Natural variations in the promoter of ZmDeSI2 encoding a deSUMOylating isopeptidase controls kernel methionine...

Improving the methionine (Met) content in maize kernels is of key importance to the animal feed industry; however, the genetic and molecular mechanisms governing maize kernel Met content remain largely unexplored. In this study, we leveraged a panel consisting of 348 diverse inbred maize lines to explore the genetic and molecular mechanisms that control kernel Met levels. A genome-wide association study followed by transcriptomic analysis identified the deSUMOylating isopeptidase gene ZmDeSI2. Further biochemical experiments revealed that ZmDeSI2 directly reduces the SUMOylation and accumulation of the sulfite reductase ZmSIR, thereby repressing Met accumulation. Natural variants in the ZmDeSI2 promoter region were found to serve as key determinants of the expression of this gene, predominantly due to the absence or presence of a ZmWRKY105 transcription factor binding site. The elite ZmDeSI2^Hap2 haplotype without this binding site in the ZmDeSI2 promoter was associated with a 1.36-fold increase in Met levels in the kernels of modified near-isogenic lines generated through marker-assisted breeding. Taken together, these results provide new insights into the molecular processes that control Met biosynthesis, highlighting an elite natural variant suitable for application in maize breeding for Met biofortification.