title: A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification.
abstract: Quantitative Trait Loci (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the S. 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. pennellii This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2and BC3lines, 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.
authors: Department of Plant Biology, University of California at Davis, California 95616.
authors: Daniel
authors: 0000-0002-3778-4107
authors: D
authors: Fulop
authors: Department of Plant Biology, University of California at Davis, California 95616.
authors: Aashish
authors: 0000-0003-3447-4442
authors: A
authors: Ranjan
authors: Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel.
authors: Itai
authors: I
authors: Ofner
authors: Department of Plant Biology, University of California at Davis, California 95616.
authors: Michael F
authors: 0000-0002-0555-6409
authors: MF
authors: Covington
authors: Department of Plant Biology, University of California at Davis, California 95616.
authors: Daniel H
authors: 0000-0003-4875-1447
authors: DH
authors: Chitwood
authors: Department of Plant Biology, University of California at Davis, California 95616.
authors: Donelly
authors: 0000-0003-0624-8034
authors: D
authors: West
authors: Department of Plant Biology, University of California at Davis, California 95616.
authors: Yasunori
authors: 0000-0003-1935-4397
authors: Y
authors: Ichihashi
authors: Department of Plant Biology, University of California at Davis, California 95616.
authors: Lauren
authors: L
authors: Headland
authors: Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel.
authors: Daniel
authors: D
authors: Zamir
authors: Department of Plant Biology, University of California at Davis, California 95616 nrsinha@ucdavis.edu jnmaloof@ucdavis.edu.
authors: Julin N
authors: 0000-0002-9623-2599
authors: JN
authors: Maloof
authors: Department of Plant Biology, University of California at Davis, California 95616 nrsinha@ucdavis.edu jnmaloof@ucdavis.edu.
authors: Neelima R
authors: 0000-0002-1494-7065
authors: NR
authors: Sinha
mesh_terms: D002874:Chromosome Mapping; D003433:Crosses, Genetic; D004843:Epistasis, Genetic; D017343:Genes, Plant; D056726:Genetic Association Studies / Q000379:methods; D005838:Genotype; D007178:Inbreeding; D018551:Solanum lycopersicum / Q000235:genetics*; D008390:Markov Chains; D008957:Models, Genetic; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics*; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
keywords: epistatic QTL; fine-mapping QTL; heterogeneous Hidden Markov Model; regularized regression; variable selection