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

Genome Biology

Zhangjun Fei¹  Kejiao Zhao²  Jiaying Zhang²  Bobo Song²  Manyi Sun²  Yongsong Xue²  Mengfan Qin²  Jiaming Li²  Jun Wu²  Runze Wang²  Xiaolong Li³  Mingyue Zhang⁴  Qun Lian⁵  Tao Lin⁶  Xu Chen⁷  Hongju Hu⁸  Jing Fan⁸  Cheng Xue⁹  Jia-Long Yao^1,10 

[1] Boyce Thompson Institute, Cornell University, 14853, Ithaca, NY, USA;USDA-ARS, Robert W. Holley Center for Agriculture and Health, 14853, Ithaca, NY, USA;College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China;College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China;Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518124, Shenzhen, China;College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China;State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271018, Tai’an, China;Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518124, Shenzhen, China;Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518124, Shenzhen, China;College of Horticulture, China Agricultural University, 100083, Beijing, China;Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, 350002, Fuzhou, China;Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, 430072, Wuhan, China;State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271018, Tai’an, China;The New Zealand Institute for Plant & Food Research Limited, 1025, Auckland, New Zealand;

关键词: Pear fruit;    Co-expression network;    eQTL;    Stone cell formation;    NAC transcription factor;    Transcriptional regulation;   

DOI  :  10.1186/s13059-021-02531-8

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY