title: MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii.
abstract: Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions missing from the reference (gaps) cannot be identified by simple alignment. Here we report on a method called 'MutMap-Gap', which involves delineating a candidate region harboring a mutation of interest using the recently reported MutMap method, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. We applied MutMap-Gap to isolate the blast resistant gene Pii from the rice cv Hitomebore using mutant lines that have lost Pii function. MutMap-Gap should prove useful for cloning genes that exhibit significant structural variations such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class.
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.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Aiko
authors.initials: A
authors.lastname: Uemura
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Yaegashi
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Muluneh
authors.initials: M
authors.lastname: Tamiru
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Abe
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Chikako
authors.initials: C
authors.lastname: Mitsuoka
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Hiroe
authors.initials: H
authors.lastname: Utsushi
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.|United Graduate School of Iwate University, Morioka, Iwate, 020-8550, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Natsume
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanzaki
authors.affiliation: Shinshu University, Ueda, Nagano, 386-8567, Japan.
authors.forename: Hideo
authors.initials: H
authors.lastname: Matsumura
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Hiromasa
authors.initials: H
authors.lastname: Saitoh
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.|The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yoshida
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.
authors.forename: Liliana M
authors.initials: LM
authors.lastname: Cano
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.
authors.forename: Sophien
authors.initials: S
authors.lastname: Kamoun
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Ryohei
authors.initials: R
authors.lastname: Terauchi
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant; D018745:Genome, Plant; D020082:Magnaporthe; D009154:Mutation; D012275:Oryza / Q000235:genetics* / Q000382:microbiology; D051922:PII Nitrogen Regulatory Proteins / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D010940:Plant Proteins / Q000235:genetics*
chemical_list: D051922:PII Nitrogen Regulatory Proteins; D010940:Plant Proteins
keywords: MutMap; R-gene; de novo assembly; next-generation sequencing; rice; whole-genome sequencing