title: QTL map meets population genomics: an application to rice.
abstract: Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance.
authors.affiliation: Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Fawcett
authors.affiliation: Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Kado
authors.affiliation: Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
authors.forename: Eriko
authors.initials: E
authors.lastname: Sasaki
authors.affiliation: Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
authors.forename: Shohei
authors.initials: S
authors.lastname: Takuno
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yoshida
authors.affiliation: Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
authors.forename: Ryuichi P
authors.initials: RP
authors.lastname: Sugino
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, Japan.
authors.forename: Shunichi
authors.initials: S
authors.lastname: Kosugi
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Natsume
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, Japan.
authors.forename: Chikako
authors.initials: C
authors.lastname: Mitsuoka
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, Japan.
authors.forename: Aiko
authors.initials: A
authors.lastname: Uemura
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takagi
authors.affiliation: Iwate Agricultural Research Center, Kitakami, Iwate, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Abe
authors.affiliation: Faculty of Agriculture, Kobe University, Kobe, Japan.
authors.forename: Takashige
authors.initials: T
authors.lastname: Ishii
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, Japan.
authors.forename: Ryohei
authors.initials: R
authors.lastname: Terauchi
authors.affiliation: Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Innan
mesh_terms: D002874:Chromosome Mapping; D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D012641:Selection, Genetic