DOI: 10.5061/dryad.2fqz612wx
title: Data from: Solanum pennellii (LA5240) backcross inbred lines (BILs) for high resolution mapping in tomato

description: Wild species are an invaluable source of new traits for crop improvement.
 Over the years the tomato community bred cultivated lines that carry
 introgressions from different species of the tomato tribe to facilitate
 trait discovery and mapping. The next phase in such projects is to find
 the genes that drive the identified phenotypes. This can be achieved by
 genotyping a few thousand individuals resulting in fine-mapping that can
 potentially identify the causative gene. To couple trait discovery and
 fine mapping we are presenting large, recombination-rich, Backcross Inbred
 Line (BIL) populations involving an unexplored accession of the wild,
 green-fruited species Solanum pennellii (LA5240; the Lost Accession) with
 two modern tomato inbreds: LEA, determinate, and TOP
 indeterminate. The LEA and TOP BILs are in BC2F6-8 generation and include
 1,400 and 500 lines respectively. The BILs were genotyped with ~5,000 SPET
 markers, showing that in the euchromatic regions there was one recombinant
 every 17-18 Kb while in the heterochromatin a recombinant every 600-700 Kb
 (TOP and LEA respectively). To gain perspective on the topography of
 recombination we compared five independent members of the self-pruning
 gene family with their respective neighboring genes; based on PCR markers,
 in all cases we found recombinants. Further mapping analysis of two known
 morphological mutations that segregated in the BILs (Self-pruning and
 Hair), showed that the maximal delimited intervals were 73 Kb and 210 Kb
 respectively and included the known causative genes. The LOST_BILs provide
 a solid framework to study traits derived from a tolerant
 wild tomato.
description: # Solanum pennellii (LA5240) backcross inbred lines (BILs) for high
 resolution mapping in tomato # Author(s): Shai Torgeman The Hebrew
 University of Jerusalem Faculty of Agriculture Institute of Plant Sciences
 P.O.Box 12, Rehovot 76100, Israel 
 Dani Zamir The Hebrew University of Jerusalem Faculty of Agriculture
 Institute of Plant Sciences P.O.Box 12, Rehovot 76100, Israel
 # File list:
 Genotype&Phenotype.LEA.csv Genotype&Phenotype.TOP.csv Rqtl.txt #
 Files descriptions: Genotype&Phenotype.LEA/TOP - Genotypic data for
 all the BILs population got from Single Primer Enrichment Technology
 (SPET). The first row refer to the marker name and its physical position.
 The second row refer to the chromosome number. the third row refer to the
 genetic distance(CM) calculated from the number of recombination between
 neighbor markers. NA are missing genotype data points genotype = 1 refer
 to cultivated allele genotype = 3 refer to wild species allele Throughout
 the autumn 2017, the LEA BILs (1389) and the TOP BILs (490) were grown in
 a greenhouse in Chatzav, Israel and scored for plant habit (determinate
 and indeterminate) and hairiness on stem (Hairy and hair absent). Genome
 scan for trait mapping analysis in the bi-parental populations was
 performed in R/qtl and R/qtl2 packages (Broman et al., 2003) by
 Haley-Knott regression (Haley & Knott, 1992) and validated using
 single marker analysis (ANOVA) in JMP pro 16 software (SAS Institute,
 Cary, NC, USA). The Genotype and Phenotypes data combined for upload in R
 format for QTL analysis. script add in R file. Rqtl.R - script for QTL
 analysis Genotype&Phenotype.csv file. # notes: Our analysis done by
 combine of R software to detect the QTLs and by JMP software for the
 t-test and multiple comparisons analysis.