnology Information (NCBI). When the GWAS analysis was applied the 43,565 (of the purebred Landrace population) and 41,700 (of the purebred Yorkshire population) SNP markers, 1, 2, and 1 significant SNP markers were identified for the traits of feeding frequency (LOC110262254), locomotion time (LOC110260361), and locomotion frequency (LOC110260361) of the purebred Landrace population, respectively. Meanwhile, 1 and 7 significant SNP markers were identified for the traits of drinking time (LOC 110260090) and feeding frequency (MAP3K19; LOC110257013; ACMSD; TMEM163; RAB3GAP1) of the purebred Yorkshire population, respectively. The results of this study may suggest that the GWAS analysis of the ethological traits of purebred Landrace and Yorkshire populations could be used to perform a GWAS analysis on non-economic traits, and the results can thus be provided as basic data for GWAS analyses of other non-economic traits in the future.

According to Livestock Inspection Standards, the piglets enter the feedlot at approximately 30 kg, and the inspection starts after the preliminary feeding period. The reason for applying the preliminary feeding period is to select inspection piglets with no diseases after the complete growth of the internal organs until 10 weeks of age. Furthermore, the age of 10 week is the time when the muscle fibers grow to their maximum size and the piglets are prepared for fat deposition at the later fattening period. In the study, a genome-wide association study (GWAS) was performed through the mlma command of the genome-wide complex trait analysis (GCTA) program with 703 purebred Landrace population, and the candidate genes associated with the weight of 10 week were searched. The GWAS identified 3 single nucleotide polymorphism (SNP) markers, which have a significant genome-wide suggestive level, on chromosome 6 (DIAS0002615; p-value=1.62×10-6, MARC0083933; p-value=4.94×10-6, ASGA0028717; p-value=5.40×10-6). The 2 genes (Ubiquitin protein ligase E3 component n-recognin 4; UBR4, WD and tetratricopeptide repeats 1; WDTC1) in which these 3 SNP markers are located are positional candidate genes of the weight of 10 week of the purebred Landrace population. 2 candidate genes have been reported to be associated with fattening. Therefore, the positional candidate genes in this study, UBR4 and WDTC1, are expected to be usable as genes for traits associated with the weight of 10 week weight and fattening through additional experimental research with other population.

돼지의 생시체중은 생존율과 폐사율에 밀접한 관련이 있어 양돈산업에서 자돈 관리와 직결된 중요한 경제형질이다. 본 연구는 Genome-Wide Association Study(GWAS) 분석을 통해 순종 랜드레이스의 생 시체중과 관련된 위치상 후보유전자 탐색을 실시하였다. 생시체중의 유의적 관련 분석 결과, genomewide suggestive level에서 유의성 있는 single nucleotide polymorphism(SNP) marker는 3번 염색체 (ASGA0098921, P=2.41×10-5)와 4번 염색체(H3GA0013451, P=2.47×10-5)에서 각각 1개씩 동정되었다. 이들 SNP marker가 위치한 3개의 유전자(LOC110260055, LOC100156472, LOC100157689)들은 순종 랜드레이스 생시체중의 위치상 후보 유전자이며, 이들 유전자 정보를 이용해서 순종 랜드레이스 생시 체중을 선발할 수 있는 기초 연구 자료가 될 것으로 사료된다.

Alterations affecting the status of robustness and health can bring about physiological changes including hematological parameters in pigs. To identify quantitative trait loci (QTL) associated with 8 hematological phenotypes (one leukocyte trait, six erythrocyte traits, and one platelet trait), we performed a genome-wide association study using the Porcine SNP 60K BeadChip in an intercross population between Landrace and Korean native pigs. A total of 36,740 SNPs from 816 F2 offspring were analysed for each blood related traits after filtering by quality control. Data were analysed genome-wide rapid association using the mixed model and regression (GRAMMAR) approach. A total of 257 significant SNPs (P<1.36x10-6) on SSC3, 6, 8, 13, and 17 were detected for blood related traits in this study. Interestingly, the genomic region between 17.9 and 130 Mb on SSC8 was found to be significantly associated with RBC, MCV, and MCH. Our results include 5 significant SNPs within five candidate genes (KIT, IL15, TXK, ARAP2, and ERG) for hematopoiesis. Further validation of these identified SNPs could give valuable information for understanding the variation of hematological traits in swine.

