NGS 기술 활용 돌연변이체 해석 및 연구현황
Current status and prospects to identify mutations responsible for mutant phenotypes by using NGS technology
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초록
NGS 기술은 전체 게놈 시퀀싱 및 reference 게놈에 alignment 에 의해 돌연변이 표현형에 관련된 돌연변이 식별에 이용한다. 그러나 품종 및 계통들을 resequence 하였을 경우기존의 reference 게놈에 구조적 변이가 보이며, reference 와 맞지 않는 게놈지역에서 돌연변이들은 단순한 alignment 로 찾을 수 없다. 본 리뷰에서는 NGS 기술을 이용하여돌연변이체로부터 변이 관련 유전자를 식별하는 MutMap, MutMap-Gap 및 MutMap+ 방법을 기술하였고 지금까지의연구현황에 대해 기술하였다. 아울러 이들 방법은 nucleotidebinding site-leucine rich repeat (NBS-LRR) 그룹들의 병 저항성 유전자와 같이 구조적 변이를 가진 유전자를 분리하는 등 유용성에 대해 고찰하였다.
Abstract
Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole- genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions absent in the reference cannot be identified by simple alignment. In this review, we report the current status and prospects in identification of genes in mutant phenotypes, by using the methods MutMap, MutMap-Gap, and MutMap+. These methods delineate a candidate region harboring a mutation of interest, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. These methods are likely to prove useful for cloning genes that exhibit significant structural variations, such as disease resistance genes of the nucleotide- binding site-leucine rich repeat (NBS-LRR) class.
참고문헌 (24)
- Abe A, "Genome sequencing reveals gronomically important loci in rice using MutMap", Nature Biotechnology, 30, pp.174~178 (2012)
- Altshule D, "Genetic mapping in human disease", Science, 322(5903), pp.881~888 (2008)
- Austin RS, "Next-generation mapping of Arabidopsis genes", Plant Journal, 67, pp.715~725 (2011)
- Baxter SW, "Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism", PLoS One, 6, pp.e19315~ (2011)
- Boetzer M, "Scaffolding pre-assembled contigs using SSPACE", Bioinformatics, 27, pp.578~579 (2011)
- Clark RM, "Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana", Science, 317, pp.338~342 (2007)
- Elshir RJ, "A robust, simple genotyping-bysequencing (GBS) approach for high diversity species", PLoS One, 6, pp.e19379~ (2011)
- Fekih R, "MutMap+: genetic mapping and mutant identification without crossing in rice", PLoS One, 8, pp.e68529~ (2013)
- Harper AL, "Associative transcriptomics of traits in the polyploid crop species Brassica napus", Nature Biotechnol, 30, pp.798~802 (2012)
- Huang X, "Genome-wide association studies of 14 agronomic traits in rice landraces", Nature Genet, 42, pp.961~967 (2010)
- Hunter KW, "The future of mouse QTL mapping to diagnose disease in mice in the age of wholegenome association studies", Annu. Rev. Genet, 42, pp.131~141 (2008)
- Li H, "Fast and accurate short read alignment with Burrows-Wheeler transform", Bioinformatics, 25, pp.1754~1760 (2009)
- Li H, "The sequence alignment", map format and samtools, 2009, pp.25, 2078~2079
- Lister R, "Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond", Curr. Opin. Plant Biol, 12, pp.107~118 (2009)
- Morishige DT, "Digital genotyping of sorghum-a diverse plant species with a large repeat-rich genome", BMC Genomics, 14, pp.448~ (2013)
- Lupski JR, "Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy", N. Engl. J. Med, 362, pp.1181~1191 (2010)
- Takagi H, "MutMap-Gap: whole-genome resequencing of mutant F2progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii", New Phytol, 200, pp.276~283 (2013)
- 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 accelerates breeding of a salt-tolerant rice cultivar", Nat. Biotechnol, 33, pp.445~449 (2015)
- Tian F, "Genome-wide association study of leaf architecture in the maize nested association mapping population", Nature Genet, 43, pp.6~11 (2011)
- Wallace JG, "Entering the second century of maize quantitative genetics", Heredity, 112, pp.30~38 (2014)
- Yan J, "Genetic Characterization and linkage disequilibrium estimation of a global maize collection using SNP markers", Plos One, 4(12), pp.e8451~ (2009)
- Zhou T, "Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes", Molecular Genetics and Genomics, 271, pp.402~405 (2004)
- Zhu C, "Status and prospects of association mapping in plants", Plant Genome, 1, pp.5~20 (2008)