유전자 단위 haplotype을 대변하는 토마토 Tag-SNP 선발 및 웹 데이터베이스 구축

• 영문명: Tag-SNP selection and online database construction for haplotype-based marker development in tomato
• 발행기관: (사)한국식물생명공학회
• 저자명: 정혜리(Hye-ri Jeong) 이보미(Bo-Mi Lee) 이봉우(Bong-Woo Lee) 오재은(Jae-Eun Oh) 이정희(Jeong-Hee Lee) 김지은(Ji-Eun Kim
• 간행물 정보: 『Journal of Plant Biotechnology』47권 3호, 218~226쪽, 전체 9쪽
• 주제분류: 농수해양 > 기타농수해양
• 파일형태: PDF
• 발행일자: 2020.09.30

영문 초록

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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키워드

tag-SNP Haplotype Molecular marker NGS tomato