In the swine industry, growth related traits are important economic traits directly linked to profitability. Representative growth traits include daily gain, back fat thickness, and carcass weight. This study was conducted to search for positional candidate genes associated with the carcass weight through a genome-wide association study(GWAS) using suggestive levels of statistical thresholds in pigs. As a result of the genome-wide analysis of the associations with carcass weight, the single nucleotide polymorphism(SNP) markers with suggestive significance were identified in 1 SNP marker on chromosome 2(ALGA0015365) and 1 SNP marker on chromosome 4(ALGA0023678). We could select positional 2 candidate genes, located close to the SNP markers with suggestive significance levels. The SNP markers in adjacent to the 2 genes(LOC100519538, LOC100737583) may provide basic data regarding the marker-assisted selection for the carcass weight trait in pigs.

Data on primal cuts were collected from 1,829 steers of Hanwoo progeny testing programs, between 2010 and 2015 for the ssGWAS. SNP data were analyzed by using Illumina Bovine 50K Beadchip. The SNP data that matches with phenotype data was 674 animals. As a first step, the genomic estimated breeding value(GEBV) of the loin and rib cuts were estimated, which was used in the estimation of SNP marker effects and their variances related to the traits. Then, the estimated variance explained by each marker was expressed as a proportion to the total genetic variance. Finally, the SNP loci and their significance to any possible QTL were examined. Among the 20 best SNP loci explaining a larger proportion of SNP variance to the total genetic variance for tender loin yield, the region between 12,812,193 ~ 12,922,313bp on BTA 10 harbored a cluster of SNPs that explained about 7.32 to 7.34% of the total genetic variance. For strip loin yield, a peak for higher effects for multiple SNPs was found in BTA24, between 38,158,543 and 38,347,278bp distances, which explained about 8.36 to 8.56% of the observed variance for this trait. For loin yield had relatively smaller effects in terms of the total genetic variance. Therefore, loin yield might be affected by a few loci with moderate effects and many other loci with smaller effects across the genome.

Copy number variation (CNV) is one of structural variation types that shows various numbers of copies in segments of the DNA. This study aimed to identify the association between copy number variation regions (CNVRs) and carcass traits in Hanwoo. We analyzed a total of 571 Hanwoo steers with the four carcass traits (marbling score (MS), backfat thickness (BF), carcass weight (CW), loineye muscle area (LMA)). PennCNV program was used to identify the CNVs and CNVRuler program was used to analyze the association between CNVRs and carcass traits. A total of 1,659 CNVRs were identified in the whole genome of Hanwoo. These 1,659 CNVRs divided into 415 Gain, 1082 Loss and 162 Gain/Loss events. A genome wide association analysis between the CNVRs and the carcass traits was performed using CNVRuler program. The number of significant CNVR at a threshold of p<1×10-4 was 2, 7, 2 and 1 loci for MS, BF, CW and LMA, respectively. We performed gene ontology (GO) analysis for the genes in the significant CNVRs using DAVID. ABCA2 and EDF1 were related to regulation of lipid metabolic process. C8G, TRAF2 and STAB2 were related to immune. CHST11 was related to developmental growth. Our results may provide an important resource for molecular breeding research in Hanwoo.

혈청 내 존재하는 효소 중 Glutamic pyruvic transaminase(GPT)는 근육이나 간세포의 손상에 대한 임상 화학적 지표로 사용 된다. 본 연구는 Landrace와 한국재래돼지의 F2 교잡 축군(N=1,105)에 대해 Porcine SNP 60K beadchip을 사용하여 유전자형 분석을 실시하고, GPT 형질과의 관련성을 검증하기 위해 Genome-Wide Association Study(GWAS)를 수행하였다. F2 교잡축군의 가계구조를 보정한 GWAS를 수행하기 위하여 혼합모형과 회귀분석을 조합한 GRAMMAR방법을 관련성 분석에 사용 하였다. 유의성 있는 SNP 표지들은 Sus scrofa chromosome(SSC) 6, 7, 그리고 13에서 동정되었다. 이들유의성 있는 SNP marker들에 가장 근접한 염색체상 위치의 유전자를 그 유전자의 기능을 고려하여 SSC7에서 2개의 위치후보유전자(BCL11B, AHNAK2)를 선정하였다. Pyrosequencing법을 통하여 이 들유전자 내에 존재하는 4개 SNP 표지들의 유전자형을 분석하여 GPT 형질간의 관련성 분석에 이용하였다. 관련성 분석결과, BCL11B g.267 T>C에서 nominal P=7.23×10-8 과 AHNAK2 g.1439 C>T에서 nominal P=5.64×10-6, g.1736 C>A에서 nominal P=3.51×10-6의 결과를 얻었다. 이 들 중 가장 유의한 결과를 얻은 BCL11B 유전자의 g.267 T>C SNP 표지는 추가 연구를 통하여 혈청 GPT 변이에 영향을 미치는 위치상 후보 유전자 표지로 사용 되어 질 수 있을 것이라 사료되어진다.

