Exome sequencing of bulked segregants identified a novel TaMKK3- A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype

Abstract

Key message

Using bulked segregant analysis of exome sequence, we fine-mapped the ABA-hypersensitive mutant ERA8 in a wheat backcross population to the TaMKK3- A locus of chromosome 4A.

Abstract

Preharvest sprouting (PHS) is the germination of mature grain on the mother plant when it rains before harvest. The ENHANCED RESPONSE TO ABA8 ( ERA8) mutant increases seed dormancy and, consequently, PHS tolerance in soft white wheat ‘Zak.’ ERA8 was mapped to chromosome 4A in a Zak/‘Zak ERA8’ backcross population using bulked segregant analysis of exome sequenced DNA (BSA-exome-seq). ERA8 was fine-mapped relative to mutagen-induced SNPs to a 4.6 Mb region containing 70 genes. In the backcross population, the ERA8 ABA-hypersensitive phenotype was strongly linked to a missense mutation in TaMKK3- A- G1093A (LOD 16.5), a gene associated with natural PHS tolerance in barley and wheat. The map position of ERA8 was confirmed in an ‘Otis’/Zak ERA8 but not in a ‘Louise’/Zak ERA8 mapping population. This is likely because Otis carries the same natural PHS susceptible MKK3- A- A660 ^S allele as Zak, whereas Louise carries the PHS-tolerant MKK3- A-C660 ^R allele. Thus, the variation for grain dormancy and PHS tolerance in the Louise/Zak ERA8 population likely resulted from segregation of other loci rather than segregation for PHS tolerance at the MKK3 locus. This inadvertent complementation test suggests that the MKK3- A- G1093A mutation causes the ERA8 phenotype. Moreover, MKK3 was a known ABA signaling gene in the 70-gene 4.6 Mb ERA8 interval. None of these 70 genes showed the differential regulation in wild-type Zak versus ERA8 expected of a promoter mutation. Thus, the working model is that the ERA8 phenotype results from the MKK3- A- G1093A mutation.

Electronic supplementary material

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