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...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.展开更多
Development of wheat(Triticum aestivum L.)grain mainly depends on the processes of starch synthesis and storage protein accumulation,which are critical for grain yield and quality.However,the regulatory network underl...Development of wheat(Triticum aestivum L.)grain mainly depends on the processes of starch synthesis and storage protein accumulation,which are critical for grain yield and quality.However,the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear.Here,we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes.We found that the chromatin accessibility changes are tightly associated with differential transcriptomic expressions,and the proportion of distal ACRs was increased gradually during grain development.Specific transcription factor(TF)binding sites were enriched at different stages and were diversified among the 3 subgenomes.We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles.Overall,our findings have provided numerous resources and illustrated the regulatory network during wheat grain development,which would shed light on the improvement of wheat yields and qualities.展开更多
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+2 种基金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。
文摘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.
基金This project was financially supported by the Outstanding Young Scientist Foundation of NSFC(Overseas)the Central Public-interest Scientific Institution Basic Research Found(S2022ZD02)+1 种基金the Fundamental Research Funds from Institute of Crop Sciences,Chinese Academy of Agricultural Sciences(S2020YC07 and S2021YC03)CAAS Agricultural Science and Technology Innovation Program,China(CAAS-ZDRW202002).
文摘Development of wheat(Triticum aestivum L.)grain mainly depends on the processes of starch synthesis and storage protein accumulation,which are critical for grain yield and quality.However,the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear.Here,we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes.We found that the chromatin accessibility changes are tightly associated with differential transcriptomic expressions,and the proportion of distal ACRs was increased gradually during grain development.Specific transcription factor(TF)binding sites were enriched at different stages and were diversified among the 3 subgenomes.We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles.Overall,our findings have provided numerous resources and illustrated the regulatory network during wheat grain development,which would shed light on the improvement of wheat yields and qualities.
