The gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH-type zinc finger protein as a key regulator of lignin biosynthesis and stone cell formation in pear fruit

Yunpeng Cao; Xiaofeng Feng; Baopeng Ding; Heqiang Huo; Muhammad Abdullah; Jiayi Hong; Lan Jiang; Han Wang; Risheng Li; Yongping Cai; Xiaoxu Li; Zhichao Xia; Rajeev K. Varshney; Haifei Hu; Mengfei Lin; Fei Shen

doi:10.1016/j.xplc.2024.101238

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The gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH-type zinc finger protein as a key regulator of lignin biosynthesis and stone cell formation in pear fruit

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The gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH-type zinc finger protein as a key regulator of lignin biosynthesis and stone cell formation in pear fruit

Yunpeng Cao, Xiaofeng Feng, Baopeng Ding, Heqiang Huo, Muhammad Abdullah, Jiayi Hong, Lan Jiang, Han Wang, Risheng Li, Yongping Cai, …

Plant communications, Vol.6(3), 101238

2024

DOI: https://doi.org/10.1016/j.xplc.2024.101238

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Abstract

The Chinese white pear (Pyrus bretschneideri) is an economically significant fruit crop worldwide. Previous genomic versions of P. bretschneideri contained numerous gaps and unanchored genetic regions. Here, we generated two high-quality, gap-free genome assemblies for 'Dangshansu' (DS; 503.92 Mb) and 'Lianglizaosu' (ZS; 509.01 Mb), each anchored to 17 chromosomes, achieving a BUSCO completeness score of nearly 99.0%. Our genome-wide association studies (GWAS) explored the associations between genetic variations and stone cell traits, revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene, designated as the PbdsZF. Through genetic transformation, we verified the pivotal role of PbdsZF in regulating both lignin biosynthesis and stone cell formation, as it transcriptionally activated multiple genes involved in these processes. By binding to CT-rich motifs, CT1 (CTTTTTTCT) and CT2 (CTCTTTTT), PbdsZF significantly influenced the transcription of genes essential for lignin production, underscoring its regulatory importance in plant lignin metabolism. Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation, thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.

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Title: The gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH-type zinc finger protein as a key regulator of lignin biosynthesis and stone cell formation in pear fruit
Authors/Creators: Yunpeng Cao - Chinese Academy of Sciences
Xiaofeng Feng
Baopeng Ding - Shanxi Datong University
Heqiang Huo
Muhammad Abdullah
Jiayi Hong
Lan Jiang
Han Wang
Risheng Li
Yongping Cai
Xiaoxu Li
Zhichao Xia
Rajeev K. Varshney - Murdoch University, Food Futures Institute
Haifei Hu - Rice Research Institute
Mengfei Lin
Fei Shen
Publication Details: Plant communications, Vol.6(3), 101238
Publisher: Elsevier Inc. on behalf of CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, and Chinese Society for Plant Biology.
Identifiers: 991005726578407891
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre; Food Futures Institute
Language: English
Resource Type: Journal article

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