초록 ▼

Ⅳ. 연구개발결과
□ 벼 핵심집단 및 육성품종 168점에 대한 비교유전체 분석 (평균 9X)
▪ 핵심집단 및 육성품종의 개체별 염기서열(평균 40.5 million reads) 분석 완료
▪ 총 10 million (M) 이상 SNP 및 1.1 M의 InDel의 DNA 마커정보 대량확보
▪ 자포니카 및 인디카 특이 SNP의 확보 및 염색체간 분포 확인하고, 한국 고유 핵심집단의 다양성, 근연관계 및 집단구조(Population Structure)의 분석에 적용함
▪ 핵심집단에 포함된 재래종 벼와 잡초성 벼

Ⅳ. 연구개발결과
□ 벼 핵심집단 및 육성품종 168점에 대한 비교유전체 분석 (평균 9X)
▪ 핵심집단 및 육성품종의 개체별 염기서열(평균 40.5 million reads) 분석 완료
▪ 총 10 million (M) 이상 SNP 및 1.1 M의 InDel의 DNA 마커정보 대량확보
▪ 자포니카 및 인디카 특이 SNP의 확보 및 염색체간 분포 확인하고, 한국 고유 핵심집단의 다양성, 근연관계 및 집단구조(Population Structure)의 분석에 적용함
▪ 핵심집단에 포함된 재래종 벼와 잡초성 벼는 온대자포니카 생태형 이외에 Aus생태형과 열대자포니카 생태형 등 다양한 생태형에 포함되어 있음이 처음으로 밝혀짐
□ GAPIT 프로그램을 이용한 GWAS(전장유전체연관분석) 분석 기반구축 및 분석 매뉴얼 작성
▪ GWAS분석으로 Vitamin(Vit) E, 향, 출수기, 전분생합성 관련 표현형과 연관된 SNP 및 후보 유전자 탐색
▪ 향미 관련 유용유전자원 확보를 위한 GC-MS 등 정밀 표현형 분석 시스템 기반구축
□ 후보 유전자 Functional Hyplotype 분석을 통한 Vitamin E, 향, 출수기, 전분생합성 관련 유전자 변이 탐색 및 비교 유전체 정보를 활용한 분자마커 개발
□ 핵심집단/육성종 벼 유전체 염기서열 기반 대립유전자 SNP정보 DB 구축 및 생물정보분석 지원
▪ CCGRB(Center for Crop Genetic Resource and Breeding, http://ccgrb.kongju.ac.kr)신설
▪ 대용량 유전체 정보 활용을 위한 핵심집단작성프로그램 POWER CORE 64bit 버전 업데이트

Abstract ▼

Rice (Oryza sativa L.) is one of the most important staple crops in the world, providing main energy source for more than half of the world’s population. It is even closely associated with economic and political stability of many developing countries, in Asia and Africa. Moreover, amount of land sui

Rice (Oryza sativa L.) is one of the most important staple crops in the world, providing main energy source for more than half of the world’s population. It is even closely associated with economic and political stability of many developing countries, in Asia and Africa. Moreover, amount of land suitable for the agriculture is currently decreasing due to a variety factors such as rapid climate changes and industrializations, while rice eating human populations keeps growing. To meet the nutritional and socio-economic demands worldwide, dedicated efforts in developing superior rice varieties keep reinforced by accumulating and combining beneficial alleles from as vast rice genetic resources as much as possible.
Rice germplasm collections continue to grow in number and size around the world. As a good example, International Rice Research Institute(IRRI) holds more than 11,000 accessions in the collections. However maintaining and screening such massive resources remain as a great challenge. Thus, developing core collections has been proposed to simplify the germplasm conservations and their effective utilizations.
The advent of draft genome sequences of two rice subspecies, O. sativa ssp. japonica (Nipponbare) and O. sativa, along with subsequent completion of high quality indica, japonica and aus reference genomes, greatly accelerated rice functional genomics research. In addition, those reference sequences also serve as frameworks for the whole genome resequencing, which was accomplished by alignments of short sequence reads produced by the next generation sequencing (NGS) technology. Recently, the application of the genome resequencing are rapidly expanding toward various rice natural resources, providing the crop research community with unprecedented resolution and scale as to the genetic variations and relevant functional diversity, accumulated in the rice germplasm.
We previously developed the rice min core sets out of total 25,604 rice germplasms deposited in Korean genebank of Rural Development Administration (RDA). The subset of 25,604 rice accession was screened based on passport data, forming 4046 rice composite collection. The allelic diversity of the composite collection was assessed using 15 neutral SSR markers distributed throughout the genome. The heuristic algorithm was then implemented to narrow down to 166 accessions, which supposedly retains genetic diversity of the entire collection with minimum redundancy.
Here we reports the whole genome resequencing of the 137 rice min core set along with 31 Korean breeding varieties, which are implemented by the Illumina highseq 2500 platform with 9.25X depth. Comparison of the sequences with the Nipponbare reference genome yielded more than 11 million(M) SNPs and ~1 M INDEL. Phylogenetic and population analysis using 2,046,529 of high quality SNPs successfully assigned the rice accessions to the relevant rice subgroups, suggesting that those SNPs captures evolutionary signatures existing rice subpopulations, which is useful for future rice breeding, functional and evolutionary studies in the post-genomic era