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

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.

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.

Magnesium is important not only for the growth of rice itself, but also as an essential micronutrient component of half of the world population who are supported by rice. Here, we performed genome-wide association study (GWAS) with high-resolution density SNPs to identify natural allelic variation in Mg2+ increase from rice set, which is derived from a total 24,368 rice germplasms. The range of the concentration and distribution of Mg2+ in 295 core accessions of brown rice grain were wide, from 18.17mg/L to 57.11mg/L, with mean 39.71mg/L. In particular, GWAS result shows that the high peak found on chromosomes 3 and 11. The new natural variants identified through haplotyping analysis would be useful to develop new rice varieties with improved storage ability of the valuable mineral through the future molecular 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.

In order to breakthrough upcoming challenges for the food production, the efficient use of rice germplasm would be a indispensible. These rice germplasm, adapted from diverse eco-systems, are undiscovered treasures for rice breeders/researchers, potentially providing a broad array of useful alleles that enrich gene pools of current cultivated rice varieties. Although growing ex-situ conservation efforts are an important for preserving diverse rice genetic resources, the activity on finding the novel and favorable genetic variants from the vast genebank collection is greatly challenging, requiring extensive screening processes. Therefore, rice core collection is a powerful solution to accelerate utilizations of the exotic germplasm of the entire population. In addition, The application of whole genome re-sequencing technology would establish a potent platform for fast forward genetic study, such as genome wide association study (GWAS). The GWAS has been implemented to efficiently identify candidate genes related to various useful agricultural traits in many crop species including rice. Given the significant associations between genetic variations and phenotypic diversity does not require prior knowledge, GWAS using high genome coverage of SNP markers provides a genomics platform to dissect previously unknown adaptive or other useful genetic variation accumulated in plant germplasm resources over the times. Once pinpointing candidate genes, GWAS allows informed choice of parents for QTL analysis based on the haplotype information, along with suggesting targets for following mutagenesis and transgenics. Here, we are to report our current achievements and perspectives from GWAS and post-GWAS undertaken to dissect and exploit useful alleles underlying many agricultural traits from Rice core set, including PHS (Pre-Harvest Sprouting), salt tolerance and disease resistance and so forth. Also, we will introduce the integrated Omics based GWAS case study using transcriptomes, proteomes, metabolomes and ionomes of our rice core set.

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.