Multi-omics analysis reveals the pivotal role of phytohormone homeostasis in regulating maize grain water content

Grain water content (GWC) is a key determinant for mechanical harvesting of maize (Zea mays). In our previous research, we identified a quantitative trait locus, qGWC1, associated with GWC in maize. Here, we examined near-isogenic lines (NILs) NIL^L and NIL^H that differed at the qGWC1 locus. Lower GWC in NIL^L was primarily attributed to reduced grain water weight (GWW) and smaller fresh grain size, rather than the accumulation of dry matter. The difference in GWC between the NILs became more pronounced approximately 35 d after pollination (DAP), arising from a faster dehydration rate in NIL^L. Through an integrated analysis of the transcriptome, proteome, and metabolome, coupled with an examination of hormones and their derivatives, we detected a marked decrease in JA, along with an increase in cytokinin, storage forms of IAA (IAA-Glu, IAA-ASP), and IAA precursor IPA in immature NIL^L kernels. During kernel development, genes associated with sucrose synthases, starch biosynthesis, and zein production in NIL^L, exhibited an initial up-regulation followed by a gradual down-regulation, compared to those in NIL^H. This discovery highlights the crucial role of phytohormone homeostasis and genes related to kernel development in balancing GWC and dry matter accumulation in maize kernels.