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/'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 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'/ZakERA8 but not in a 'Louise'/ZakERA8 mapping population. This is likely because Otis carries the same natural PHS susceptible MKK3-A-A660 S allele as Zak, whereas Louise carries the PHStolerant MKK3-A-C660 R 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.

Identification of a major and stable QTL on chromosome 5A confers spike length in wheat (Triticum aestivum L.)

“…As an effective method, BSE-Seq has been successfully used for mapping and gene identi cation in wheat. However, the traits identi ed by BSE-Seq to date are mainly controlled by a single gene, and few results have been reported for complex traits in RIL populations (Martinez et al 2020;Dong et al 2020;Breseghello and Sorrells 2006;Harrington et al 2019). To determine the usefulness of BSE-Seq data in complex trait gene mapping, SL throughout an RIL population was analyzed.…”

“…Bulked segregant analysis (BSA) with pooled DNA samples obtained from individuals with extreme phenotypes in the RIL population provides a high-e ciency approach to the identi cation of polymorphic markers associated with target traits (Zhai et al 2016;Zou et al 2016;Win et al 2017;Ramirez-Gonzalez et al 2015). Due to the large size of the wheat genome (~ 16 Gb in hexaploid wheat) (Bennett and Smith 1976) and highly repetitive content (Lukaszewski et al 2014), whole-genome DNA resequencing for BSA is still costly (Martinez et al 2020). Exons constitute approximately 0.95% of the wheat genome and code primary protein components that play essential roles in plant growth and development (Dong et al 2020).…”

Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat

“…Using bulked segregant analysis and the exome sequence strategy, Harrington et al identified a locus controlling a dominant, environmentally dependent chlorosis phenotype within the Durum wheat ( Triticum turgidum ) cv. Kronos ( Harrington et al, 2019 ), Mo et al (2018) identified a clear peak region on chromosome arm 4BS associated with increased plant height, Martinez et al (2020) fine-mapped the ABA-hypersensitive mutant ERA8 in a wheat backcross population. Using RenSeq and MutRenSeq strategy, series resistance genes were cloned through developing the exome capture probe panel that specifically captures disease resistance (R) genes ( Jupe et al, 2013 ; Steuernagel et al, 2016 ).…”

Prospects for the accelerated improvement of the resilient crop quinoa

“…Exchange of the evolutionarily conserved amino acid N260 to T260 in MKK3 adapts barley to wet growth conditions in East Asia ( Nakamura et al , 2016 ). Additionally, the semi-dominant ethylmethane sulfonate (EMS)-induced ERA8 allele of MKK3 (in which Glu365 is substituted with Lys) was shown to increase seed dormancy and thus pre-harvest sprouting tolerance in wheat ( Martinez et al , 2020 ). The quinoa genome encodes three close homologues of MKK3 (AUR62015864, AUR62026127, and AUR62020359; Fig.…”