유전체재해석(resequencing)에 의한 통일형 벼 품종간 단일염기서열변이(SNP) 탐색
Genome-wide Detection of SNPs between Two Korean Tongil-Type Rice Varieties
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벼멸구 저항성 통일형 벼 품종인 가야벼와 벼멸구 감수성통일형 벼 품종인 태백벼와의 교배 후대집단을 이용하여 가야벼의 저항성 유전자를 mapping하기 위한 1단계 연구로 가야벼와태백벼를 resequencing하였다. 가야벼에서 약 18.5X109 bp의염기서열과, 태백벼에서 약 17.9X109 bp의 염기서열이 생산되었다. quality trimming을 거쳐 Nipponbare 표준유전체서열에mapping한 결과 가야벼에서 약 9.3X109 bp의 염기서열이 mapping되어 약 25.0X의 mapping depth를 나타내었으며, 태백벼에서 약 9.5X109 bp의 염기서열이 mapping되어 약 25.5X의mapping depth를 나타내었다. 가야벼-Nipponbare 비교에서 총1,585,880 개의 SNP가 탐지되었으며, 태백벼-Nipponbare 비교에서 총 1,416,898 개의 SNP가 탐지되었다. 가야벼와 태백벼간에는 총 284,501개의 SNP가 탐지되었다. 가야벼와 태백벼간SNP들 가운데, 21.2%의 SNP들이 유전자 영역에 있었고, 78.8%의 SNP가 비유전자 영역에 있었다. 유전자 영역에 있는SNP들 가운데 단백질 코딩 영역(CDS)에 있는 SNP들은 15,924 개이었으며, 이들 중 synonymous SNP들은 47.3%를 차지하였고, non-synonymous SNP들은 52.7%를 차지하였다. 제한효소인식부위에 있는 SNP들을 대상으로 CAPS 마커들을 디자인하여 모본들간 다형성(polymorphism)을 검정한 결과, 20개의 마커들 가운데 19개마커들이 모본들간에 다형성을 보였고 1개의마커만이 다형성을 보이지 않았다. 이 연구결과를 토대로 가야벼와 태백벼간 교배후대집단을 이용하여 벼멸구저항성 유전자를mapping 하기에 충분한 마커들을 개발할 수 있을 것이다.
Abstract
As a first step of mapping genes conferring resistance to the brown planthopper, Nilaparvata lugens Stål, in Gayabyeo using a population derived from a cross between Gayabyeo and Taebaegbyeo, we performed the whole genome resequencing of these two Tongil-type rice varieties. The amount of raw sequence data was about 18.5X109 bp and 17.9X109 bp in Gayabyeo and Taebaegbyeo, respectively. After quality trimming and read mapping onto Nipponbare reference genome sequence, 9.3X109 bp was mapped in Gayabyeo with mapping depth of 25.0X, and 9.5X109 bp was mapped in Taebaegbyeo with mapping depth of 25.5X. Between Gayabyeo and Nipponbare, 1,585,880 SNPs were detected, while 1,416,898 SNPs were detected between Taebaegbyeo and Nipponbare. Between Gayabyeo and Taebaegbyeo, 284,501 SNPs were detected. Among the SNPs between Gayabyeo and Taebaegbyeo, 21.2% were in genic region and 78.8% were in intergenic region. In CDS region, 15,924 SNPs were detected, among which synonymous SNPs covered 47.3% and non-synonymous SNPs covered 52.7%. We designed Cleaved Amplified Polymorphic Sequences (CAPS) markers with SNPs in the restriction enzyme recognition sites, and 20 CAPS markers were tested. Of the 20 markers, 19 markers showed polymorphism and one marker showed monomorphism between Gayabyeo and Taebaegbyeo. It is expected that sufficient DNA markers for mapping genes with a population derived from a cross between Gayabyeo and Taebaegbyeo can be developed based on the results of the study.
참고문헌 (19)
- Abe A, "Genome sequencing reveals agronomically important loci in rice using MutMap", Nat Biotechnol, 30, pp.174~178 (2012)
- Alexandrov N, "SNP-Seek database of SNPs derived from 3000 rice genomes", Nucleic Acids Res, 43, pp.D1023~1027 (2015)
- Arai-Kichise Y, "Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups", PLoS One, 9, pp.e86312~ (2014)
- Barabaschi D, "Next generation breeding", Plant Sci, 242, pp.3~13 (2016)
- Gao ZY, "Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences", Proc Natl Acad Sci U S A, 110, pp.14492~14497 (2013)
- Guo L, "Application of resequencing to rice genomics, functional genomics and evolutionary analysis", Rice (N Y), 7, pp.4~ (2014)
- Huang X, "A map of rice genome variation reveals the origin of cultivated rice", Nature, 490, pp.497~501 (2012)
- 정인선, "Genome-wide Detection of DNA Polymorphisms Between Two Korean Japonica Rice Varieties", Plant Breeding and Biotechnology, 3(3), pp.208~215 (2015), 한국육종학회[DOI]
- Jeong IS, "SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing", Rice (N Y), 6, pp.6~ (2013)
- Kim B, "Defining the genome structure of 'Tongil' rice, an important cultivar in the Korean "Green Revolution"", Rice (N Y), 7, pp.22~ (2014)
- Mehra P, "Genome-wide DNA polymorphisms in low Phosphate tolerant and sensitive rice genotypes", Sci Rep, 5, pp.13090~ (2015)
- Perez-de-Castro AM, "Application of genomic tools in plant breeding", Curr Genomics, 13, pp.179~195 (2012)
- Seo BY, "Planthoppers: new threats to the sustainability of intensive rice production systems in Asia", pp.303~314 (2009), International Rice Research Institute
- Takagi H, "QTL-seq : rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations", Plant J, 74, pp.174~183 (2013)
- Takagi H, "MutMap-Gap : whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii", New Phytol, 200, pp.276~283 (2013)
- Wang L, "Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines", Theor Appl Genet, 122, pp.327~340 (2011)
- Xie W, "Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing", Proc Natl Acad Sci U S A, 107, pp.10578~10583 (2010)
- Yamamoto T, "Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms", BMC Genomics, 11, pp.267~ (2010)
- Yano K, "Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice", Nat Genet, 48, pp.927~934 (2016)