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, 200 (1), 276-83

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

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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

Hiroki Takagi et al. New Phytol.

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.

Keywords: MutMap; R-gene; de novo assembly; next-generation sequencing; rice; whole-genome sequencing.

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