Aleurone layer multi-omics reveals constitutive enzyme-inhibitor imbalance in LMA-contrasting wheat cultivars.

Late maturity amylase (LMA) is a genetic defect in wheat causing premature accumulation of high-pI alpha-amylase isoforms in the aleurone during grain development, which reduces falling number, resulting in flour downgrading and price penalties. Yet, the aleurone layer proteome and metabolome remain poorly characterised across LMA-contrasting cultivars. We measured the proteome and central carbon metabolome of aleurone from three wheat cultivars differing in LMA-phenotype: Seri (susceptible), Kennedy (intermediate), and Hartog (resistant) - under abscisic acid (ABA), abscisic acid plus gibberellic acid (GA), or untreated conditions. Cultivar identity explained 65.7% of proteome variance, exceeding hormone treatment effects (13.1%), with no significant cultivar × treatment interaction. In Seri, increased numbers and abundance of alpha-amylase isoforms, glyoxylate cycle enzymes, arabinofuranosidase, malic acid, and sucrose indicate constitutive reserve mobilisation in the absence of hormone induction. The inhibitor-to-amylase ratio was higher in Hartog than Seri, suggesting LMA susceptibility reflects a broader imbalance between degradative enzymes and their regulators rather than elevated amylase production alone. The cultivar Hartog showed higher abundance of dehydrins, invertase/PME inhibitors, and sucrose-phosphate synthase, consistent with storage maintenance and cellular protection. Multi-omics integration and proteomics-phenotype integration independently converged on the same cultivar axis, with glyoxylate cycle enzymes and arabinofuranosidase consistently associated with Seri. These findings provide a molecular framework for dissecting mechanisms of LMA susceptibility and resistance.