돼지의 체장, 체폭, 체중 등의 연속적인 변이를 가지는 양적형질에 속하는 형질인 성장형질은 양돈업에 있어서 생산성과 수익성에 직결된 중요한 경제 형질이다. 성장형질로는 일당증체량, 등지방두께, 등심단면적 및 도체품질 등이 있으며, 그중에서 등심단면적과 관련이 있는 후보 유전자를 Genome-wide 수준에서 선발하기 위하여 Illumina 사의 Porcine SNP 60K chip을 이용하여 순종 Landrace 집단(수컷 : 50두, 암컷 : 440두)을 분석하였다. Plink program을 이용하여 filtering 과정을 거쳐 최종적으로 31,960개의 SNP marker를 선별하였으며, Genome-wide 임계수준을 bonferroni correction (i.e.1/31957=3.12×10-5)을 이용해서 결정했을 때, SSC16에서 유의성 있는 4개의 SNP marker들을 발견하였다. 이 중 가장 유의성 있는 SNP marker인 DRGA0016148(P=1.38×10-5)와 근접한 후보유전자로 PDE4D를 선정하였고, PDE4D에서 2개(g.9870 T>C, g3976 C>T)의 SNP를 탐색하였다. 본 연구에서는 Genome-wide association study (GWAS)를 이용하여 등심단면적과 관련성이 있는 SNP를 선발하여, 등심단면적과 후보유전자 PDE4D와의 관련성을 규명하고자 연구를 실시하였으나, PDE4D g.9870 T>C 에서는 Hardy-weinberg equilibrium P-value 0.7581로 음의 상관관계를 나타내었으며, PDE4D g.3976 C>T에서는 모두 호모타입이 확인되었다.

본 연구는 농촌진흥청 국립축산과학원에서 사육중인 제주재래돼지와 랜드레이스의 상호교차교배를 통해 생산된 417두의 F2집단을 대상으로 성장형질(생시체중, 3주령 체중, 10주령 체중, 20주령 체중)을 측정하고, 개체별 혈액으로부터 Illumina Porcine SNP 60k BeadChip을 이용하여 유전자형 분석을 실시하여 성장형질과 유전체 전장의 단일염기다형의 유전자형 간에 연관성을 알아보았다. 단일연기다형의 유전자형 분석은 돼지의 성염색체를 제외한 18개의 상염색체 내에 나타난 52,574개의 SNP표지인자 중다형성이 나타나지 않은 7,564개의 표지인자, 모든 개체에서 이형으로 나타난 47개 표지인자 및 결측률이 10 % 이상인 1,830개의 표지인자가 나타나 분석에 앞서 사전 제거를 실시하였으며, 남은 44,133개의 표지인자를 체중형질과 표지인자간 연관성 분석하는데 이용하였다. 체중에 영향하는 고정효과에 대해 일반선형모형을 설정하여 사전 보정을 실시하였으며, 여기서 얻어진 잔차값을 이용하여 표지인자와 월령별 체중간의 연관성 분석을 실시하였다. 분석결과 전장의 유전체 정보 중 통계적 판단의 오류를 고려하여 연관성이 강한(p <10-6)표지인자가 생시(BWB), 3주령(BW3), 10주령(BW10) 및 20주령(BW20) 체중에서 각각 657개, 846개, 49개, 122개로 추정되었다. 생시와 3주령 체중에 공통으로 유의적 영향을 하는 표지인자가 286개로 나타났으며, BWB와 BW10에서 5개, BWB와 BW20에서 8개, BW3와 BW10에서 13개, BW3과 BW20에서 11개, BW10과 BW20에서 1개로 나타났다. 또한 염색체별 성장형질에 영향하는 표지인자의 분포를 조사한 결과, 주령별 체중에 영향하는 표지인자는 전장의 유전체에 고르게 분포하는 것으로 조사되었으며, 특히 생시 및 3주령 체중에 영향하는 표지인자는 특정 염색체(SSC9)에서 고도의 통계적 유의차(p <10-15)를 나타내는 유전자 좌위가 있는 것으로 추정되었다.

