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논문 기본 정보
- 자료유형
- 학술저널
- 저자정보
- 발행연도
- 2020.1
- 수록면
- 218 - 226 (9page)
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This report describes methods for selecting informative single nucleotide polymorphisms (SNPs), and the development of an online Solanaceae genome database, using 234 tomato resequencing data entries deposited in the NCBI SRA database. The 126 accessions of Solanum lycopersicum, 68 accessions of Solanum lycopersicum var. cerasiforme, and 33 accessions of Solanum pimpinellifolium, which are frequently used for breeding, and some wild-species tomato accessions were included in the analysis. To select tag-SNPs, we identified 29,504,960 SNPs in 234 tomatoes and then separated the SNPs in the genic and intergenic regions according to gene annotation. All tag-SNP were selected from non-synonymous SNPs among the SNPs present in the gene region and, as a result, we obtained tag-SNP from 13,845 genes. When there were no nonsynonymous SNPs in the gene, the genes were selected from synonymous SNPs. The total number of tag-SNPs selected was 27,539. To increase the usefulness of the information, a Solanaceae genome database website, TGsol (http://tgsol. seeders.co.kr/), was constructed to allow users to search for detailed information on resources, SNPs, haplotype, and tag-SNPs. The user can search the tag-SNP and flanking sequences for each gene by searching for a gene name or gene position through the genome browser. This website can be used to efficiently search for genes related to traits or to develop molecular markers.
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참고문헌 (13)
참고문헌 신청
Barrett JC / 2009 / Haploview: Visualization and analysis of SNP genotype data / Cold Spring Harb Protoc 2009(10):pdb.ip71
Bombarely A / 2011 / The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl / Nucleic Acids Res 39(Database issue):D1149~D1155
Choe J / 2018 / A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae / Database (Oxford) :bay047
Collard BC / 2008 / Marker-assisted selection: an approach for precision plant breeding in the twenty-first century / Philos Trans R Soc Lond B Biol Sci 363(1491):557~572
Cox MP / 2010 / SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data / BMC Bioinformatics 11:485
Bombarely A / 2011 / The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl / Nucleic Acids Res 39(Database issue):D1149~D1155
Choe J / 2018 / A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae / Database (Oxford) :bay047
Collard BC / 2008 / Marker-assisted selection: an approach for precision plant breeding in the twenty-first century / Philos Trans R Soc Lond B Biol Sci 363(1491):557~572
Cox MP / 2010 / SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data / BMC Bioinformatics 11:485
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