Wheat quality defects, such as pre-harvest sprouting (PHS) and late maturity amylase (LMA), directly impact growers’ profitability. Unlike PHS, LMA is a genetic defect present in specific wheat genotypes, with high expression of one or more alpha-amylase subtypes triggered by cold stress and temperature shock during the post-anthesis period. Both PHS and LMA, are complex traits involving interactions between genotype and environment, and the underlying interactions between genome and phenome are poorly understood.

Here, we selected five wheat cultivars representing resistant, intermediate, susceptible and control genotypes of LMA expression and performed transcriptomics across two-time points (dormant and 48h germination) and collected global proteome data across three-time points (dormant, 2 h imbibed and 48 h germination). The comparative analysis of dormant seeds between constituent expresser and LMA-resistant varieties showed the 710 upregulated and 1403 downregulated genes (Fold change=2; Adj. p value=0.05), where the upregulated genes were associated with galactose metabolism and increased ion transporter activity, evidencing the initiation of vacuolation and α-amylase activity. While the comparison between the constitutive expresser and intermediate genotype showed minimal changes.

Notably, the resistant cultivar retained the functions associated with nutrient reservoir activity, while the constitutive and intermediate expresser cultivars were high in carbohydrate metabolism and positive regulation of nutrient levels during the 48h germination period. The comparative analysis of the proteomics dataset between the wheat cultivars showed enrichment of peroxidase, antioxidant and oxidoreductase activities in the resistant varieties, suggesting their role in blocking starch catabolism and hydrolase activities at the 0, 2 and 48 h times compared to the constituent LMA expresser genotype.

The Weighted Gene Network Correlation Analysis on the proteomics dataset reveals that the LMA-resistant cultivars have a significantly higher abundance of endopeptidase inhibitors, peroxidases and nutrient reservoir proteins, explaining the role of protease inhibitors and the peroxidases in protecting the nutrient reservoirs in the seed.

We found a module (Pearson r=0.76) that positively correlates transcriptomics and proteomics analysis with seed germination and time (h). This module is overrepresented by genes and proteins involved in starch and sucrose metabolism and fatty acid degradation, which provide energy and carbon skeleton for seedling establishment.

The identification of a higher abundance of antagonistic regulatory proteins and the decrease of carbohydrate metabolism events associated with LMA-resistant varieties further enhances our understanding of additional mechanisms that regulate starch breakdown, hydrolase activities and nutrient mobilisation beyond the expression of alpha-amylase expression within the dormant seed.