@article {Fulop040923, author = {Daniel Fulop and Aashish Ranjan and Itai Ofner and Michael F. Covington and Daniel H. Chitwood and Donnelly West and Yasunori Ichihashi and Lauren Headland and Daniel Zamir and Julin N. Maloof and Neelima R. Sinha}, title = {A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification}, elocation-id = {040923}, year = {2016}, doi = {10.1101/040923}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Quantitative Trait Locus (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the Solanum pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennelli. This socalled Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous Hidden Markov Model for genotyping the lines, and by using state of the art sparse regression techniques for QTL mapping.Summary: Determining the genes responsible for species differences is central to biology. Finding such genes is typically done using experimental populations derived from crossing closely-related species and correlating phenotypes to genotypes in the progeny of these crosses. In this work we present a powerful new experimental population for tomato, derived from a cross between a modern cultivated tomato variety (M82) and the wild species Solanum pennelli. This Backcrossed Inbred Line (BIL) population was derived through repeated backcrossing to the M82 parent. We demonstrate that compared to other populations available for tomato, this BIL population has substantially smaller segments of S. pennelli DNA, that can enable the identification of single or few candidates genes for traits of interest. Using the BILs we determined the genomic regions controlling dissection of the leaves into leaflets, leaflet shape, and time to flower. Moreover, we demonstrated the benefit of populations with multiple introgressions per line, such as the BILs, for finding putative epistatic interactions among loci. Finally, we present newly developed statistical inference and visualization tools, and demonstrate how state of the art regression techniques can assist in analyzing populations of this type.}, URL = {https://www.biorxiv.org/content/early/2016/04/22/040923}, eprint = {https://www.biorxiv.org/content/early/2016/04/22/040923.full.pdf}, journal = {bioRxiv} }