Single-nucleus RNA and ATAC sequencing analyses provide molecular insights into early pod development of peanut fruit  

作　　者：Yuanyuan Cui Yanning Su Jianxin Bian Xue Han Haosong Guo Zhiyuan Yang Yijun Chen Lihui Li Tianyu Li Xing Wang Deng Xiaoqin Liu 

机构地区：[1]Peking University Institute of Advanced Agricultural Sciences,Shandong Laboratory for Advanced Agricultural Sciences at Weifang,Shandong 261325,China [2]School of Advanced Agricultural Sciences,Peking University,Beijing 100083,China

出　　处：《Plant Communications》2024年第8期50-68,共19页植物通讯（英文）

基　　金：supported by grants from the Taishan Scholar Foundation of Shandong Province(tsqn202103161);the Natural Science Foundation of Shandong Province(ZR202103010405);the Key R&D Program of Shandong Province,China(ZR202211070163);the Foundation of President of the Peking University Institute of Advanced Agricultural Sciences(ZR202211070163);the Peanut Seed Industry Project in Shandong Province,China(2022LZGC007)to X.L;It was also funded by the National Natural Science Foundation of China(NSFC)Key Program(32230006)to X.W.D.

摘　　要：Peanut(Arachis hypogaea L.)is an important leguminous oil and economic crop that produces flowers aboveground and fruits belowground.Subterranean fruit-pod development,which significantly affects peanut production,involves complex molecular mechanisms that likely require the coordinated regulation of multiple genes in different tissues.To investigate the molecular mechanisms that underlie peanut fruitpod development,we characterized the anatomical features of early fruit-pod development and integrated single-nucleus RNA-sequencing(snRNA-seq)and single-nucleus assay for transposase-accessible chromatin with sequencing(snATAC-seq)data at the single-cell level.We identified distinct cell types,such as meristem,embryo,vascular tissue,cuticular layer,and stele cells within the shell wall.These specific cell types were used to examine potential molecular changes unique to each cell type during pivotal stages of fruit-pod development.snRNA-seq analyses of differentially expressed genes revealed cell-type-specific insights that were not previously obtainable from transcriptome analyses of bulk RNA.For instance,we identified MADS-box genes that contributes to the formation of parenchyma cells and gravity-related genes that are present in the vascular cells,indicating an essential role for the vascular cells in peg gravitropism.Overall,our single-nucleus analysis provides comprehensive and novel information on specific cell types,gene expression,and chromatin accessibility during the early stages of fruit-pod development.This information will enhance our understanding of the mechanisms that underlie fruit-pod development in peanut and contribute to efforts aimed at improving peanut production.

关 键 词：PEANUT pod development single-nucleus RNA-seq single-nucleus ATAC-seq in situ RNA hybridization 

分 类 号：Q94[生物学—植物学]