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.
New Phytol
; 200(1): 276-283, 2013 Oct.
Article
in En
| MEDLINE
| ID: mdl-23790109
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.
Key words
Full text:
1
Database:
MEDLINE
Main subject:
Plant Proteins
/
Oryza
/
Chromosome Mapping
/
Genes, Plant
/
Genome, Plant
/
Disease Resistance
/
Mutation
Language:
En
Journal:
New Phytol
Journal subject:
BOTANICA
Year:
2013
Type:
Article
Affiliation country:
Japan