본 연구는 벼의 밝혀진 개화 유전자의 정보를 정리하여, 벼 핵심집단의 GWAS분석 및 진화론적 방법에 의해 개화기와 관련된 후보유전자 탐색을 통해 개화에 관련된 유용유전자 확보 및 allele 조합의 신규 분자마커정보를 제공하며, allele marker를 이용한 유전체 육종을 통해 품종육성 및 육종효율을 개선하는데 기초자료로 이용하는데 목적을 두고 있다. 1. 벼 전체 유전체재분석 집단 295점의 유전체 재분석 결과, Sequence read는 42,414,594개이며, ...
본 연구는 벼의 밝혀진 개화 유전자의 정보를 정리하여, 벼 핵심집단의 GWAS분석 및 진화론적 방법에 의해 개화기와 관련된 후보유전자 탐색을 통해 개화에 관련된 유용유전자 확보 및 allele 조합의 신규 분자마커정보를 제공하며, allele marker를 이용한 유전체 육종을 통해 품종육성 및 육종효율을 개선하는데 기초자료로 이용하는데 목적을 두고 있다. 1. 벼 전체 유전체재분석 집단 295점의 유전체 재분석 결과, Sequence read는 42,414,594개이며, Mapping rate는 96.40%로 나타났다. 평균 Coverage는 9.83X이며, SNP의 total 개수는 11,632,676, InDel의 total 개수는 1,285,506으로 나타났다. 2. 벼 전장유전체연관분석(GWAS)은 집단과 집단내 생태형 별로 반복되어 나타나는 -log10(P) 5이상의 높은 유의성을 보이는 후보유전자를 Chromosome 1번에서 Os01g0773350 유전자, Chromosome 6번에서 Os06g0259850, Os06g0259901, Os06g0260000 유전자, Os08g0203350, Os08g0203400 유전자로서, 총 6개의 개화기와 연관된 후보유전자를 선발하였다. 3. 벼 진화론적 연구를 통해 벼 핵심집단 295 점과 Brachypodium distachyon간 10,887 개의 orthologous gene에 대해 MKT 방법을 이용하여 총 68개의 유전자를 선발하였으며, DAVID와 Q-TARO 데이터 베이스를 이용하여 총 3개의 functional한 후보유전자 Os04g0201900, Os08g0159500, Os11g0689300를 선발하였다. Os11g0689300 유전자에 대해 27,993,759bp 의 C/T SNP와의 유의한 association이 확인되었다. Key Words: 개화기, 벼, 이종상동유전자, 전장유전체연관분석, 핵심집단
본 연구는 벼의 밝혀진 개화 유전자의 정보를 정리하여, 벼 핵심집단의 GWAS분석 및 진화론적 방법에 의해 개화기와 관련된 후보유전자 탐색을 통해 개화에 관련된 유용유전자 확보 및 allele 조합의 신규 분자마커정보를 제공하며, allele marker를 이용한 유전체 육종을 통해 품종육성 및 육종효율을 개선하는데 기초자료로 이용하는데 목적을 두고 있다. 1. 벼 전체 유전체재분석 집단 295점의 유전체 재분석 결과, Sequence read는 42,414,594개이며, Mapping rate는 96.40%로 나타났다. 평균 Coverage는 9.83X이며, SNP의 total 개수는 11,632,676, InDel의 total 개수는 1,285,506으로 나타났다. 2. 벼 전장유전체연관분석(GWAS)은 집단과 집단내 생태형 별로 반복되어 나타나는 -log10(P) 5이상의 높은 유의성을 보이는 후보유전자를 Chromosome 1번에서 Os01g0773350 유전자, Chromosome 6번에서 Os06g0259850, Os06g0259901, Os06g0260000 유전자, Os08g0203350, Os08g0203400 유전자로서, 총 6개의 개화기와 연관된 후보유전자를 선발하였다. 3. 벼 진화론적 연구를 통해 벼 핵심집단 295 점과 Brachypodium distachyon간 10,887 개의 orthologous gene에 대해 MKT 방법을 이용하여 총 68개의 유전자를 선발하였으며, DAVID와 Q-TARO 데이터 베이스를 이용하여 총 3개의 functional한 후보유전자 Os04g0201900, Os08g0159500, Os11g0689300를 선발하였다. Os11g0689300 유전자에 대해 27,993,759bp 의 C/T SNP와의 유의한 association이 확인되었다. Key Words: 개화기, 벼, 이종상동유전자, 전장유전체연관분석, 핵심집단
This dissertation is a series of work mainly focus on identifying candidate genes and alleles associated with rice flowering time using GWAS (genome-wide association study) and evolutionary study. A Korean authentic set of 295 rice accessions, which including a core set with 137 accessions, was rese...
