ArticleScience China. Life sciences2023
Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat.
Article in Science China. Life sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 41 citations in OpenAlex.
- Integration of the D-Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Anthocyanin biosynthesis in blueberry is regulated by light and abscisic acid signaling via a VcABF2-miR156-VcSPL9 feedback loop.The New phytologist · 2026Article
- Dynamic chromatin accessibility reveals BrKAN2 as a key regulator of Chinese cabbage leaf heading.Molecular horticulture · 2026Article
- DNA hypomethylation enables the transcriptional repressor SlSPL-CNR to control fruit flavor ester biosynthesis.Nature communications · 2026Article
- The miR171a-TaSCL6-1 Module Acts Downstream of miR164-Targeted TaNAC21/22 to Regulate Leaf Rust Resistance in Wheat.Plant biotechnology journal · 2026Article
- Wheat TaSPL13-2B Improves Floret Fertility and Enhances Grain Number per Spikelet Through Jasmonic Acid Signalling Pathway.Plant biotechnology journal · 2026Article
- Non-Random Distribution of EMS-Induced Mutations Reveals Preference for Open Chromatin and Expressed Genes in Rice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Comparative analyses highlight wheat TaSPL4-D as a promising candidate gene to optimize plant architecture traits in rice.Plant cell reports · 2025Article
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators.Cell reports · 2025Article
- Overexpression of AtbZIP69 in transgenic wheat confers tolerance to nitrogen and drought stress.Planta · 2025Article
- Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat.Nature communications · 2024Article
- Diversification and conservation of DNA binding specificities of SPL family of transcription factors.bioRxiv : the preprint server for biology · 2024Article
- Epigenomic identification of vernalization cis-regulatory elements in winter wheat.Genome biology · 2024Article
- TaSPL6B, a member of the Squamosa promoter binding protein-like family, regulates shoot branching and florescence in Arabidopsis thaliana.BMC plant biology · 2024Article
- An overview of detecting gene-trait associations by integrating GWAS summary statistics and eQTLs.Science China. Life sciences · 2024Review
- Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat.Plant communications · 2024Article
- Age-dependent seasonal growth cessation inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis.Genome biology · 2023Article
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10 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat (Triticum aestivum. L., BBAADD) is hypothesized to increase its adaptability and/or plasticity. However, the molecular basis of expression divergence remains unclear. Squamosa promoter-binding protein-like (SPL) transcription factors are critical for a wide array of biological processes. In this study, we constructed expression regulatory networks by combining DAP-seq for 40 SPLs, ATAC-seq, and RNA-seq. Our findings indicate that a group of low-affinity SPL binding regions (SBRs) were targeted by diverse SPLs and caused different sequence preferences around the core GTAC motif. The SBRs including the low-affinity ones are evolutionarily conserved, enriched GWAS signals related to important agricultural traits. However, those SBRs are highly diversified among the cis-regulatory regions (CREs) of syntenic genes, with less than 8% SBRs coexisting in triad genes, suggesting that CRE variations are critical for subgenome differentiations. Knocking out of TaSPL7A/B/D and TaSPL15A/B/D subfamily further proved that both high- and low-affinity SBRs played critical roles in the differential expression of genes regulating tiller number and spike sizes. Our results have provided baseline data for downstream networks of SPLs and wheat improvements and revealed that CRE variations are critical sources for subgenome divergence in the allohexaploid wheat.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.