Genome sequencing reveals agronomically-important loci in rice using MutMap

The majority of agronomic traits are controlled by multiple genes that cause minor phenotypic effects making gene isolation challenging. Here we introduce a novel method for isolation of crop genes termed MutMap. Following mutagenesis, a mutant with a useful phenotype is crossed to the original wild-type line allowing unequivocal segregation in the F2 progeny even of subtle phenotypic differences. Bulked DNA of 20 F2 progeny showing the mutant phenotype is subjected to whole genome resequencing. Scanning of the genome for regions exhibiting higher frequencies of sequence reads originating from the mutant identifies loci harboring the mutation. We applied MutMap to mutants of a Japanese elite rice cultivar and identified the unique genomic positions most likely harboring the causal mutations for seven mutants, including those encoding agronomically-relevant traits. These results demonstrate the power of MutMap to accelerate the genetic improvement of rice and other crop plants, ultimately providing sufficient food for a growing world population. none provided