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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
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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
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Journal Article
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
2013
Overview
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 (NBSLRR) class.
Publisher
New Phytologist Trust,Wiley Subscription Services, Inc
Subject
/ Assembly
/ Chromosome Mapping - methods
/ Cloning
/ Disease Resistance - genetics
/ DNA
/ Exons
/ Genes
/ Genomes
/ Genomics
/ Introns
/ Leucine
/ Methods
/ Mutants
/ Mutation
/ MutMap
/ PII Nitrogen Regulatory Proteins - genetics
/ Plant Diseases - microbiology
/ Progeny
/ Regions
/ Rice
/ R‐gene
