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

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

机构地区：[1]Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China [2]State Key Laboratory of Crop Biology,College of Life Sciences,Shandong Agricultural University,Tai’an 271018,China [3]Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,Beijing 100101,China [4]The State Key Laboratory for Plant Cell and Chromosome Engineering,the Innovative Academy of Seed Design,Chinese Academy of Sciences,Beijing 100101,China

出　　处：《Science China(Life Sciences)》2023年第4期819-834,共16页中国科学（生命科学英文版）

基　　金：supported by the Central Publicinterest Scientific Institution Basic Research Found(S2022ZD02);the Excellent Young Scientists Fund(Overseas)of National Natural Science Foundation of China;the Fundamental Research Funds from the Institute of Crop Sciences,Chinese Academy of Agricultural Sciences(S2020YC07,S2021YC03);the Major Basic Research Program of Shandong Natural Science Foundation(ZR2019ZD15);the Top Talents Program“One Case One Discussion(Yishiyiyi)”of Shandong Province,China。

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,ATACseq,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 Ta SPL7A/B/D and Ta SPL15A/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.

关 键 词：wheat(Triticum aestivum L.) squamosa promoter-binding protein-like(SPL) transcriptional regulation cis-regulatory regions POLYPLOIDIZATION low-affinity binding sites 

分 类 号：S512.1[农业科学—作物学]