Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat

文献类型： 外文期刊

第一作者： Pei, Hongcui

作者： Pei, Hongcui;Gao, Lifeng;Ren, Xueni;Liu, Yanhong;Jia, Jizeng;Lu, Zefu;Gao, Hengbin;Wang, Yonghong;Teng, Wan;Tong, Yiping;Wang, Yonghong;Teng, Wan;Tong, Yiping

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关键词： wheat (Triticum aestivum L; ); squamosa promoter-binding protein-like (SPL); transcriptional regulation; cis-regulatory regions; polyploidization; low-affinity binding sites

期刊名称：SCIENCE CHINA-LIFE SCIENCES （ 影响因子：10.372； 五年影响因子：7.587 ）

ISSN： 1674-7305

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收录情况： SCI

摘要： 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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