title: QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations.
abstract: The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time-consuming and labor-intensive. Here we report the rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines and F2 populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan; United Graduate School of Iwate University, Morioka, Iwate, 020-8550, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takagi
authors.forename: Akira
authors.initials: A
authors.lastname: Abe
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yoshida
authors.forename: Shunichi
authors.initials: S
authors.lastname: Kosugi
authors.forename: Satoshi
authors.initials: S
authors.lastname: Natsume
authors.forename: Chikako
authors.initials: C
authors.lastname: Mitsuoka
authors.forename: Aiko
authors.initials: A
authors.lastname: Uemura
authors.forename: Hiroe
authors.initials: H
authors.lastname: Utsushi
authors.forename: Muluneh
authors.initials: M
authors.lastname: Tamiru
authors.forename: Shohei
authors.initials: S
authors.lastname: Takuno
authors.forename: Hideki
authors.initials: H
authors.lastname: Innan
authors.forename: Liliana M
authors.initials: LM
authors.lastname: Cano
authors.forename: Sophien
authors.initials: S
authors.lastname: Kamoun
authors.forename: Ryohei
authors.initials: R
authors.lastname: Terauchi
mesh_terms: D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D016415:Sequence Alignment
chemical_list: D018744:DNA, Plant