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 Academic Article uri icon


  • 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.


  • Takagi, H
  • Uemura, A
  • Yaegashi, H
  • Tamiru, M
  • Abe, A
  • Mitsuoka, C
  • Utsushi, H
  • Natsume, S
  • Kanzaki, H
  • Matsumura, H
  • Saitoh, H
  • Yoshida, K
  • Cano, LM
  • Kamoun, S
  • Terauchi, R

publication date

  • 2013