A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae

Abstract

It is necessary for molecular breeders to overcome the difficulties in applying abundant genomic information to crop breeding. Candidate orthologs would be discovered more efficiently in less-studied crops if the information gained from studies of related crops were used. We developed a comparative analysis tool and web-based genome viewer to identify orthologous genes based synteny as well as sequence similarity between tomato, pepper and potato. The tool has a step-by-step interface with multiple viewing levels to support the easy and accurate exploration of functional orthologs. Furthermore, it provides access to single nucleotide-polymorphism markers from the massive genetic resource pool in order to accelerate the development of molecular markers for candidate orthologs in the Solanaceae. This tool provides a bridge between genome data and breeding by supporting effective marker development, data utilization and communication.Database URL: http://tgsol.seeders.co.kr/scomp/

Analysis of differentially expressed genes induced by drought stress in tef (Eragrostistef) root

“…Tef is one of the most drought-tolerant cereals, providing a useful platform to understand the mystery of root elongation under drought stress. Since many of the monocot genomes had high synteny (Choe et al, 2018), it is feasible to use rice chips to do hybridization with tef RNAs. However, from the hybridization of tef and rice transcripts, only 171 genes are differentially regulated.…”

Tag-SNP selection and online database construction for haplotype-based marker development in tomato

“…인간 유전체 분야에서 처음 연구가 시작된 tag-SNP의 개념은 haplotype을 대표하는 마커로서 Hapmap project에서 활발히 연구되었다 (Willer et al 2006). 유전체 내 에서 haplotype block을 선발하는 방법은 LD (linkage disequilibrium) block based methods와 genome-wide approaches의 크 게 2가지의 카테고리로 나누어 개발되고 있다 (Choe et al 2018). LD block 기반의 방식은 미리 정의된 haplotype block structure에 의존한다.…”