ArticleGenome biology2025
HebQTLs reveal intra-subgenome regulation inducing unbalanced expression and function among bread wheat homoeologs.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Evolutionary characteristics of the GAPDH gene family and functional characterization of TaGAPDH5 in wheat.BMC plant biology · 2026Article
- Nonadditive gene expression and reduced homoeolog expression bias in an intraspecific hexaploid wheat hybrid.BMC plant biology · 2026Article
- Regulatory divergence of homoeologs underlies network optimization for fiber improvement in domesticated cotton.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The TaSDIR1-4A-TaASR4-3D module regulates ABA-related drought responses in wheat seedlings.The New phytologist · 2026Article
- Integrated phenomic and genomic analyses unveil modes of altered phenotypic plasticity during wheat improvement.Genome biology · 2025Article
- HebQTLs reveal intra-subgenome regulation inducing unbalanced expression and function among bread wheat homoeologs.Genome biology · 2025Article
- Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations.Genome biology · 2025Article
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Authors and funding
11 authors.
Funding
Abstract
backgroundPolyploidy contains multiple gene copies, known as homoeologs. Differential expression of homoeologs confers expression plasticity and facilitates the adaptation and domestication of major polyploid crops. However, how this homoeolog expression bias is produced and genetically regulated remains elusive.
resultsHere we uncover substantial variation in homoeolog expression bias among the root transcriptomes of a natural population of 406 bread wheat (Triticum aestivum ssp. aestivum) accessions collected worldwide. We develop a new model allowing us to identify 14,727 quantitative trait loci regulating the variation in homoeolog expression bias (hebQTLs), indicating that homoeolog expression bias is genetically regulated and can be predicted using genotyping data. The hebQTLs mostly regulate the expression of homoeologs in the same subgenome and downregulate expression to produce homoeolog expression bias, suggesting that intra-subgenomic rather than inter-subgenomic interactions induce homoeolog expression bias. Furthermore, we determine that hebQTL-regulated homoeologs exhibit higher genetic diversity and weaker biological functions than their counterparts. Notably, the downregulation of 38.4% of hebQTL-regulated homoeologs is compensated for by the upregulation of other homoeologs within the triad.
conclusionsOur findings reveal how homoeolog expression is coordinated at the genetic level and provide an avenue for leveraging homoeolog expression bias to improve polyploid crops.
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