TITLE

Genome-wide SNP Database for Marker-assisted Background Selection in Tomato

AUTHOR(S)
Ji-Eun Kim; Bong-Woo Lee; Sang-Mi Kim; Bo-Mi Lee; Jeong-Hee Lee; Sung-Hwan Jo
PUB. DATE
September 2013
SOURCE
Korean Journal of Breeding Science;2013, Vol. 45 Issue 3, p232
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Backcrossing is a plant breeding method most commonly used to incorporate one or a few genes into an adapted or elite variety. To facilitate MAB (marker-assisted backcrossing) in a practice breeding program, we developed a SNP database and a program for providing selected markers for background selection from genome-wide SNPs of seven tomato accessions downloaded from NCBI-SRA. We identified 410,074 SNPs among 21 parental combinations with data from seven transcriptomes and developed a SNP database. To select the optimized number of markers for background selection, we divided 12 chromosomes according to physical length and genetic length. Initially, each chromosome was equally divided into five blocks according to physical length, and three SNPs were positioned per block. Additionally, we applied the genetic distance from tomato-EXPEN 2000 map because the frequency of recombination can vary greatly among chromosomal regions. When considering genetic distance, each chromosome was divided into fifteen blocks unequally and one SNP was positioned per block. The program for background selection was designed to be simple and easy to use, and it is available at http://tgsol.seeders.co.kr/index.php/tg/mab. When the user selects the parental combination, the program provides selected markers with primer information. The value of this program for tomato breeding will further increase if more accession numbers are added to the database.
ACCESSION #
93400681

 

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