본 연구는 국내에서 육성 또는 도입된 재배국화 85점을 4 개의 분자마커(SSR marker)를 이용해 유전자형을 분석하여 품 종판별에 대한 활용성을 검토하고, 유전관계를 분석하여 국화 품종 육성에 필요한 기초자료로 제공하기위해 본 실험을 수행 하였으며 결과를 요약하면 다음과 같다 1. 85점의 재배국화에 대하여 4개의 SSR 마커로 총 95개의 대립인자가 관찰되었다. 대립인자의 수는 11개 (KNUCRY-35) 에서 34개(KNUCRY-84)로 비교적 다양하게 나타났으며, 평균 대립인자 수는 23.8개였다. 유전적 다양성을 나타내는 gene diversity (GD)와 PIC 값의 범위는 0.81-0.89, 0.79-0.89로 관 찰되었다 2. 국화의 이용에 따라 재배국화를 관상국, 스탠다드국, 스 프레이국, 분화국, 화단국으로 그룹을 나눠 집단간의 유전적 다양성을 분석하였다. 각 집단의 평균 expected heterozygosity (H)와 PIC 값을 비교하였을 때 화단국이 0.25와 0.42로 가장 낮 게 나타났고 스프레이국이 0.80과 0.79로 가장 높게 나타났다. 3. SSR마커 4개 중 allele수, 특이적 allele 수, gene diversity 및 PIC 값이 높은 마커 KNUCRY-84, KNUCRY-98, KNUCRY- 77, KNUCRY-35를 단계별로 이용하여 단계별 phylogenetic tree를 작성하여 재배국화 85점을 모두 판별하였다.

In rice (Oryza sativa L.), there is a diversity in flowering time that is strictly genetically regulated. The floral transition from vegetative to reproductive development is a very important step in the life cycle of a flowering plant. Although the genetic pathway for short-day flowering in rice is relatively well understood, the naturally occurring molecular mechanisms underlying flowering time diversity of the cultivated rice are still not clear. Resequencing of 295 rice accessions including 137 HS and 158 KB rice accessions, was recently finished with an average of approximately 10x depth and > 90% coverage. A wide range of variation in flowering time was observed within a diversity research set of 295 accessions ranging from 28 to 72 days. GWAS was performed using the resequencing data to investigate the candidate genes associated with flowering time in rice. Our GWAS result suggests that two SNPs in the promoter or 3’ UTR of the ‘Arabidopsis CO’ homolog FBH1 are potentially associated with early flowering. The new SNPs found in the FBH1 locus would be useful in developing markers to screen the varieties with early flowering time in the future molecular breeding.

Rice is the most important staple food crop of almost half of the world`s population. In rice, seed longevity is major factor for production and storage potential of seeds. But it is faced with grain degradation and loss of seed viability. Lipoxygenases(LOX) are a family of enzymes related to the seed longevity. LOX activity in rice grain is present in a bran-milling fraction. It is also observed that rice embryos contains three isozymes activites, Lox1, Lox2 and Lox3. Among those, the Lox3 isozyme is known as the major component in the embryonic tissue. In this study, genetic structure variability of three seed longevity related genes, Lox1, Lox2 and Lox3 were examined by using whole-genome resequencing data of 137 accessions of rice core set. The new SNPs and InDels in the exon regions identified through haplotyping analysis would be useful to develop new varieties with improved storage ability of rice in the future molecular breeding.

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.

Direct seeding of rice is increasingly being practiced in both rainfed and irrigated areas because of labor shortage for transplanting and opportunities for crop intensification. However, slow seed germination and delayed seedling establishment will become a major problem for rice production in flood-prone lowland areas as sowing method shifts from transplanting to direct seeding. Identification of anoxia-induced ethylene response factors is suggestive because genes belonging to this gene family play a crucial role in rice tolerance to submergence. In this study, genetic structure variability of three AG related genes, Sub1 (Sub1A, Sub1B, Sub1C), Sub2 (OsGAPPH) and Ramy3D were examined by using whole-genome resequencing data of 84 accessions of rice core set. Some new SNPs and InDels found in exon part of anaerobic germination related genes in the present study would be useful in developing markers to identify the submergence resistant varieties in the future molecular breeding.

Preharvest sprouting (PHS) not only causes reduction of grain yield, but also affects the quality of grains, resulting into significant economic losses. PHS is governed by multiple genes. Little is known about the large genetic variation of preharvest sprouting in rice. In the present study, genetic variations of four PHS genes, OsVP1, Osaba1, Alpha-amylase3D and OsGA20ox1 were studied by using whole-genome resequencing data of 84 accessions of rice core set. A total of haplotype groups; 27, 29, 6 and 14, for OsVP1, Osaba1, Alpha-amylase3D and OsGA20ox1, respectively, were detected among the 84 accessions. Some new SNPs and InDels were found in exon part of PHS related genes were expected to result in amino acid changes following analysis of the genetic code variations, and the germplasm or varieties which are resistant to preharvest sprouting were explored. Based on this step, phenotyping for PHS is ongoing, and the association mapping of PHS will be conducted by using SNPs resulted from the haplotyping data. The present results will be ultimately useful to the molecular breeding for the development of PHS resistant rice cultivars.

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.