This dissertation is a series of work mainly focus on identifying candidate genes and alleles associated with rice flowering time using GWAS (genome-wide association study) and evolutionary study. A Korean authentic set of 295 rice accessions, which including a core set with 137 accessions, was resequenced, and the SNPs/Indels generated were used for GWAS in rice flowering time. The genomic data and the candidate genes, as well as the natural variations in our rice collections will be used as an elementary research material to improve breeding efficiency on developing new varieties and also useful for the further rice genomics and functional studies The main results and conclusions are as follow: 1. By using whole genome re-sequencing, total 42,414,594 sequence reads from 295 rice core population were generated, along with 11,632,676 SNPs and 1,285,506 InDels were identified with 96.40% mapping rate and ~9.83x of mean coverage. 2. Total 6 genes, Os01g0773350 in chromosome 1, Os06g0259850, Os06g0259901, Os06g0260000, Os08g0203350 and Os08g0203400 in chromosome 6 were characterized that were significantly associated with flowering time in the GWAS with -log10 (P-value) > more than 5. 3. Total 68 genes were positively selected form the McDonald-Kreitman test, which were investigated using 10,887 orthologous genes between Rice (Oryza sativa L.) and Brachypodium distachyon (outgroup) based on different phenotypic groups in 295 rice core population. Three groups which represented the long flowering time (group 1), medium flowering time (group 2) and short flowering time (group 3) were separated based on the phenotype and each group was examined with the outgroup for MKT. Three candidate genes (Os04g0201900, Os08g0159500, Os11g0689300) were functionally annotated by DAVID and Q-TARO database, which shown fast evolutionary process . In addition, a C/T SNP at Os11g0689300 was significantly associated with flowering time. Key words：Orthologues, McDonald-Kreitman Test, Oryza sativa, Flowering Time, Evolution
This dissertation is a series of work mainly focus on identifying candidate genes and alleles associated with rice flowering time using GWAS (genome-wide association study) and evolutionary study. A Korean authentic set of 295 rice accessions, which including a core set with 137 accessions, was resequenced, and the SNPs/Indels generated were used for GWAS in rice flowering time. The genomic data and the candidate genes, as well as the natural variations in our rice collections will be used as an elementary research material to improve breeding efficiency on developing new varieties and also useful for the further rice genomics and functional studies The main results and conclusions are as follow: 1. By using whole genome re-sequencing, total 42,414,594 sequence reads from 295 rice core population were generated, along with 11,632,676 SNPs and 1,285,506 InDels were identified with 96.40% mapping rate and ~9.83x of mean coverage. 2. Total 6 genes, Os01g0773350 in chromosome 1, Os06g0259850, Os06g0259901, Os06g0260000, Os08g0203350 and Os08g0203400 in chromosome 6 were characterized that were significantly associated with flowering time in the GWAS with -log10 (P-value) > more than 5. 3. Total 68 genes were positively selected form the McDonald-Kreitman test, which were investigated using 10,887 orthologous genes between Rice (Oryza sativa L.) and Brachypodium distachyon (outgroup) based on different phenotypic groups in 295 rice core population. Three groups which represented the long flowering time (group 1), medium flowering time (group 2) and short flowering time (group 3) were separated based on the phenotype and each group was examined with the outgroup for MKT. Three candidate genes (Os04g0201900, Os08g0159500, Os11g0689300) were functionally annotated by DAVID and Q-TARO database, which shown fast evolutionary process . In addition, a C/T SNP at Os11g0689300 was significantly associated with flowering time. Key words：Orthologues, McDonald-Kreitman Test, Oryza sativa, Flowering Time, Evolution
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