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

Authors: MARTINEZ, SHANTEL - Washington State University; SHORINOLA, OLUWAYESI - John Innes Center; CONSELMAN, SAMANTHA - Washington State University; See, Deven; SKINNER, DANIEL - Retired ARS Employee; UAUY, CRISTOBAL - John Innes Center; Steber, Camille

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2019
Publication Date: 1/28/2020
Citation: Martinez, S.A., Shorinola, O., Conselman, S., See, D.R., Skinner, D.Z., Uauy, C., Steber, C.M. 2020. Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype. Theoretical and Applied Genetics. 133:719-736. https://doi.org/10.1007/s00122-019-03503-0.
DOI: https://doi.org/10.1007/s00122-019-03503-0

Interpretive Summary: Wheat is one of the most widely cultivate crops responsible for 20% of human caloric intake. One reason for the population of wheat is that it can be used to make diverse products including bread, cake, cookies, and noodles. Unfortunately, the quality of these products can be damaged by preharvest sprouting, the initiation of wheat grain germination on the mother plant when rain occurs before harvest. The wheat ERA8 (enhanced response to ABA) gene provides increased resistance to preharvest sprouting through increased seed dormancy. This study mapped ERA8, and found that the preharvest spouting tolerance likely results from a single amino acid change in a Map Kinase Kinase gene called TaMKK3-A. Identifying the single nucleotide change in MKK3 creates a perfect marker in order to introduce preharvest sprouting resistance from ERA8 into new wheat varieties. It also open the door to understanding the underying mechanisms of resistance. Preharvest sprouting tolerance will help prevent financial losses for farmers due to preharvest sprouting and low falling numbers (a measure of sprout damage).

Technical 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/‘ZakERA8’ 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 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’/ZakERA8 but not in a ‘Louise’/ZakERA8 mapping population. This is likely because Otis carries the same natural PHS susceptible MKK3-A-A660S allele as Zak, whereas Louise carries the PHS tolerant MKK3-A-C660R allele. Thus, the variation for grain dormancy and PHS tolerance in the Louise/ZakERA8 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.