Late maturity amylase (LMA) is a recessive trait with increased alpha-amylase enzyme expression (TaAMY1 and TaAMY4) triggered by abiotic stress like cold shock. This leads to a decrease in the falling number and downgrading of wheat grains.

Here, we performed transcriptomics analysis on dormant (0h) and germinated (48h) seeds from two multi-parent advanced generation inter-cross (MAGIC) population subsets of tall lines (MT9 and MT10) growing for two generations (Generations 3 and 4) in glass house using the same conditions, which showed unpredictable LMA phenotypes between the two generations. The preliminary assessment showed that MT9 has higher LMA phenotype expression than the MT10 lines.

However, the LMA phenotype is unpredictable in these lines, with generations 3 and 4 showing high variability. Generation 3 had very high LMA expression, whereas LMA was absent in generation 4, but the underlying molecular mechanism for this unpredictable LMA phenotype remains unknown.

The comparison between two germination time points, 0h and 48h, for one generation (MT9-generation 3) showed the upregulation of 19,239 genes and the downregulated 10,767 genes (Fold change = 2, adj. p-value< 0.05). In the germinated grains (48h), phenylpropanoid biosynthesis, metabolic and amino and nucleotide sugar pathways were enriched. The comparison between two genotypes, MT9 and MT10, on dormant grains (0h) from generation 3 resulted in a limited change (~8%) of genes that were differentially expressed.

As expected, the seed dormancy breakdown-related pathways, such as metabolic processes and sugar metabolism pathways, were downregulated, while the spliceosome pathway was significantly enriched, indicating their critical role in maintaining seed dormancy through the catalysis of mature mRNA processing.

The comparison of dormant grains between two generations, 3 and 4, showed that the generation 4 seeds of MT9 were involved in strigolactone biosynthesis and metabolism processes and shoot system morphogenesis, indicating the underlying role of these genes’ molecular functions in defining the LMA phenotype characteristics between two generations.

Overall, the enrichment of dormancy-breakdown-related pathways, increased ion transporters and sucrose metabolism between the two generations for the same genotype further elucidate the underpinning mechanism for the unpredicted LMA expression.

Key Words: Genotype, Phenotype, LMA resistance, RNA-Seq, Temporal expression profiles