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KMID : 0578320140370010036
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Molecules and Cells
2014 Volume.37 No. 1 p.36 ~ p.42
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Genome-Wide SNP Calling Using Next Generation Sequencing Data in Tomato
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Kim Ji-Eun
Oh Sang-Keun
Lee Jeong-Hee
Lee Bo-Mi
Jo Sung-Hwan
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Abstract
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The tomato ( L.) is a model plant for genome research in , 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 transcriptome 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 , which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of . Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient 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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KEYWORD
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next generation sequencing (NGS), single nucleotide polymorphism (SNP), tomato
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