Objective of this study was to investigate the difference of cadmium (Cd) levels in rice grains from non-polluted fields and to define the gene associated with Cd uptake for producing safety food. Cd was analyzed by Inductively Coupled Plasma Mass Spectrometer (ICP-MS). The average concentration of Cd in rice grains was 0.943 μg/kg and Cd levels ranged from 0.050 to 5.699 μg/kg. Genome-Wide Association study (GWAS) based on phenotype data for Cd levels was performed. However, results of GWAS were affected by subpopulation structure and caused false positive. Therefore, GWAS for rice ecotypes (temperate Japonica, tropical Japonica, Indica, Aus, Aromatic, and Admixture) was performed to minimize false positive. GWAS results showed that Os01g0611300, Os01g0611900, Os01g0611950, Os01g0612000, Os01g0612200, Os11g0444400, Os11g0444700, Os11g0444800, and Os11g0444900 genes have significant correlation with Cd levels in rice grains. The sequences of these genes were compared to sequence positions of each other gene (haplotype analysis). According to the results of haplotype analysis, Cd levels of non-synonymous group were higher than other groups and sequence of non-synonymous group was similar to that of Indica. These results were corresponding to the previous research result that Cd levels of Indica were higher than Japonica. Therefore, candidate genes detected through GWAS need to be examined by knock-out or cross breeding.

The Cucurbitaceae (Cucurbits) family has 825 species in 118 genera, predominantly distributed in tropical and subtropical regions. Major cucurbit crops including cucumber (Cucumis sativa), melon (Cucumis melo), watermelon (Citrullus lanatus), and squash/pumpkin (Cucumis pepo) are important in the human diet and the rural economy. In recent years, large amount of genome information has been analyzed and reported in major cucurbit crops, such as cucumber, melon, and watermelon. To construct high quality reference genome sequence of Korean melon (Chamoe), genomic and transcriptomic sequence data were generated from Korean native (Gotgam) and elite (SW3) Chamoe inbred line using Illumina HiSeq2000 platform. In case of genome analysis, 4,773 scaffolds covering 98% of Gotgam Chamoe were assembled through de novo genome assembly and reference-based assembly. Large number of simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were detected between two inbred lines and these markers were used for construction of genetic maps and discrimination of cultivars or species. In addition, genome sequence of other Chamoe and melon including Chang Bougi, Sakata’s Sweet, Prescott Fond Blanc and Banana melon will be constructed by de novo genome analysis. Genetic markers of these will also be detected and used for marker-assisted breeding and further analysis to investigate major traits of Chamoe, fruit color and flesh color. In conclusion, the newly constructed reference genome will provide genome information for comparative genomics and breeding of other cucurbit crops.

GWAS (Genome-wide association study) provides a useful to associate phenotypic variation to genetic variation. It has emerged as a powerful approach for identifying genes underlying complex diseases or morphological traits at an unprecedented rate. Despite benefits, there are only a few examples applied in crop plants due to lack of effective genotyping techniques and well prepared resources for developing high density haplotype maps. In this study, 350 core accessions selected from almost 5,000 Capsicum accessions were used for GWAS. We are planning to construct a high-density haplotype map using GBS platform and perform GWAS for various agronomic traits including fruit traits and metabolites related to pungency to identify genes controlling the traits. These results will not only provide a list of candidate loci but also a powerful tools for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits.

