A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

Runze Wang,Jun Wu,Mingyue Zhang,Bobo Song,Zhangjun Fei,Jing Fan,Kejiao Zhao,Qun Lian,Cheng Xue,Mengfan Qin,Xu Chen,Manyi Sun,Yongsong Xue,Tao Lin,Hongju Hu,Jia-Long Yao,Jiaying Zhang,Xiaolong Li,Jiaming Li

doi:10.1186/s13059-021-02531-8

Abstract

BackgroundStone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh.ResultsWe generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules. Focusing on regulatory factors and using a co-expression network comprising 39 structural genes, we identify PbrNSC as a candidate regulator of stone cell formation. We then verify the function of PbrNSC in regulating lignocellulose formation using both pear fruit and Arabidopsis plants and further show that PbrNSC can transcriptionally activate multiple target genes involved in secondary cell wall formation.ConclusionsThis study generates a large resource for studying stone cell formation and provides insights into gene regulatory networks controlling the formation of stone cell and lignocellulose.

Highlights

Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh
Phenotypic determination and global gene expression profiling of pear fruit We collected fruit flesh samples at 49 days after full bloom (DAFB) from a total of 206 sand pear cultivars (P. pyrifolia) that collectively represented a broad scope of genetic diversity and large phenotypic variability (Additional file 1)
Among genes mapped with RNA sequencing (RNA-seq) reads, an average of 84.5% had more than 50% of the CDS length covered by RNA-seq reads (Additional file 2: Fig. S1a; Additional file 3)

Summary

Introduction

Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh. Different from other Rosaceae species, pear accumulates a large number of stone cells in the flesh of its fruits. These cell clusters with thickened cell wall materials cause a gritty texture and a poor fruit taste and negatively impact on consumer satisfaction. The formation of stone cells is known to be closely related to the biosynthesis, transfer, and deposition of lignin and cellulose in pear fruit flesh [8,9,10,11,12]

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Results

Discussion

Conclusion