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

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. Preharvest sprouting (PHS) is the germination of mature grain on the mother plant when it rains before harvest. T...

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Published in:	Theoretical and applied genetics Vol. 133; no. 3; pp. 719 - 736
Main Authors:	Martinez, Shantel A., Shorinola, Oluwayesi, Conselman, Samantha, See, Deven, Skinner, Daniel Z., Uauy, Cristobal, Steber, Camille M.
Format:	Journal Article
Language:	English
Published:	Berlin/Heidelberg Springer Berlin Heidelberg 01-03-2020 Springer Springer Nature B.V
Subjects:	Abscisic Acid Agriculture Alleles Analysis Biochemistry Biomedical and Life Sciences Biotechnology Chromosome Mapping Complementation Crosses, Genetic Dormancy Exome Gene mapping Gene regulation Genes Genes, Plant Genetic aspects Genetic Linkage Genotype & phenotype Germination Life Sciences MAP Kinase Kinase 3 - genetics Missense mutation Mutants Mutation Mutation, Missense Nucleotide sequence Original Original Article Phenotype Phenotypes Plant Biochemistry Plant Breeding/Biotechnology Plant Genetics and Genomics Population Quantitative Trait Loci Single-nucleotide polymorphism Triticum - genetics Triticum - physiology Wheat Israel
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Summary:	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. 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.
Bibliography:	Communicated by Mark E. Sorrells.
ISSN:	0040-5752 1432-2242
DOI:	10.1007/s00122-019-03503-0