Identifying the genetic and epigenetic basis for asymmetric bZIP expression in temperature-stressed bread wheat

Abstract

Asymmetric gene expression in a polyploid plant refers to the differential expression of the homeologs of a gene. Bread wheat (Triticum aestivum) with three subgenomes, A, B, and D, is a hexaploid crop with six copies of each chromosome (6n, n = 7). This complexity can result in unequal expression of genes from each parental genome, leading to asymmetry in gene expression. In other polyploid crops like cotton, transcription factors (TF) exhibit genome-biased expression; however, there are no comparable studies for bread wheat. One of plants' most prominent TF gene families is the basic Leucine Zippers (bZIP), which are eukaryote-specific proteins and regulate various biological processes, including stress-related responses. bZIP proteins are dimeric and several heptads long. They exhibit typical coiled-coil structures with strategically placed amino acids in each heptad, responsible for their stability and specificity. Here, we aim to decipher the structural basis of the asymmetric expression of the bZIP TFs in wheat under low and high-temperature conditions. Furthermore, 19 highly expressed stress-related TabZIP TFs were analysed for their asymmetric expression profiles as plants were exposed to temperature-stress conditions. Two benchmarks were used to examine the bZIPs asymmetric gene expression, i.e., (a) the promoter's occupancy by the epigenetic marker histones, namely, H3K4me3 and H3k9ac (both active) and H3K27me3 (repressive), (b) density and diversity of cis-regulatory elements in the promoters. Notably, the genetic basis of the differences in protein sequences of bZIP triads was explored, which may impart structural stability to a specific homeolog, enabling the plant to endure the stress conditions.