The differential expression of homoeologous genes confers expression plasticity and facilitates the adaptation and domestication of major polyploid crops. However, how this homoeolog expression bias (HEB) is regulated remains elusive. Here, transcriptome analysis of 406 worldwide wheat (Triticum aestivum) accessions revealed great variation in HEB among accessions.

We identified 14,727 QTLs regulating HEB (hebQTLs) by developing a region-based model to quantify HEB among accessions, indicating that HEB is genetically regulated and can be predicted using genotyping data. The hebQTLs only regulate the expression of homoeologs in the same subgenome and downregulate their expression to result in HEB, suggesting that intra-subgenomic rather than inter-subgenomic interactions drive subgenome expression bias.

Furthermore, non-hebQTL-regulated homoeologs have stronger biological functions, are under higher selection pressure and exhibit lower genetic diversity than hebQTL-regulated homoeologs. Significantly, the downregulations of 38.38% hebQTL-regulated homoeologs are compensated for by the upregulation of other homoeologs within a triad.

Our findings reveal how homoeolog expression is coordinated at the genetic level and provide an avenue for leveraging HEB to improve agronomic traits in polyploid crops.