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학술연구/단체지원/교육 등 연구자 활동을 지속하도록 DBpia가 지원하고 있어요.
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논문 기본 정보
- 자료유형
- 학술저널
- 저자정보
- 발행연도
- 2014.1
- 수록면
- 36 - 42 (7page)
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The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven tran-scriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the suffi-cient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies.
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참고문헌 (21)
참고문헌 신청
Agarwal, G. / 2012 / Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers / PLoS One 7:e52443
Altshuler, D. / 2000 / An SNP map of the human genome generated by reduced representation shotgun sequencing / Nature 407:513~516
Barbazuk, W. B. / 2007 / SNP discovery via 454 transcriptome sequencing / Plant J 51:910~918
Bundock, P. C. / 2009 / Targeted single nucleotide polymorphism(SNP)discovery in a highly polyploid plant species using 454 sequencing / Plant Biotechnol. J 7:347~354
Cox, M. P. / 2010 / SolexaQA : At-aglance quality assessment of Illumina second-generation sequencing data / BMC Bioinformatics 11:485
Altshuler, D. / 2000 / An SNP map of the human genome generated by reduced representation shotgun sequencing / Nature 407:513~516
Barbazuk, W. B. / 2007 / SNP discovery via 454 transcriptome sequencing / Plant J 51:910~918
Bundock, P. C. / 2009 / Targeted single nucleotide polymorphism(SNP)discovery in a highly polyploid plant species using 454 sequencing / Plant Biotechnol. J 7:347~354
Cox, M. P. / 2010 / SolexaQA : At-aglance quality assessment of Illumina second-generation sequencing data / BMC Bioinformatics 11:485
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