Salt toxicity is the major factor limiting crop productivity in saline soils. Rice is an important staple food crop of nearly half of the world population and is well known to be a salt sensitive crop. The completion and enhanced annotations of rice genome sequence has provided the opportunity to study functional genomics of rice. With the rapid development of the biotechnology techniques, we can use more accurate and reliable methods to study the mechanism and function in different stress conditions. In present study, 295 rice accessions of diverse origin were re-sequenced and used for genome-wide association study (GWAS) with several germination-related traits, including germination percentage (GP), germination energy (GE), germination rate (GR), germination index (GI), salt tolerance index (STI) in salt tolerant germination stage. Phenotyping of the rice accessions were carried out at 200mM NaCl to screen salt tolerance levels. GWAS was applied to detect the associated genes related to salt tolerance in rice germination stage. Variations and haplotypes of the associated genes were detected and correlation between the phenotypes and genotypes were validated using qRT-PCR.

Preharvest sprouting resistance (PHS) causes the reduction of grain yield and also affects the quality of grains, resulting significant economic losses. PHS and its related traits were evaluated and observed in wide range among the 137 diverse rice accessions. To mine the associated signals for PHS resistance, genome wide association study (GWAS) was performed using phenotype data and whole genome resequencing data of 137 diverse rice accessions. This study not only could detect the previously identified dormancy and PHS associated genes but also explore the new candidate genes associated with the PHS and related traits. An example of them is seed dormancy 4 (Sdr4) gene which was found to be associated with germination % at day 14 (D14). This study provided the potential associated candidate genes which might be very useful to improve the PHS resistance in future rice breeding.

One of the biotic stresses in rice production is rice blast disease caused by Magnaporthe oryzae, which is one of the most destructive fungal diseases in rice. We outlined an approach towards genome wide association study for the blast disease resistance in rice. In total, 295 rice accessions including 137 Heuristic Set accessions (HS) and 158 Korean Bred varieties (KB) were screened for the rice blast disease resistance. Firstly, Magnaporthe oryzae were inoculated to the rice seedlings of two weeks after germinations. Then, evaluation of the disease symptoms and checking the crossing point (CP) value were conducted one week after inoculation. To quantify the CP value, real-time polymerase chain reaction (PCR) was employed in combination with the primer pair and Taqman probe specific to Magnaporthe oryzae HYDROPHOBIN class 1 (MHP1) which is an indispensable unigene encoding HYDROPHOBIN for normal virulence expression. Based on these CP values from the PCR reactions containing a series of increasing concentration of cloned amplicon or fungal genomic DNA, correlation among the template’s copy number or its amount and amplification pattern was calculated. Reliability of this equation was further confirmed using the DNA samples from the rice leaves infected with compatible or incompatible strains of M. oryzae. These steps are still being undertaken, and after the complete process of disease resistance phenotyping for the whole population containing 295 accessions, GWAS will be performed to examine the associated genes involving in blast resistance mechanism using the whole genome resequencing data of 295 accessions. This approach would be a useful technique for identifying genetic loci responsible for natural variation in rice blast disease resistance and ultimately, new R genes which can improve the blast resistance in rice.

AGenome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in rice. With the fast developed next-generation sequencing technology, it is possible for people to carry out GWAS by phenotyping different traits. However, how to make full use of huge data, abandon unnecessary data, and solve the problem of data application effectively seems still an obstacle for many researchers. Taking the case of whole-genome resequencing of Korean authentic rice core set, here we present a general technological path of GWAS including: 1) a schematic view of sequencing-based GWAS in rice; 2) a user-friendly and interactive web application for GWAS in rice by the aid of experience from Arabidopsis; 3) Haplotype and association analysis of candidate genes in a certain mechanism pathway, giving 10 starch synthesis genes as example; and 4) functional validation by Trans- and Mata-Omics analysis.

Genome-wide association study (GWAS) is a very powerful method to identify the natural allelic variation present in crop plants causing variation to economically important traits. The recent advances in high throughput genotyping and sequencing technology supplemented greatly to GWAS. Taking this advantage, we selected a total of 382 Chinese cabbage inbred lines for GWAS study. The selected inbred lines are being sequenced using next generation sequencing technology to develop genome wide gene specific single nucleotide polymorphism markers. The morphological and quality traits data were taken from field grown inbred lines. The phenotype and genotype association study will be done with more environmental grown data’s and developed SNP. At the end of this project, gene specific SNP markers will be developed for Chinese cabbage breeding for morphological and quality traits.